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Add support for of-type token modifier (#3309) 

* Add support for of-type token modifier

* Add changelog

* Clean up hash calculation logic

* Test fix

* Rework hash generation

* Work on hash generation

* Test fix

* Avoid redundant hash calculations

* Revert some useless changes

* Cleanup

* Test fixes
This commit is contained in:
James Agnew 2022-01-21 11:10:51 -05:00 committed by GitHub
parent 48caff30d9
commit 3fa76a9027
No known key found for this signature in database
GPG Key ID: 4AEE18F83AFDEB23
48 changed files with 730 additions and 318 deletions
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4
hapi-fhir-base/src/main/java/ca/uhn/fhir/context/ParserOptions.java
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@ -55,7 +55,7 @@ public class ParserOptions {
* serialized.
* </p>
*
* @since 6.0.0
* @since 5.7.0
*/
public boolean isAutoContainReferenceTargetsWithNoId() {
return myAutoContainReferenceTargetsWithNoId;
@ -72,7 +72,7 @@ public class ParserOptions {
* serialized.
* </p>
*
* @since 6.0.0
* @since 5.7.0
*/
public void setAutoContainReferenceTargetsWithNoId(boolean theAllowAutoContainedReferences) {
myAutoContainReferenceTargetsWithNoId = theAllowAutoContainedReferences;

1
hapi-fhir-base/src/main/java/ca/uhn/fhir/rest/api/Constants.java
View File

@ -217,6 +217,7 @@ public class Constants {
public static final String PARAMQUALIFIER_STRING_EXACT = ":exact";
public static final String PARAMQUALIFIER_TOKEN_TEXT = ":text";
public static final String PARAMQUALIFIER_MDM = ":mdm";
public static final String PARAMQUALIFIER_TOKEN_OF_TYPE = ":of-type";
public static final int STATUS_HTTP_200_OK = 200;
public static final int STATUS_HTTP_201_CREATED = 201;
public static final int STATUS_HTTP_204_NO_CONTENT = 204;

4
hapi-fhir-base/src/main/java/ca/uhn/fhir/rest/param/TokenParamModifier.java
View File

@ -62,7 +62,7 @@ public enum TokenParamModifier {
/**
* :of-type
*/
OF_TYPE(":of-type");
OF_TYPE(Constants.PARAMQUALIFIER_TOKEN_OF_TYPE);
private static final Map<String, TokenParamModifier> VALUE_TO_ENUM;
@ -86,5 +86,5 @@ public enum TokenParamModifier {
public static TokenParamModifier forValue(String theValue) {
return VALUE_TO_ENUM.get(theValue);
}
}

5
hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/5_7_0/1892-add-of-type-to-jpa.yaml Normal file
View File

@ -0,0 +1,5 @@
---
type: add
issue: 1892
title: "In the JPA server, the token `:of-type` modifier is now supported. This is an optional feature and
must be explicitly enabled (default is disabled)."

4
hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/5_7_0/1892-avoid-redundant-hash-calculation.yaml Normal file
View File

@ -0,0 +1,4 @@
---
type: perf
issue: 1892
title: "A redundant set of hash calculations in the JPA server was eliminated."

7
hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/5_7_0/1892-drop-text-identifer-search.yaml Normal file
View File

@ -0,0 +1,7 @@
---
type: remove
issue: 1892
title: "In the JPA server, searching using the token `:text` modifier will no longer index and match
values in `Identifier.type.text`. Previously we indexed this element, but the FHIR specification does not
actually show this field as being indexed for this modifier, and intuitively it doesn't make sense to
do so."

70
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/BaseHapiFhirDao.java
View File

@ -11,6 +11,7 @@ import ca.uhn.fhir.context.RuntimeSearchParam;
import ca.uhn.fhir.interceptor.api.HookParams;
import ca.uhn.fhir.interceptor.api.IInterceptorBroadcaster;
import ca.uhn.fhir.interceptor.api.Pointcut;
import ca.uhn.fhir.interceptor.model.RequestPartitionId;
import ca.uhn.fhir.jpa.api.config.DaoConfig;
import ca.uhn.fhir.jpa.api.dao.DaoRegistry;
import ca.uhn.fhir.jpa.api.dao.IDao;
@ -134,7 +135,6 @@ import javax.persistence.criteria.CriteriaQuery;
import javax.persistence.criteria.Root;
import javax.xml.stream.events.Characters;
import javax.xml.stream.events.XMLEvent;
import java.nio.charset.StandardCharsets;
import java.util.ArrayList;
import java.util.Arrays;
import java.util.Collection;
@ -1229,7 +1229,16 @@ public abstract class BaseHapiFhirDao<T extends IBaseResource> extends BaseStora
if (thePerformIndexing || ((ResourceTable) theEntity).getVersion() == 1) {
newParams = new ResourceIndexedSearchParams();
mySearchParamWithInlineReferencesExtractor.populateFromResource(newParams, theTransactionDetails, entity, theResource, existingParams, theRequest, thePerformIndexing);
RequestPartitionId requestPartitionId;
if (!myPartitionSettings.isPartitioningEnabled()) {
requestPartitionId = RequestPartitionId.allPartitions();
} else if (entity.getPartitionId() != null) {
requestPartitionId = entity.getPartitionId().toPartitionId();
} else {
requestPartitionId = RequestPartitionId.defaultPartition();
}
mySearchParamWithInlineReferencesExtractor.populateFromResource(requestPartitionId, newParams, theTransactionDetails, entity, theResource, existingParams, theRequest, thePerformIndexing);
changed = populateResourceIntoEntity(theTransactionDetails, theRequest, theResource, entity, true);
@ -1656,20 +1665,23 @@ public abstract class BaseHapiFhirDao<T extends IBaseResource> extends BaseStora
myConfig = theDaoConfig;
}
private class AddTagDefinitionToCacheAfterCommitSynchronization implements TransactionSynchronization {
private final TagDefinition myTagDefinition;
private final MemoryCacheService.TagDefinitionCacheKey myKey;
public AddTagDefinitionToCacheAfterCommitSynchronization(MemoryCacheService.TagDefinitionCacheKey theKey, TagDefinition theTagDefinition) {
myTagDefinition = theTagDefinition;
myKey = theKey;
public void populateFullTextFields(final FhirContext theContext, final IBaseResource theResource, ResourceTable theEntity, ResourceIndexedSearchParams theNewParams) {
if (theEntity.getDeleted() != null) {
theEntity.setNarrativeText(null);
theEntity.setContentText(null);
} else {
theEntity.setNarrativeText(parseNarrativeTextIntoWords(theResource));
theEntity.setContentText(parseContentTextIntoWords(theContext, theResource));
if (myDaoConfig.isAdvancedLuceneIndexing()) {
ExtendedLuceneIndexData luceneIndexData = myFulltextSearchSvc.extractLuceneIndexData(theResource, theNewParams);
theEntity.setLuceneIndexData(luceneIndexData);
}
}
}
@Override
public void afterCommit() {
myMemoryCacheService.put(MemoryCacheService.CacheEnum.TAG_DEFINITION, myKey, myTagDefinition);
}
@VisibleForTesting
public void setPartitionSettingsForUnitTest(PartitionSettings thePartitionSettings) {
myPartitionSettings = thePartitionSettings;
}
@Nonnull
@ -1706,20 +1718,6 @@ public abstract class BaseHapiFhirDao<T extends IBaseResource> extends BaseStora
return retVal.toString();
}
public void populateFullTextFields(final FhirContext theContext, final IBaseResource theResource, ResourceTable theEntity, ResourceIndexedSearchParams theNewParams) {
if (theEntity.getDeleted() != null) {
theEntity.setNarrativeText(null);
theEntity.setContentText(null);
} else {
theEntity.setNarrativeText(parseNarrativeTextIntoWords(theResource));
theEntity.setContentText(parseContentTextIntoWords(theContext, theResource));
if (myDaoConfig.isAdvancedLuceneIndexing()) {
ExtendedLuceneIndexData luceneIndexData = myFulltextSearchSvc.extractLuceneIndexData(theResource, theNewParams);
theEntity.setLuceneIndexData(luceneIndexData);
}
}
}
public static String decodeResource(byte[] theResourceBytes, ResourceEncodingEnum theResourceEncoding) {
String resourceText = null;
switch (theResourceEncoding) {
@ -1804,4 +1802,20 @@ public abstract class BaseHapiFhirDao<T extends IBaseResource> extends BaseStora
}
}
private class AddTagDefinitionToCacheAfterCommitSynchronization implements TransactionSynchronization {
private final TagDefinition myTagDefinition;
private final MemoryCacheService.TagDefinitionCacheKey myKey;
public AddTagDefinitionToCacheAfterCommitSynchronization(MemoryCacheService.TagDefinitionCacheKey theKey, TagDefinition theTagDefinition) {
myTagDefinition = theTagDefinition;
myKey = theKey;
}
@Override
public void afterCommit() {
myMemoryCacheService.put(MemoryCacheService.CacheEnum.TAG_DEFINITION, myKey, myTagDefinition);
}
}
}

8
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/dstu3/FhirResourceDaoCodeSystemDstu3.java
View File

@ -89,7 +89,7 @@ public class FhirResourceDaoCodeSystemDstu3 extends BaseHapiFhirResourceDao<Code
public IValidationSupport.LookupCodeResult lookupCode(IPrimitiveType<String> theCode, IPrimitiveType<String> theSystem, Coding theCoding, RequestDetails theRequestDetails) {
return lookupCode(theCode, theSystem, theCoding, null, theRequestDetails);
}
@Nonnull
@Override
public IValidationSupport.LookupCodeResult lookupCode(IPrimitiveType<String> theCode, IPrimitiveType<String> theSystem, Coding theCoding, IPrimitiveType<String> theDisplayLanguage, RequestDetails theRequestDetails) {
@ -97,7 +97,7 @@ public class FhirResourceDaoCodeSystemDstu3 extends BaseHapiFhirResourceDao<Code
boolean haveCode = theCode != null && theCode.isEmpty() == false;
boolean haveSystem = theSystem != null && theSystem.isEmpty() == false;
boolean haveDisplayLanguage = theDisplayLanguage != null && theDisplayLanguage.isEmpty() == false;
if (!haveCoding && !(haveSystem && haveCode)) {
throw new InvalidRequestException("No code, coding, or codeableConcept provided to validate");
}
@ -119,11 +119,11 @@ public class FhirResourceDaoCodeSystemDstu3 extends BaseHapiFhirResourceDao<Code
system = theSystem.getValue();
}
String displayLanguage = null;
String displayLanguage = null;
if (haveDisplayLanguage) {
displayLanguage = theDisplayLanguage.getValue();
}
ourLog.debug("Looking up {} / {}", system, code);
if (myValidationSupport.isCodeSystemSupported(new ValidationSupportContext(myValidationSupport), system)) {

1
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/index/DaoSearchParamSynchronizer.java
View File

@ -121,7 +121,6 @@ public class DaoSearchParamSynchronizer {
// Take a row we were going to remove, and repurpose its ID
T entityToReuse = theIndexesToRemove.remove(theIndexesToRemove.size() - 1);
entityToReuse.copyMutableValuesFrom(targetEntity);
entityToReuse.calculateHashes();
theIndexesToAdd.set(addIndex, entityToReuse);
}
}

3
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/index/IdHelperService.java
View File

@ -131,6 +131,7 @@ public class IdHelperService {
@Nonnull
public IResourceLookup resolveResourceIdentity(@Nonnull RequestPartitionId theRequestPartitionId, String theResourceType, String theResourceId) throws ResourceNotFoundException {
assert myDontCheckActiveTransactionForUnitTest || TransactionSynchronizationManager.isSynchronizationActive();
assert theRequestPartitionId != null;
IdDt id = new IdDt(theResourceType, theResourceId);
Map<String, List<IResourceLookup>> matches = translateForcedIdToPids(theRequestPartitionId,
@ -377,6 +378,8 @@ public class IdHelperService {
}
private Map<String, List<IResourceLookup>> translateForcedIdToPids(@Nonnull RequestPartitionId theRequestPartitionId, Collection<IIdType> theId) {
assert theRequestPartitionId != null;
theId.forEach(id -> Validate.isTrue(id.hasIdPart()));
if (theId.isEmpty()) {

29
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/index/SearchParamWithInlineReferencesExtractor.java
View File

@ -31,7 +31,6 @@ import ca.uhn.fhir.jpa.dao.MatchResourceUrlService;
import ca.uhn.fhir.jpa.dao.data.IResourceIndexedComboStringUniqueDao;
import ca.uhn.fhir.jpa.model.config.PartitionSettings;
import ca.uhn.fhir.jpa.model.entity.BaseResourceIndexedSearchParam;
import ca.uhn.fhir.jpa.model.entity.PartitionablePartitionId;
import ca.uhn.fhir.jpa.model.entity.ResourceIndexedComboStringUnique;
import ca.uhn.fhir.jpa.model.entity.ResourceIndexedComboTokenNonUnique;
import ca.uhn.fhir.jpa.model.entity.ResourceLink;
@ -56,12 +55,12 @@ import com.google.common.annotations.VisibleForTesting;
import org.hl7.fhir.instance.model.api.IBaseReference;
import org.hl7.fhir.instance.model.api.IBaseResource;
import org.hl7.fhir.instance.model.api.IIdType;
import javax.annotation.Nullable;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.context.annotation.Lazy;
import org.springframework.stereotype.Service;
import javax.annotation.Nonnull;
import javax.annotation.Nullable;
import javax.persistence.EntityManager;
import javax.persistence.PersistenceContext;
import javax.persistence.PersistenceContextType;
@ -104,6 +103,8 @@ public class SearchParamWithInlineReferencesExtractor {
private IResourceIndexedComboStringUniqueDao myResourceIndexedCompositeStringUniqueDao;
@Autowired
private PartitionSettings myPartitionSettings;
@Autowired
private MemoryCacheService myMemoryCacheService;
@VisibleForTesting
public void setPartitionSettings(PartitionSettings thePartitionSettings) {
@ -120,17 +121,10 @@ public class SearchParamWithInlineReferencesExtractor {
mySearchParamRegistry = theSearchParamRegistry;
}
public void populateFromResource(ResourceIndexedSearchParams theParams, TransactionDetails theTransactionDetails, ResourceTable theEntity, IBaseResource theResource, ResourceIndexedSearchParams theExistingParams, RequestDetails theRequest, boolean theFailOnInvalidReference) {
public void populateFromResource(RequestPartitionId theRequestPartitionId, ResourceIndexedSearchParams theParams, TransactionDetails theTransactionDetails, ResourceTable theEntity, IBaseResource theResource, ResourceIndexedSearchParams theExistingParams, RequestDetails theRequest, boolean theFailOnInvalidReference) {
extractInlineReferences(theResource, theTransactionDetails, theRequest);
RequestPartitionId partitionId;
if (myPartitionSettings.isPartitioningEnabled()) {
partitionId = PartitionablePartitionId.toRequestPartitionId(theEntity.getPartitionId());
} else {
partitionId = RequestPartitionId.allPartitions();
}
mySearchParamExtractorService.extractFromResource(partitionId, theRequest, theParams, theEntity, theResource, theTransactionDetails, theFailOnInvalidReference);
mySearchParamExtractorService.extractFromResource(theRequestPartitionId, theRequest, theParams, theEntity, theResource, theTransactionDetails, theFailOnInvalidReference);
Set<Map.Entry<String, RuntimeSearchParam>> activeSearchParams = mySearchParamRegistry.getActiveSearchParams(theEntity.getResourceType()).entrySet();
if (myDaoConfig.getIndexMissingFields() == DaoConfig.IndexEnabledEnum.ENABLED) {
@ -183,8 +177,8 @@ public class SearchParamWithInlineReferencesExtractor {
Set<String> queryStringsToPopulate = extractParameterCombinationsForComboParam(theParams, theResourceType, theParam);
for (String nextQueryString : queryStringsToPopulate) {
ourLog.trace("Adding composite unique SP: {}", nextQueryString);
theParams.myComboStringUniques.add(new ResourceIndexedComboStringUnique(theEntity, nextQueryString, theParam.getId()));
ourLog.trace("Adding composite unique SP: {}", nextQueryString);
theParams.myComboStringUniques.add(new ResourceIndexedComboStringUnique(theEntity, nextQueryString, theParam.getId()));
}
}
@ -299,13 +293,12 @@ public class SearchParamWithInlineReferencesExtractor {
if (paramsListForCompositePart != null) {
paramsListForCompositePart = paramsListForCompositePart
.stream()
.filter(t->t.getParamName().equals(nextCompositeOf.getName()))
.filter(t -> t.getParamName().equals(nextCompositeOf.getName()))
.collect(Collectors.toList());
}
return paramsListForCompositePart;
}
@VisibleForTesting
public void setDaoConfig(DaoConfig theDaoConfig) {
myDaoConfig = theDaoConfig;
@ -316,12 +309,6 @@ public class SearchParamWithInlineReferencesExtractor {
myContext = theContext;
}
@Autowired
private MemoryCacheService myMemoryCacheService;
/**
* Handle references within the resource that are match URLs, for example references like "Patient?identifier=foo". These match URLs are resolved and replaced with the ID of the
* matching resource.

19
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/r4/FhirResourceDaoCodeSystemR4.java
View File

@ -61,15 +61,14 @@ import static org.hl7.fhir.common.hapi.validation.support.ValidationConstants.LO
public class FhirResourceDaoCodeSystemR4 extends BaseHapiFhirResourceDao<CodeSystem> implements IFhirResourceDaoCodeSystem<CodeSystem, Coding, CodeableConcept> {
private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(FhirResourceDaoCodeSystemR4.class);
@Autowired
private IValidationSupport myValidationSupport;
@Autowired
protected ITermCodeSystemStorageSvc myTerminologyCodeSystemStorageSvc;
@Autowired
private FhirContext myFhirContext;
@Autowired
protected ITermDeferredStorageSvc myTermDeferredStorageSvc;
@Autowired
private IValidationSupport myValidationSupport;
@Autowired
private FhirContext myFhirContext;
@Override
public List<IIdType> findCodeSystemIdsContainingSystemAndCode(String theCode, String theSystem, RequestDetails theRequest) {
@ -88,7 +87,7 @@ public class FhirResourceDaoCodeSystemR4 extends BaseHapiFhirResourceDao<CodeSys
public IValidationSupport.LookupCodeResult lookupCode(IPrimitiveType<String> theCode, IPrimitiveType<String> theSystem, Coding theCoding, RequestDetails theRequestDetails) {
return lookupCode(theCode, theSystem, theCoding, null, theRequestDetails);
}
@Nonnull
@Override
public IValidationSupport.LookupCodeResult lookupCode(IPrimitiveType<String> theCode, IPrimitiveType<String> theSystem, Coding theCoding, IPrimitiveType<String> theDisplayLanguage, RequestDetails theRequestDetails) {
@ -118,11 +117,11 @@ public class FhirResourceDaoCodeSystemR4 extends BaseHapiFhirResourceDao<CodeSys
system = theSystem.getValue();
}
String displayLanguage = null;
String displayLanguage = null;
if (haveDisplayLanguage) {
displayLanguage = theDisplayLanguage.getValue();
}
ourLog.debug("Looking up {} / {}", system, code);
if (myValidationSupport.isCodeSystemSupported(new ValidationSupportContext(myValidationSupport), system)) {
@ -170,8 +169,8 @@ public class FhirResourceDaoCodeSystemR4 extends BaseHapiFhirResourceDao<CodeSys
@Override
public CodeValidationResult validateCode(IIdType theCodeSystemId, IPrimitiveType<String> theCodeSystemUrl,
IPrimitiveType<String> theVersion, IPrimitiveType<String> theCode, IPrimitiveType<String> theDisplay,
Coding theCoding, CodeableConcept theCodeableConcept, RequestDetails theRequestDetails) {
IPrimitiveType<String> theVersion, IPrimitiveType<String> theCode, IPrimitiveType<String> theDisplay,
Coding theCoding, CodeableConcept theCodeableConcept, RequestDetails theRequestDetails) {
return myTerminologySvc.codeSystemValidateCode(theCodeSystemId, toStringOrNull(theCodeSystemUrl), toStringOrNull(theVersion), toStringOrNull(theCode), toStringOrNull(theDisplay), theCoding, theCodeableConcept);

2
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/r4/FhirResourceDaoConceptMapR4.java
View File

@ -20,9 +20,9 @@ package ca.uhn.fhir.jpa.dao.r4;
* #L%
*/
import ca.uhn.fhir.context.support.TranslateConceptResults;
import ca.uhn.fhir.jpa.api.dao.IFhirResourceDaoConceptMap;
import ca.uhn.fhir.jpa.api.model.TranslationRequest;
import ca.uhn.fhir.context.support.TranslateConceptResults;
import ca.uhn.fhir.jpa.dao.BaseHapiFhirResourceDao;
import ca.uhn.fhir.jpa.model.cross.IBasePersistedResource;
import ca.uhn.fhir.jpa.model.entity.ResourceTable;

24
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/r5/FhirResourceDaoCodeSystemR5.java
View File

@ -22,20 +22,20 @@ package ca.uhn.fhir.jpa.dao.r5;
import ca.uhn.fhir.context.FhirContext;
import ca.uhn.fhir.context.support.IValidationSupport;
import ca.uhn.fhir.context.support.ValidationSupportContext;
import ca.uhn.fhir.context.support.IValidationSupport.CodeValidationResult;
import ca.uhn.fhir.context.support.ValidationSupportContext;
import ca.uhn.fhir.jpa.api.dao.IFhirResourceDaoCodeSystem;
import ca.uhn.fhir.jpa.dao.BaseHapiFhirResourceDao;
import ca.uhn.fhir.jpa.dao.index.IdHelperService;
import ca.uhn.fhir.jpa.model.cross.IBasePersistedResource;
import ca.uhn.fhir.jpa.term.api.ITermDeferredStorageSvc;
import ca.uhn.fhir.rest.api.server.storage.ResourcePersistentId;
import ca.uhn.fhir.jpa.model.entity.ResourceTable;
import ca.uhn.fhir.rest.api.server.storage.TransactionDetails;
import ca.uhn.fhir.jpa.searchparam.SearchParameterMap;
import ca.uhn.fhir.jpa.term.api.ITermCodeSystemStorageSvc;
import ca.uhn.fhir.jpa.term.api.ITermDeferredStorageSvc;
import ca.uhn.fhir.jpa.util.LogicUtil;
import ca.uhn.fhir.rest.api.server.RequestDetails;
import ca.uhn.fhir.rest.api.server.storage.ResourcePersistentId;
import ca.uhn.fhir.rest.api.server.storage.TransactionDetails;
import ca.uhn.fhir.rest.param.TokenParam;
import ca.uhn.fhir.rest.server.exceptions.InvalidRequestException;
import org.hl7.fhir.convertors.advisors.impl.BaseAdvisor_40_50;
@ -65,11 +65,11 @@ public class FhirResourceDaoCodeSystemR5 extends BaseHapiFhirResourceDao<CodeSys
@Autowired
protected IdHelperService myIdHelperService;
@Autowired
protected ITermDeferredStorageSvc myTermDeferredStorageSvc;
@Autowired
private IValidationSupport myValidationSupport;
@Autowired
private FhirContext myFhirContext;
@Autowired
protected ITermDeferredStorageSvc myTermDeferredStorageSvc;
@Override
public List<IIdType> findCodeSystemIdsContainingSystemAndCode(String theCode, String theSystem, RequestDetails theRequest) {
@ -88,7 +88,7 @@ public class FhirResourceDaoCodeSystemR5 extends BaseHapiFhirResourceDao<CodeSys
public IValidationSupport.LookupCodeResult lookupCode(IPrimitiveType<String> theCode, IPrimitiveType<String> theSystem, Coding theCoding, RequestDetails theRequestDetails) {
return lookupCode(theCode, theSystem, theCoding, null, theRequestDetails);
}
@Nonnull
@Override
public IValidationSupport.LookupCodeResult lookupCode(IPrimitiveType<String> theCode, IPrimitiveType<String> theSystem, Coding theCoding, IPrimitiveType<String> theDisplayLanguage, RequestDetails theRequestDetails) {
@ -96,7 +96,7 @@ public class FhirResourceDaoCodeSystemR5 extends BaseHapiFhirResourceDao<CodeSys
boolean haveCode = theCode != null && theCode.isEmpty() == false;
boolean haveSystem = theSystem != null && theSystem.isEmpty() == false;
boolean haveDisplayLanguage = theDisplayLanguage != null && theDisplayLanguage.isEmpty() == false;
if (!haveCoding && !(haveSystem && haveCode)) {
throw new InvalidRequestException("No code, coding, or codeableConcept provided to validate");
}
@ -118,11 +118,11 @@ public class FhirResourceDaoCodeSystemR5 extends BaseHapiFhirResourceDao<CodeSys
system = theSystem.getValue();
}
String displayLanguage = null;
String displayLanguage = null;
if (haveDisplayLanguage) {
displayLanguage = theDisplayLanguage.getValue();
}
ourLog.info("Looking up {} / {}", system, code);
if (myValidationSupport.isCodeSystemSupported(new ValidationSupportContext(myValidationSupport), system)) {
@ -170,8 +170,8 @@ public class FhirResourceDaoCodeSystemR5 extends BaseHapiFhirResourceDao<CodeSys
@Override
public CodeValidationResult validateCode(IIdType theCodeSystemId, IPrimitiveType<String> theCodeSystemUrl,
IPrimitiveType<String> theVersion, IPrimitiveType<String> theCode, IPrimitiveType<String> theDisplay,
Coding theCoding, CodeableConcept theCodeableConcept, RequestDetails theRequestDetails) {
IPrimitiveType<String> theVersion, IPrimitiveType<String> theCode, IPrimitiveType<String> theDisplay,
Coding theCoding, CodeableConcept theCodeableConcept, RequestDetails theRequestDetails) {
return myTerminologySvc.codeSystemValidateCode(theCodeSystemId, toStringOrNull(theCodeSystemUrl), toStringOrNull(theVersion), toStringOrNull(theCode), toStringOrNull(theDisplay), theCoding, theCodeableConcept);
}

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

@ -20,9 +20,9 @@ package ca.uhn.fhir.jpa.dao.r5;
* #L%
*/
import ca.uhn.fhir.context.support.TranslateConceptResults;
import ca.uhn.fhir.jpa.api.dao.IFhirResourceDaoConceptMap;
import ca.uhn.fhir.jpa.api.model.TranslationRequest;
import ca.uhn.fhir.context.support.TranslateConceptResults;
import ca.uhn.fhir.jpa.dao.BaseHapiFhirResourceDao;
import ca.uhn.fhir.jpa.model.cross.IBasePersistedResource;
import ca.uhn.fhir.jpa.model.entity.ResourceTable;

23
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/search/builder/predicate/TokenPredicateBuilder.java
View File

@ -28,6 +28,7 @@ import ca.uhn.fhir.interceptor.model.RequestPartitionId;
import ca.uhn.fhir.jpa.dao.LegacySearchBuilder;
import ca.uhn.fhir.jpa.dao.predicate.SearchFilterParser;
import ca.uhn.fhir.jpa.model.entity.BaseResourceIndexedSearchParam;
import ca.uhn.fhir.jpa.model.entity.ModelConfig;
import ca.uhn.fhir.jpa.model.entity.ResourceIndexedSearchParamToken;
import ca.uhn.fhir.jpa.search.builder.QueryStack;
import ca.uhn.fhir.jpa.search.builder.sql.SearchQueryBuilder;
@ -35,16 +36,19 @@ import ca.uhn.fhir.jpa.term.api.ITermReadSvc;
import ca.uhn.fhir.model.api.IQueryParameterType;
import ca.uhn.fhir.model.base.composite.BaseCodingDt;
import ca.uhn.fhir.model.base.composite.BaseIdentifierDt;
import ca.uhn.fhir.rest.api.Constants;
import ca.uhn.fhir.rest.param.NumberParam;
import ca.uhn.fhir.rest.param.TokenParam;
import ca.uhn.fhir.rest.param.TokenParamModifier;
import ca.uhn.fhir.rest.server.exceptions.InvalidRequestException;
import ca.uhn.fhir.rest.server.exceptions.MethodNotAllowedException;
import ca.uhn.fhir.util.FhirVersionIndependentConcept;
import com.google.common.collect.Sets;
import com.healthmarketscience.sqlbuilder.BinaryCondition;
import com.healthmarketscience.sqlbuilder.Condition;
import com.healthmarketscience.sqlbuilder.InCondition;
import com.healthmarketscience.sqlbuilder.dbspec.basic.DbColumn;
import org.apache.commons.lang3.StringUtils;
import org.hl7.fhir.instance.model.api.IBaseResource;
import org.springframework.beans.factory.annotation.Autowired;
@ -73,7 +77,8 @@ public class TokenPredicateBuilder extends BaseSearchParamPredicateBuilder {
@Autowired
private ITermReadSvc myTerminologySvc;
@Autowired
private ModelConfig myModelConfig;
/**
* Constructor
@ -129,7 +134,7 @@ public class TokenPredicateBuilder extends BaseSearchParamPredicateBuilder {
if (nextParameter instanceof TokenParam) {
TokenParam id = (TokenParam) nextParameter;
system = id.getSystem();
code = (id.getValue());
code = id.getValue();
modifier = id.getModifier();
} else if (nextParameter instanceof BaseIdentifierDt) {
BaseIdentifierDt id = (BaseIdentifierDt) nextParameter;
@ -171,6 +176,20 @@ public class TokenPredicateBuilder extends BaseSearchParamPredicateBuilder {
system = determineSystemIfMissing(theSearchParam, code, system);
validateHaveSystemAndCodeForToken(paramName, code, system);
codes.addAll(myTerminologySvc.findCodesBelow(system, code));
} else if (modifier == TokenParamModifier.OF_TYPE) {
if (!myModelConfig.isIndexIdentifierOfType()) {
throw new MethodNotAllowedException("The :of-type modifier is not enabled on this server");
}
if (isBlank(system) || isBlank(code)) {
throw new InvalidRequestException("Invalid parameter value for :of-type query");
}
int pipeIdx = code.indexOf('|');
if (pipeIdx < 1 || pipeIdx == code.length() - 1) {
throw new InvalidRequestException("Invalid parameter value for :of-type query");
}
paramName = paramName + Constants.PARAMQUALIFIER_TOKEN_OF_TYPE;
codes.add(new FhirVersionIndependentConcept(system, code));
} else {
if (modifier == TokenParamModifier.NOT && operation == null) {
operation = SearchFilterParser.CompareOperation.ne;

17
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/BaseJpaTest.java
View File

@ -15,6 +15,7 @@ import ca.uhn.fhir.jpa.dao.data.IForcedIdDao;
import ca.uhn.fhir.jpa.dao.data.IResourceHistoryTableDao;
import ca.uhn.fhir.jpa.dao.data.IResourceIndexedComboTokensNonUniqueDao;
import ca.uhn.fhir.jpa.dao.data.IResourceIndexedSearchParamDateDao;
import ca.uhn.fhir.jpa.dao.data.IResourceIndexedSearchParamStringDao;
import ca.uhn.fhir.jpa.dao.data.IResourceIndexedSearchParamTokenDao;
import ca.uhn.fhir.jpa.dao.data.IResourceLinkDao;
import ca.uhn.fhir.jpa.dao.data.IResourceTableDao;
@ -94,6 +95,7 @@ import javax.persistence.EntityManager;
import java.io.IOException;
import java.io.InputStream;
import java.util.ArrayList;
import java.util.Arrays;
import java.util.HashMap;
import java.util.HashSet;
import java.util.List;
@ -168,6 +170,8 @@ public abstract class BaseJpaTest extends BaseTest {
@Autowired
protected IResourceIndexedSearchParamTokenDao myResourceIndexedSearchParamTokenDao;
@Autowired
protected IResourceIndexedSearchParamStringDao myResourceIndexedSearchParamStringDao;
@Autowired
protected IResourceIndexedSearchParamDateDao myResourceIndexedSearchParamDateDao;
@Autowired
protected IResourceIndexedComboTokensNonUniqueDao myResourceIndexedComboTokensNonUniqueDao;
@ -346,6 +350,19 @@ public abstract class BaseJpaTest extends BaseTest {
});
}
protected void logAllStringIndexes(String... theParamNames) {
String messageSuffix = theParamNames.length > 0 ? " containing " + Arrays.asList(theParamNames) : "";
runInTransaction(() -> {
String message = myResourceIndexedSearchParamStringDao
.findAll()
.stream()
.filter(t->theParamNames.length == 0 ? true : Arrays.asList(theParamNames).contains(t.getParamName()))
.map(t -> t.toString())
.collect(Collectors.joining("\n * "));
ourLog.info("String indexes{}:\n * {}", messageSuffix, message);
});
}
protected void logAllResourceTags() {
runInTransaction(() -> {
ourLog.info("Token tags:\n * {}", myResourceTagDao.findAll().stream().map(t -> t.toString()).collect(Collectors.joining("\n * ")));

4
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/r4/ChainingR4SearchTest.java
View File

@ -1193,8 +1193,12 @@ public class ChainingR4SearchTest extends BaseJpaR4Test {
String url = "/Observation?subject.organization.partof.name=HealthCo";
logAllStringIndexes();
// execute
myCaptureQueriesListener.clear();
List<String> oids = searchAndReturnUnqualifiedVersionlessIdValues(url);
myCaptureQueriesListener.logSelectQueriesForCurrentThread();
// validate
assertEquals(1L, oids.size());

10
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/r4/FhirResourceDaoR4QueryCountTest.java
View File

@ -303,7 +303,7 @@ public class FhirResourceDaoR4QueryCountTest extends BaseResourceProviderR4Test
List<ResourceTable> resources = myResourceTableDao.findAll();
String versions = "Resource Versions:\n * " + resources
.stream()
.map(t->"Resource " + t.getIdDt() + " has version: " + t.getVersion())
.map(t -> "Resource " + t.getIdDt() + " has version: " + t.getVersion())
.collect(Collectors.joining("\n * "));
for (ResourceTable next : resources) {
@ -368,7 +368,7 @@ public class FhirResourceDaoR4QueryCountTest extends BaseResourceProviderR4Test
List<ResourceTable> resources = myResourceTableDao.findAll();
String versions = "Resource Versions:\n * " + resources
.stream()
.map(t->"Resource " + t.getIdDt() + " has version: " + t.getVersion())
.map(t -> "Resource " + t.getIdDt() + " has version: " + t.getVersion())
.collect(Collectors.joining("\n * "));
for (ResourceTable next : resources) {
@ -554,9 +554,9 @@ public class FhirResourceDaoR4QueryCountTest extends BaseResourceProviderR4Test
public void assertNoPartitionSelectors() {
List<SqlQuery> selectQueries = myCaptureQueriesListener.getSelectQueriesForCurrentThread();
for (SqlQuery next : selectQueries) {
assertEquals(0, StringUtils.countMatches(next.getSql(true, true).toLowerCase(), "partition_id is null"));
assertEquals(0, StringUtils.countMatches(next.getSql(true, true).toLowerCase(), "partition_id="));
assertEquals(0, StringUtils.countMatches(next.getSql(true, true).toLowerCase(), "partition_id ="));
assertEquals(0, StringUtils.countMatches(next.getSql(true, true).toLowerCase(), "partition_id is null"), () -> next.getSql(true, true));
assertEquals(0, StringUtils.countMatches(next.getSql(true, true).toLowerCase(), "partition_id="), () -> next.getSql(true, true));
assertEquals(0, StringUtils.countMatches(next.getSql(true, true).toLowerCase(), "partition_id ="), () -> next.getSql(true, true));
}
}

76
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/r4/FhirResourceDaoR4SearchNoFtTest.java
View File

@ -125,7 +125,6 @@ import org.hl7.fhir.r4.model.Substance;
import org.hl7.fhir.r4.model.Task;
import org.hl7.fhir.r4.model.Timing;
import org.hl7.fhir.r4.model.ValueSet;
import org.junit.Ignore;
import org.junit.jupiter.api.AfterEach;
import org.junit.jupiter.api.BeforeAll;
import org.junit.jupiter.api.BeforeEach;
@ -170,6 +169,7 @@ import static org.hamcrest.Matchers.hasSize;
import static org.hamcrest.Matchers.not;
import static org.junit.jupiter.api.Assertions.assertEquals;
import static org.junit.jupiter.api.Assertions.assertFalse;
import static org.junit.jupiter.api.Assertions.assertNotNull;
import static org.junit.jupiter.api.Assertions.assertNull;
import static org.junit.jupiter.api.Assertions.assertTrue;
import static org.junit.jupiter.api.Assertions.fail;
@ -193,9 +193,11 @@ public class FhirResourceDaoR4SearchNoFtTest extends BaseJpaR4Test {
myDaoConfig.setAllowContainsSearches(new DaoConfig().isAllowContainsSearches());
myDaoConfig.setSearchPreFetchThresholds(new DaoConfig().getSearchPreFetchThresholds());
myDaoConfig.setIndexMissingFields(new DaoConfig().getIndexMissingFields());
myModelConfig.setNormalizedQuantitySearchLevel(NormalizedQuantitySearchLevel.NORMALIZED_QUANTITY_SEARCH_NOT_SUPPORTED);
myModelConfig.setNormalizedQuantitySearchLevel(NormalizedQuantitySearchLevel.NORMALIZED_QUANTITY_SEARCH_NOT_SUPPORTED);
myModelConfig.setAutoSupportDefaultSearchParams(true);
myModelConfig.setIndexIdentifierOfType(new ModelConfig().isIndexIdentifierOfType());
mySearchParamRegistry.resetForUnitTest();
}
@ -3793,6 +3795,8 @@ public class FhirResourceDaoR4SearchNoFtTest extends BaseJpaR4Test {
patient.addIdentifier().setSystem("urn:system").setValue("TOKENB");
String idBoth = myPatientDao.create(patient, mySrd).getId().toUnqualifiedVersionless().getValue();
logAllTokenIndexes();
patient = new Patient();
patient.addIdentifier().setSystem("urn:system").setValue("TOKENA");
String idA = myPatientDao.create(patient, mySrd).getId().toUnqualifiedVersionless().getValue();
@ -5135,6 +5139,74 @@ public class FhirResourceDaoR4SearchNoFtTest extends BaseJpaR4Test {
runInTransaction(() -> assertEquals(2, mySearchEntityDao.count()));
}
@Test
public void testTokenOfType() {
myModelConfig.setIndexIdentifierOfType(true);
Patient patient = new Patient();
patient
.addIdentifier()
.setSystem("http://foo1")
.setValue("bar1")
.getType()
.addCoding()
.setSystem("http://terminology.hl7.org/CodeSystem/v2-0203")
.setCode("MR");
IIdType id1 = myPatientDao.create(patient).getId().toUnqualifiedVersionless();
runInTransaction(()->{
List<ResourceIndexedSearchParamToken> params = myResourceIndexedSearchParamTokenDao
.findAll()
.stream()
.filter(t -> t.getParamName().equals("identifier:of-type"))
.collect(Collectors.toList());
assertEquals(1, params.size());
assertNotNull(params.get(0).getHashSystemAndValue());
assertNull(params.get(0).getHashSystem());
assertNull(params.get(0).getHashValue());
});
// Shouldn't match
patient = new Patient();
patient
.addIdentifier()
.setSystem("http://terminology.hl7.org/CodeSystem/v2-0203")
.setValue("MR|bar1");
myPatientDao.create(patient);
TokenParam param = new TokenParam()
.setSystem("http://terminology.hl7.org/CodeSystem/v2-0203")
.setValue("MR|bar1")
.setModifier(TokenParamModifier.OF_TYPE);
SearchParameterMap map = SearchParameterMap.newSynchronous("identifier", param);
logAllTokenIndexes();
myCaptureQueriesListener.clear();
IBundleProvider outcome = myPatientDao.search(map, mySrd);
List<IIdType> ids = toUnqualifiedVersionlessIds(outcome);
myCaptureQueriesListener.logSelectQueries();
assertThat(ids, contains(id1));
}
@Test
public void testTokenOfType_Disabled() {
try {
TokenParam param = new TokenParam()
.setSystem("http://terminology.hl7.org/CodeSystem/v2-0203")
.setValue("MR|bar1")
.setModifier(TokenParamModifier.OF_TYPE);
SearchParameterMap map = SearchParameterMap.newSynchronous("identifier", param);
myPatientDao.search(map, mySrd);
fail();
} catch (MethodNotAllowedException e) {
assertEquals("The :of-type modifier is not enabled on this server", e.getMessage());
}
}
@Test
public void testTokenTextDisabled_Global() {
myModelConfig.setSuppressStringIndexingInTokens(true);

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

@ -1,9 +1,7 @@
package ca.uhn.fhir.jpa.dao.r4;
import ca.uhn.fhir.jpa.api.config.DaoConfig;
import ca.uhn.fhir.jpa.dao.BaseJpaTest;
import ca.uhn.fhir.jpa.dao.data.ISearchDao;
import ca.uhn.fhir.jpa.entity.TermValueSet;
import ca.uhn.fhir.jpa.model.config.PartitionSettings;
import ca.uhn.fhir.jpa.model.entity.NormalizedQuantitySearchLevel;
import ca.uhn.fhir.jpa.model.entity.ResourceIndexedSearchParamDate;
@ -102,7 +100,6 @@ import org.junit.jupiter.api.BeforeEach;
import org.junit.jupiter.api.Disabled;
import org.junit.jupiter.api.Test;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.test.context.TestPropertySource;
import org.springframework.transaction.TransactionDefinition;
import org.springframework.transaction.TransactionStatus;
import org.springframework.transaction.support.TransactionCallback;

7
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/r4/FhirResourceDaoR4SearchWithElasticSearchIT.java
View File

@ -387,13 +387,6 @@ public class FhirResourceDaoR4SearchWithElasticSearchIT extends BaseJpaTest {
assertObservationSearchMatches(":text matches code.display", map, id2);
}
{
// Identifier Type
SearchParameterMap map = new SearchParameterMap();
map.add("identifier", new TokenParam("Random").setModifier(TokenParamModifier.TEXT));
assertObservationSearchMatches(":text matches identifier text", map, id4);
}
{
// multiple values means or
SearchParameterMap map = new SearchParameterMap();

9
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/r4/PartitioningSqlR4Test.java
View File

@ -1318,8 +1318,11 @@ public class PartitioningSqlR4Test extends BasePartitioningR4Test {
@Test
public void testSearch_IdParamSecond_ForcedId_SpecificPartition() {
IIdType patientIdNull = createPatient(withPartition(null), withId("PT-NULL"), withActiveTrue());
// FIXME: move down
IIdType patientId1 = createPatient(withPartition(1), withId("PT-1"), withActiveTrue());
logAllTokenIndexes();
IIdType patientIdNull = createPatient(withPartition(null), withId("PT-NULL"), withActiveTrue());
IIdType patientId2 = createPatient(withPartition(2), withId("PT-2"), withActiveTrue());
/* *******************************
@ -2198,6 +2201,8 @@ public class PartitioningSqlR4Test extends BasePartitioningR4Test {
IIdType patientId1 = createPatient(withPartition(1), withFamily("FAMILY"));
createPatient(withPartition(2), withFamily("FAMILY"));
logAllStringIndexes();
addReadPartition(1);
myCaptureQueriesListener.clear();
@ -2207,7 +2212,7 @@ public class PartitioningSqlR4Test extends BasePartitioningR4Test {
IBundleProvider results = myPatientDao.search(map, mySrd);
List<IIdType> ids = toUnqualifiedVersionlessIds(results);
myCaptureQueriesListener.logSelectQueriesForCurrentThread();
assertThat(ids, contains(patientId1));
assertThat(ids.toString(), ids, contains(patientId1));
String searchSql = myCaptureQueriesListener.getSelectQueriesForCurrentThread().get(0).getSql(true, true);
ourLog.info("Search SQL:\n{}", searchSql);

94
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/r4/SearchParamExtractorR4Test.java
View File

@ -224,57 +224,6 @@ public class SearchParamExtractorR4Test {
}
@Test
public void testTokenText_Enabled_Identifier() {
Observation obs = new Observation();
obs.addIdentifier().setSystem("sys").setValue("val").getType().setText("Help Im a Bug");
SearchParamExtractorR4 extractor = new SearchParamExtractorR4(new ModelConfig(), myPartitionSettings, ourCtx, mySearchParamRegistry);
List<BaseResourceIndexedSearchParam> tokens = extractor.extractSearchParamTokens(obs)
.stream()
.filter(t -> t.getParamName().equals("identifier"))
.sorted(comparing(o -> o.getClass().getName()).reversed())
.collect(Collectors.toList());
assertEquals(2, tokens.size());
ResourceIndexedSearchParamToken token = (ResourceIndexedSearchParamToken) tokens.get(0);
assertEquals("identifier", token.getParamName());
assertEquals("sys", token.getSystem());
assertEquals("val", token.getValue());
ResourceIndexedSearchParamString string = (ResourceIndexedSearchParamString) tokens.get(1);
assertEquals("identifier", string.getParamName());
assertEquals("Help Im a Bug", string.getValueExact());
}
@Test
public void testTokenText_DisabledInSearchParam_Identifier() {
RuntimeSearchParam existingCodeSp = mySearchParamRegistry.getActiveSearchParams("Observation").get("identifier");
RuntimeSearchParam codeSearchParam = new RuntimeSearchParam(existingCodeSp);
codeSearchParam.addExtension(HapiExtensions.EXT_SEARCHPARAM_TOKEN_SUPPRESS_TEXT_INDEXING, new Extension(HapiExtensions.EXT_SEARCHPARAM_TOKEN_SUPPRESS_TEXT_INDEXING, new BooleanType(true)));
mySearchParamRegistry.addSearchParam(codeSearchParam);
Observation obs = new Observation();
obs.addIdentifier().setSystem("sys").setValue("val").getType().setText("Help Im a Bug");
SearchParamExtractorR4 extractor = new SearchParamExtractorR4(new ModelConfig(), myPartitionSettings, ourCtx, mySearchParamRegistry);
List<BaseResourceIndexedSearchParam> tokens = extractor.extractSearchParamTokens(obs)
.stream()
.filter(t -> t.getParamName().equals("identifier"))
.sorted(comparing(o -> o.getClass().getName()).reversed())
.collect(Collectors.toList());
assertEquals(1, tokens.size());
ResourceIndexedSearchParamToken token = (ResourceIndexedSearchParamToken) tokens.get(0);
assertEquals("identifier", token.getParamName());
assertEquals("sys", token.getSystem());
assertEquals("val", token.getValue());
}
@Test
public void testReferenceWithResolve() {
Encounter enc = new Encounter();
@ -394,6 +343,49 @@ public class SearchParamExtractorR4Test {
assertEquals(2, list.size());
}
@Test
public void testExtractIdentifierOfType() {
ModelConfig modelConfig = new ModelConfig();
modelConfig.setIndexIdentifierOfType(true);
Patient patient = new Patient();
patient
.addIdentifier()
.setSystem("http://foo1")
.setValue("bar1")
.getType()
.addCoding()
.setSystem("http://terminology.hl7.org/CodeSystem/v2-0203")
.setCode("MR");
patient
.addIdentifier()
.setSystem("http://foo2")
.setValue("bar2")
.getType()
.addCoding()
.setSystem("http://terminology.hl7.org/CodeSystem/v2-0203")
.setCode("MR");
SearchParamExtractorR4 extractor = new SearchParamExtractorR4(modelConfig, new PartitionSettings(), ourCtx, mySearchParamRegistry);
List<ResourceIndexedSearchParamToken> list = extractor
.extractSearchParamTokens(patient)
.stream()
.map(t->(ResourceIndexedSearchParamToken)t)
.collect(Collectors.toList());
list.forEach(t->t.calculateHashes());
ourLog.info("Found tokens:\n * {}", list.stream().map(t->t.toString()).collect(Collectors.joining("\n * ")));
assertThat(list, containsInAnyOrder(
new ResourceIndexedSearchParamToken(new PartitionSettings(), "Patient", "deceased", null, "false"),
new ResourceIndexedSearchParamToken(new PartitionSettings(), "Patient", "identifier", "http://foo1", "bar1"),
new ResourceIndexedSearchParamToken(new PartitionSettings(), "Patient", "identifier", "http://foo2", "bar2"),
new ResourceIndexedSearchParamToken(new PartitionSettings(), "Patient", "identifier:of-type", "http://terminology.hl7.org/CodeSystem/v2-0203", "MR|bar1"),
new ResourceIndexedSearchParamToken(new PartitionSettings(), "Patient", "identifier:of-type", "http://terminology.hl7.org/CodeSystem/v2-0203", "MR|bar2")
));
}
private static class MySearchParamRegistry implements ISearchParamRegistry, ISearchParamRegistryController {

7
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/provider/r4/ResourceProviderR4SearchContainedTest.java
View File

@ -859,6 +859,7 @@ public class ResourceProviderR4SearchContainedTest extends BaseResourceProviderR
obs.getSubject().setReference("#patient1");
oid1 = myObservationDao.create(obs, mySrd).getId().toUnqualifiedVersionless();
logAllStringIndexes("subject.family");
ourLog.info("Input: {}", myFhirCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(obs));
@ -877,7 +878,9 @@ public class ResourceProviderR4SearchContainedTest extends BaseResourceProviderR
}
// -- update
oid1 = myObservationDao.update(createdObs, mySrd).getId().toUnqualifiedVersionless();
myObservationDao.update(createdObs, mySrd).getId().toUnqualifiedVersionless();
logAllStringIndexes("subject.family");
}
{
@ -891,10 +894,12 @@ public class ResourceProviderR4SearchContainedTest extends BaseResourceProviderR
obs.getSubject().setReference("#patient1");
myObservationDao.create(obs, mySrd).getId().toUnqualifiedVersionless();
logAllStringIndexes("subject.family");
ourLog.info("Input: {}", myFhirCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(obs));
}
{
Patient p = new Patient();
p.setId("patient1");

75
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/provider/r4/ResourceProviderSearchModifierR4Test.java
View File

@ -1,12 +1,15 @@
package ca.uhn.fhir.jpa.provider.r4;
import static org.junit.jupiter.api.Assertions.assertEquals;
import static org.junit.jupiter.api.Assertions.fail;
import java.io.IOException;
import java.nio.charset.StandardCharsets;
import java.util.ArrayList;
import java.util.List;
import ca.uhn.fhir.jpa.model.entity.ModelConfig;
import ca.uhn.fhir.rest.server.exceptions.InvalidRequestException;
import org.apache.commons.io.IOUtils;
import org.apache.http.client.methods.CloseableHttpResponse;
import org.apache.http.client.methods.HttpGet;
@ -44,7 +47,9 @@ public class ResourceProviderSearchModifierR4Test extends BaseResourceProviderR4
myDaoConfig.setSearchPreFetchThresholds(new DaoConfig().getSearchPreFetchThresholds());
myDaoConfig.setAllowContainsSearches(new DaoConfig().isAllowContainsSearches());
myDaoConfig.setIndexMissingFields(new DaoConfig().getIndexMissingFields());
myModelConfig.setIndexIdentifierOfType(new ModelConfig().isIndexIdentifierOfType());
myClient.unregisterInterceptor(myCapturingInterceptor);
}
@ -199,7 +204,75 @@ public class ResourceProviderSearchModifierR4Test extends BaseResourceProviderR4
assertEquals(obsList.get(5).toString(), ids.get(3));
}
@Test
public void testSearch_OfType_PartialBlocked() {
myModelConfig.setIndexIdentifierOfType(true);
try {
String uri = ourServerBase + "/Patient?identifier:of-type=A";
myClient.search().byUrl(uri).execute();
fail();
} catch (InvalidRequestException e) {
assertEquals("HTTP 400 Bad Request: Invalid parameter value for :of-type query", e.getMessage());
}
try {
String uri = ourServerBase + "/Patient?identifier:of-type=A|B";
myClient.search().byUrl(uri).execute();
fail();
} catch (InvalidRequestException e) {
assertEquals("HTTP 400 Bad Request: Invalid parameter value for :of-type query", e.getMessage());
}
try {
String uri = ourServerBase + "/Patient?identifier:of-type=A|B|";
myClient.search().byUrl(uri).execute();
fail();
} catch (InvalidRequestException e) {
assertEquals("HTTP 400 Bad Request: Invalid parameter value for :of-type query", e.getMessage());
}
try {
String uri = ourServerBase + "/Patient?identifier:of-type=|B|C";
myClient.search().byUrl(uri).execute();
fail();
} catch (InvalidRequestException e) {
assertEquals("HTTP 400 Bad Request: Invalid parameter value for :of-type query", e.getMessage());
}
try {
String uri = ourServerBase + "/Patient?identifier:of-type=||C";
myClient.search().byUrl(uri).execute();
fail();
} catch (InvalidRequestException e) {
assertEquals("HTTP 400 Bad Request: Invalid parameter value for :of-type query", e.getMessage());
}
try {
String uri = ourServerBase + "/Patient?identifier:of-type=|B|";
myClient.search().byUrl(uri).execute();
fail();
} catch (InvalidRequestException e) {
assertEquals("HTTP 400 Bad Request: Invalid parameter value for :of-type query", e.getMessage());
}
try {
String uri = ourServerBase + "/Patient?identifier:of-type=A||";
myClient.search().byUrl(uri).execute();
fail();
} catch (InvalidRequestException e) {
assertEquals("HTTP 400 Bad Request: Invalid parameter value for :of-type query", e.getMessage());
}
try {
String uri = ourServerBase + "/Patient?identifier:of-type=||";
myClient.search().byUrl(uri).execute();
fail();
} catch (InvalidRequestException e) {
assertEquals("HTTP 400 Bad Request: Invalid parameter value for :of-type query", e.getMessage());
}
}
private List<String> searchAndReturnUnqualifiedVersionlessIdValues(String uri) throws IOException {
List<String> ids;

8
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/stresstest/GiantTransactionPerfTest.java
View File

@ -182,7 +182,7 @@ public class GiantTransactionPerfTest {
myTransactionProcessor.setModelConfig(myDaoConfig.getModelConfig());
myTransactionProcessor.setHapiTransactionService(myHapiTransactionService);
myTransactionProcessor.setDaoRegistry(myDaoRegistry);
myTransactionProcessor.setPartitionSettingsForUnitTest(myPartitionSettings);
myTransactionProcessor.setPartitionSettingsForUnitTest(this.myPartitionSettings);
myTransactionProcessor.setIdHelperServiceForUnitTest(myIdHelperService);
myTransactionProcessor.setFhirContextForUnitTest(myCtx);
myTransactionProcessor.start();
@ -190,6 +190,7 @@ public class GiantTransactionPerfTest {
mySystemDao = new FhirSystemDaoR4();
mySystemDao.setTransactionProcessorForUnitTest(myTransactionProcessor);
mySystemDao.setDaoConfigForUnitTest(myDaoConfig);
mySystemDao.setPartitionSettingsForUnitTest(myPartitionSettings);
mySystemDao.start();
when(myAppCtx.getBean(eq(IInstanceValidatorModule.class))).thenReturn(myInstanceValidatorSvc);
@ -228,7 +229,7 @@ public class GiantTransactionPerfTest {
mySearchParamExtractor = new SearchParamExtractorR4();
mySearchParamExtractor.setContext(myCtx);
mySearchParamExtractor.setSearchParamRegistry(mySearchParamRegistry);
mySearchParamExtractor.setPartitionSettings(myPartitionSettings);
mySearchParamExtractor.setPartitionSettings(this.myPartitionSettings);
mySearchParamExtractor.setModelConfig(myDaoConfig.getModelConfig());
mySearchParamExtractor.start();
@ -243,7 +244,7 @@ public class GiantTransactionPerfTest {
mySearchParamWithInlineReferencesExtractor = new SearchParamWithInlineReferencesExtractor();
mySearchParamWithInlineReferencesExtractor.setDaoConfig(myDaoConfig);
mySearchParamWithInlineReferencesExtractor.setContext(myCtx);
mySearchParamWithInlineReferencesExtractor.setPartitionSettings(myPartitionSettings);
mySearchParamWithInlineReferencesExtractor.setPartitionSettings(this.myPartitionSettings);
mySearchParamWithInlineReferencesExtractor.setSearchParamExtractorService(mySearchParamExtractorSvc);
mySearchParamWithInlineReferencesExtractor.setSearchParamRegistry(mySearchParamRegistry);
mySearchParamWithInlineReferencesExtractor.setDaoSearchParamSynchronizer(myDaoSearchParamSynchronizer);
@ -263,6 +264,7 @@ public class GiantTransactionPerfTest {
myEobDao.setDaoSearchParamSynchronizer(myDaoSearchParamSynchronizer);
myEobDao.setDaoConfigForUnitTest(myDaoConfig);
myEobDao.setIdHelperSvcForUnitTest(myIdHelperService);
myEobDao.setPartitionSettingsForUnitTest(myPartitionSettings);
myEobDao.start();
myDaoRegistry.setResourceDaos(Lists.newArrayList(myEobDao));

12
hapi-fhir-jpaserver-model/src/main/java/ca/uhn/fhir/jpa/model/entity/BaseResourceIndex.java
View File

@ -20,6 +20,8 @@ package ca.uhn.fhir.jpa.model.entity;
* #L%
*/
import org.apache.commons.lang3.ObjectUtils;
import javax.persistence.MappedSuperclass;
import java.io.Serializable;
@ -32,6 +34,16 @@ public abstract class BaseResourceIndex extends BasePartitionable implements Ser
public abstract void calculateHashes();
public abstract void clearHashes();
@Override
public void setPartitionId(PartitionablePartitionId thePartitionId) {
if (ObjectUtils.notEqual(getPartitionId(), thePartitionId)) {
super.setPartitionId(thePartitionId);
clearHashes();
}
}
/**
* Subclasses must implement
*/

9
hapi-fhir-jpaserver-model/src/main/java/ca/uhn/fhir/jpa/model/entity/BaseResourceIndexedSearchParam.java
View File

@ -31,6 +31,7 @@ import com.google.common.hash.HashCode;
import com.google.common.hash.HashFunction;
import com.google.common.hash.Hasher;
import com.google.common.hash.Hashing;
import org.apache.commons.lang3.StringUtils;
import org.hibernate.search.mapper.pojo.mapping.definition.annotation.FullTextField;
import org.hibernate.search.mapper.pojo.mapping.definition.annotation.GenericField;
@ -97,7 +98,10 @@ public abstract class BaseResourceIndexedSearchParam extends BaseResourceIndex {
}
public void setParamName(String theName) {
myParamName = theName;
if (!StringUtils.equals(myParamName, theName)) {
myParamName = theName;
clearHashes();
}
}
public ResourceTable getResource() {
@ -222,6 +226,7 @@ public abstract class BaseResourceIndexedSearchParam extends BaseResourceIndex {
}
HashCode hashCode = hasher.hash();
return hashCode.asLong();
long retVal = hashCode.asLong();
return retVal;
}
}

38
hapi-fhir-jpaserver-model/src/main/java/ca/uhn/fhir/jpa/model/entity/ModelConfig.java
View File

@ -50,12 +50,7 @@ public class ModelConfig {
* <li><code>"http://hl7.org/fhir/StructureDefinition/*"</code></li>
* </ul>
*/
public static final Set<String> DEFAULT_LOGICAL_BASE_URLS = Collections.unmodifiableSet(new HashSet<>(Arrays.asList(
"http://hl7.org/fhir/ValueSet/*",
"http://hl7.org/fhir/CodeSystem/*",
"http://hl7.org/fhir/valueset-*",
"http://hl7.org/fhir/codesystem-*",
"http://hl7.org/fhir/StructureDefinition/*")));
public static final Set<String> DEFAULT_LOGICAL_BASE_URLS = Collections.unmodifiableSet(new HashSet<>(Arrays.asList("http://hl7.org/fhir/ValueSet/*", "http://hl7.org/fhir/CodeSystem/*", "http://hl7.org/fhir/valueset-*", "http://hl7.org/fhir/codesystem-*", "http://hl7.org/fhir/StructureDefinition/*")));
public static final String DEFAULT_WEBSOCKET_CONTEXT_PATH = "/websocket";
@ -101,6 +96,7 @@ public class ModelConfig {
private boolean myIndexOnContainedResourcesRecursively = false;
private boolean myAllowMdmExpansion = false;
private boolean myAutoSupportDefaultSearchParams = true;
private boolean myIndexIdentifierOfType = false;
/**
* Constructor
@ -111,6 +107,32 @@ public class ModelConfig {
setNormalizedQuantitySearchLevel(NormalizedQuantitySearchLevel.NORMALIZED_QUANTITY_SEARCH_NOT_SUPPORTED);
}
/**
* If set to <code>true</code> (default is <code>false</code>) the
* <code>:of-type</code> modifier on token search parameters for
* identifiers will be supported. Enabling this causes additional
* indexing overhead (although very minor) so it is disabled unless it is
* actually needed.
*
* @since 5.7.0
*/
public boolean isIndexIdentifierOfType() {
return myIndexIdentifierOfType;
}
/**
* If set to <code>true</code> (default is <code>false</code>) the
* <code>:of-type</code> modifier on token search parameters for
* identifiers will be supported. Enabling this causes additional
* indexing overhead (although very minor) so it is disabled unless it is
* actually needed.
*
* @since 5.7.0
*/
public void setIndexIdentifierOfType(boolean theIndexIdentifierOfType) {
myIndexIdentifierOfType = theIndexIdentifierOfType;
}
/**
* If set to {@code true} the default search params (i.e. the search parameters that are
* defined by the FHIR specification itself) may be overridden by uploading search
@ -816,7 +838,7 @@ public class ModelConfig {
* Disabling this obviously reduces the options for searching however.
* </p>
*
* @since 6.0.0
* @since 5.7.0
*/
public boolean isAutoSupportDefaultSearchParams() {
return myAutoSupportDefaultSearchParams;
@ -832,7 +854,7 @@ public class ModelConfig {
* Disabling this obviously reduces the options for searching however.
* </p>
*
* @since 6.0.0
* @since 5.7.0
*/
public void setAutoSupportDefaultSearchParams(boolean theAutoSupportDefaultSearchParams) {
myAutoSupportDefaultSearchParams = theAutoSupportDefaultSearchParams;

24
hapi-fhir-jpaserver-model/src/main/java/ca/uhn/fhir/jpa/model/entity/PartitionablePartitionId.java
View File

@ -21,6 +21,8 @@ package ca.uhn.fhir.jpa.model.entity;
*/
import ca.uhn.fhir.interceptor.model.RequestPartitionId;
import org.apache.commons.lang3.builder.EqualsBuilder;
import org.apache.commons.lang3.builder.HashCodeBuilder;
import javax.annotation.Nonnull;
import javax.annotation.Nullable;
@ -63,6 +65,21 @@ public class PartitionablePartitionId implements Cloneable {
return this;
}
@Override
public boolean equals(Object theO) {
if (!(theO instanceof PartitionablePartitionId)) {
return false;
}
PartitionablePartitionId that = (PartitionablePartitionId) theO;
return new EqualsBuilder().append(myPartitionId, that.myPartitionId).append(myPartitionDate, that.myPartitionDate).isEquals();
}
@Override
public int hashCode() {
return new HashCodeBuilder(17, 37).append(myPartitionId).append(myPartitionDate).toHashCode();
}
@Nullable
public LocalDate getPartitionDate() {
return myPartitionDate;
@ -85,6 +102,13 @@ public class PartitionablePartitionId implements Cloneable {
return RequestPartitionId.fromPartitionId(getPartitionId(), getPartitionDate());
}
@Override
public String toString() {
return "[" +
getPartitionId() +
"]";
}
@Nonnull
public static RequestPartitionId toRequestPartitionId(@Nullable PartitionablePartitionId theRequestPartitionId) {
if (theRequestPartitionId != null) {

10
hapi-fhir-jpaserver-model/src/main/java/ca/uhn/fhir/jpa/model/entity/ResourceIndexedComboTokenNonUnique.java
View File

@ -82,6 +82,7 @@ public class ResourceIndexedComboTokenNonUnique extends BaseResourceIndex implem
myPartitionSettings = thePartitionSettings;
myResource = theEntity;
myIndexString = theQueryString;
calculateHashes();
}
public String getIndexString() {
@ -125,8 +126,17 @@ public class ResourceIndexedComboTokenNonUnique extends BaseResourceIndex implem
myId = theId;
}
@Override
public void clearHashes() {
myHashComplete = null;
}
@Override
public void calculateHashes() {
if (myHashComplete != null) {
return;
}
PartitionSettings partitionSettings = getPartitionSettings();
PartitionablePartitionId partitionId = getPartitionId();
String queryString = myIndexString;

14
hapi-fhir-jpaserver-model/src/main/java/ca/uhn/fhir/jpa/model/entity/ResourceIndexedSearchParamBaseQuantity.java
View File

@ -60,12 +60,26 @@ public abstract class ResourceIndexedSearchParamBaseQuantity extends BaseResourc
@Column(name = "HASH_IDENTITY", nullable = true)
private Long myHashIdentity;
/**
* Constructor
*/
public ResourceIndexedSearchParamBaseQuantity() {
super();
}
@Override
public void clearHashes() {
myHashIdentity = null;
myHashIdentityAndUnits = null;
myHashIdentitySystemAndUnits = null;
}
@Override
public void calculateHashes() {
if (myHashIdentity != null || myHashIdentityAndUnits != null || myHashIdentitySystemAndUnits != null) {
return;
}
String resourceType = getResourceType();
String paramName = getParamName();
String units = getUnits();

10
hapi-fhir-jpaserver-model/src/main/java/ca/uhn/fhir/jpa/model/entity/ResourceIndexedSearchParamCoords.java
View File

@ -26,7 +26,6 @@ import org.apache.commons.lang3.builder.EqualsBuilder;
import org.apache.commons.lang3.builder.HashCodeBuilder;
import org.apache.commons.lang3.builder.ToStringBuilder;
import org.apache.commons.lang3.builder.ToStringStyle;
import org.hibernate.search.mapper.pojo.mapping.definition.annotation.FullTextField;
import javax.persistence.Column;
import javax.persistence.Embeddable;
@ -79,8 +78,17 @@ public class ResourceIndexedSearchParamCoords extends BaseResourceIndexedSearchP
calculateHashes();
}
@Override
public void clearHashes() {
myHashIdentity = null;
}
@Override
public void calculateHashes() {
if (myHashIdentity != null) {
return;
}
String resourceType = getResourceType();
String paramName = getParamName();
setHashIdentity(calculateHashIdentity(getPartitionSettings(), getPartitionId(), resourceType, paramName));

11
hapi-fhir-jpaserver-model/src/main/java/ca/uhn/fhir/jpa/model/entity/ResourceIndexedSearchParamDate.java
View File

@ -22,7 +22,6 @@ package ca.uhn.fhir.jpa.model.entity;
import java.text.ParseException;
import java.text.SimpleDateFormat;
import java.util.Calendar;
import java.util.Date;
import javax.persistence.Column;
@ -129,7 +128,6 @@ public class ResourceIndexedSearchParamDate extends BaseResourceIndexedSearchPar
reComputeValueHighDate(theHigh, theHighString);
myOriginalValue = theOriginalValue;
calculateHashes();
}
private void computeValueHighDateOrdinal(String theHigh) {
@ -202,8 +200,17 @@ public class ResourceIndexedSearchParamDate extends BaseResourceIndexedSearchPar
myHashIdentity = source.myHashIdentity;
}
@Override
public void clearHashes() {
myHashIdentity = null;
}
@Override
public void calculateHashes() {
if (myHashIdentity != null) {
return;
}
String resourceType = getResourceType();
String paramName = getParamName();
setHashIdentity(calculateHashIdentity(getPartitionSettings(), getPartitionId(), resourceType, paramName));

7
hapi-fhir-jpaserver-model/src/main/java/ca/uhn/fhir/jpa/model/entity/ResourceIndexedSearchParamNumber.java
View File

@ -86,9 +86,16 @@ public class ResourceIndexedSearchParamNumber extends BaseResourceIndexedSearchP
myHashIdentity = source.myHashIdentity;
}
@Override
public void clearHashes() {
myHashIdentity = null;
}
@Override
public void calculateHashes() {
if (myHashIdentity != null) {
return;
}
String resourceType = getResourceType();
String paramName = getParamName();
setHashIdentity(calculateHashIdentity(getPartitionSettings(), getPartitionId(), resourceType, paramName));

1
hapi-fhir-jpaserver-model/src/main/java/ca/uhn/fhir/jpa/model/entity/ResourceIndexedSearchParamQuantity.java
View File

@ -39,7 +39,6 @@ import javax.persistence.Table;
import org.apache.commons.lang3.builder.EqualsBuilder;
import org.apache.commons.lang3.builder.ToStringBuilder;
import org.apache.commons.lang3.builder.ToStringStyle;
import org.hibernate.search.mapper.pojo.mapping.definition.annotation.FullTextField;
import org.hibernate.search.mapper.pojo.mapping.definition.annotation.ScaledNumberField;
import ca.uhn.fhir.jpa.model.config.PartitionSettings;

20
hapi-fhir-jpaserver-model/src/main/java/ca/uhn/fhir/jpa/model/entity/ResourceIndexedSearchParamString.java
View File

@ -29,10 +29,6 @@ import org.apache.commons.lang3.builder.EqualsBuilder;
import org.apache.commons.lang3.builder.HashCodeBuilder;
import org.apache.commons.lang3.builder.ToStringBuilder;
import org.apache.commons.lang3.builder.ToStringStyle;
import org.hibernate.search.engine.backend.types.Projectable;
import org.hibernate.search.engine.backend.types.Searchable;
import org.hibernate.search.mapper.pojo.mapping.definition.annotation.FullTextField;
import org.hibernate.search.mapper.pojo.mapping.definition.annotation.Indexed;
import javax.persistence.Column;
import javax.persistence.Embeddable;
@ -132,8 +128,20 @@ public class ResourceIndexedSearchParamString extends BaseResourceIndexedSearchP
myHashNormalizedPrefix = source.myHashNormalizedPrefix;
}
@Override
public void clearHashes() {
myHashIdentity = null;
myHashNormalizedPrefix = null;
myHashExact = null;
}
@Override
public void calculateHashes() {
if (myHashIdentity != null || myHashExact != null || myHashNormalizedPrefix != null) {
return;
}
String resourceType = getResourceType();
String paramName = getParamName();
String valueNormalized = getValueNormalized();
@ -245,6 +253,7 @@ public class ResourceIndexedSearchParamString extends BaseResourceIndexedSearchP
b.append("resourceId", getResourcePid());
b.append("hashNormalizedPrefix", getHashNormalizedPrefix());
b.append("valueNormalized", getValueNormalized());
b.append("partitionId", getPartitionId());
return b.build();
}
@ -284,7 +293,8 @@ public class ResourceIndexedSearchParamString extends BaseResourceIndexedSearchP
hashPrefixLength = 0;
}
return hash(thePartitionSettings, theRequestPartitionId, theResourceType, theParamName, StringUtil.left(theValueNormalized, hashPrefixLength));
String value = StringUtil.left(theValueNormalized, hashPrefixLength);
return hash(thePartitionSettings, theRequestPartitionId, theResourceType, theParamName, value);
}
}

31
hapi-fhir-jpaserver-model/src/main/java/ca/uhn/fhir/jpa/model/entity/ResourceIndexedSearchParamToken.java
View File

@ -23,6 +23,7 @@ package ca.uhn.fhir.jpa.model.entity;
import ca.uhn.fhir.interceptor.model.RequestPartitionId;
import ca.uhn.fhir.jpa.model.config.PartitionSettings;
import ca.uhn.fhir.model.api.IQueryParameterType;
import ca.uhn.fhir.rest.api.Constants;
import ca.uhn.fhir.rest.param.TokenParam;
import org.apache.commons.lang3.StringUtils;
import org.apache.commons.lang3.builder.EqualsBuilder;
@ -54,7 +55,7 @@ import static org.apache.commons.lang3.StringUtils.trim;
* IDX_SP_TOKEN_UNQUAL
*/
// TODO PERF Recommend to drop this index:
// TODO PERF Recommend to drop this index (added by JA - I don't actually think we even need the identity hash for this type, we could potentially drop the column too):
@Index(name = "IDX_SP_TOKEN_HASH", columnList = "HASH_IDENTITY"),
@Index(name = "IDX_SP_TOKEN_HASH_S", columnList = "HASH_SYS"),
@Index(name = "IDX_SP_TOKEN_HASH_SV", columnList = "HASH_SYS_AND_VALUE"),
@ -140,17 +141,35 @@ public class ResourceIndexedSearchParamToken extends BaseResourceIndexedSearchPa
myHashIdentity = source.myHashIdentity;
}
@Override
public void clearHashes() {
myHashIdentity = null;
myHashSystem = null;
myHashSystemAndValue = null;
myHashValue = null;
}
@Override
public void calculateHashes() {
if (myHashIdentity != null || myHashSystem != null || myHashValue != null || myHashSystemAndValue != null) {
return;
}
String resourceType = getResourceType();
String paramName = getParamName();
String system = getSystem();
String value = getValue();
setHashIdentity(calculateHashIdentity(getPartitionSettings(), getPartitionId(), resourceType, paramName));
setHashSystem(calculateHashSystem(getPartitionSettings(), getPartitionId(), resourceType, paramName, system));
setHashSystemAndValue(calculateHashSystemAndValue(getPartitionSettings(), getPartitionId(), resourceType, paramName, system, value));
setHashValue(calculateHashValue(getPartitionSettings(), getPartitionId(), resourceType, paramName, value));
// Searches using the :of-type modifier can never be partial (system-only or value-only) so don't
// bother saving these
boolean calculatePartialHashes = !StringUtils.endsWith(paramName, Constants.PARAMQUALIFIER_TOKEN_OF_TYPE);
if (calculatePartialHashes) {
setHashSystem(calculateHashSystem(getPartitionSettings(), getPartitionId(), resourceType, paramName, system));
setHashValue(calculateHashValue(getPartitionSettings(), getPartitionId(), resourceType, paramName, value));
}
}
@Override
@ -172,7 +191,7 @@ public class ResourceIndexedSearchParamToken extends BaseResourceIndexedSearchPa
return b.isEquals();
}
Long getHashSystem() {
public Long getHashSystem() {
return myHashSystem;
}
@ -216,6 +235,7 @@ public class ResourceIndexedSearchParamToken extends BaseResourceIndexedSearchPa
public void setSystem(String theSystem) {
mySystem = StringUtils.defaultIfBlank(theSystem, null);
myHashSystemAndValue = null;
}
public String getValue() {
@ -224,6 +244,7 @@ public class ResourceIndexedSearchParamToken extends BaseResourceIndexedSearchPa
public ResourceIndexedSearchParamToken setValue(String theValue) {
myValue = StringUtils.defaultIfBlank(theValue, null);
myHashSystemAndValue = null;
return this;
}
@ -261,6 +282,7 @@ public class ResourceIndexedSearchParamToken extends BaseResourceIndexedSearchPa
b.append("hashSystem", myHashSystem);
b.append("hashValue", myHashValue);
b.append("hashSysAndValue", myHashSystemAndValue);
b.append("partition", getPartitionId());
return b.build();
}
@ -292,6 +314,7 @@ public class ResourceIndexedSearchParamToken extends BaseResourceIndexedSearchPa
return retVal;
}
public static long calculateHashSystem(PartitionSettings thePartitionSettings, PartitionablePartitionId theRequestPartitionId, String theResourceType, String theParamName, String theSystem) {
RequestPartitionId requestPartitionId = PartitionablePartitionId.toRequestPartitionId(theRequestPartitionId);
return calculateHashSystem(thePartitionSettings, requestPartitionId, theResourceType, theParamName, theSystem);

10
hapi-fhir-jpaserver-model/src/main/java/ca/uhn/fhir/jpa/model/entity/ResourceIndexedSearchParamUri.java
View File

@ -107,9 +107,19 @@ public class ResourceIndexedSearchParamUri extends BaseResourceIndexedSearchPara
myHashIdentity = source.myHashIdentity;
}
@Override
public void clearHashes() {
myHashIdentity = null;
myHashUri = null;
}
@Override
public void calculateHashes() {
if (myHashIdentity != null || myHashUri != null) {
return;
}
String resourceType = getResourceType();
String paramName = getParamName();
String uri = getUri();

5
hapi-fhir-jpaserver-model/src/main/java/ca/uhn/fhir/jpa/model/entity/ResourceLink.java
View File

@ -235,6 +235,11 @@ public class ResourceLink extends BaseResourceIndex {
myId = theId;
}
@Override
public void clearHashes() {
// nothing right now
}
@Override
public void calculateHashes() {
// nothing right now

220
hapi-fhir-jpaserver-searchparam/src/main/java/ca/uhn/fhir/jpa/searchparam/extractor/BaseSearchParamExtractor.java
View File

@ -42,6 +42,7 @@ import ca.uhn.fhir.jpa.model.entity.ResourceIndexedSearchParamUri;
import ca.uhn.fhir.jpa.model.util.UcumServiceUtil;
import ca.uhn.fhir.jpa.searchparam.SearchParamConstants;
import ca.uhn.fhir.model.primitive.BoundCodeDt;
import ca.uhn.fhir.rest.api.Constants;
import ca.uhn.fhir.rest.api.RestSearchParameterTypeEnum;
import ca.uhn.fhir.rest.server.exceptions.InternalErrorException;
import ca.uhn.fhir.rest.server.util.ISearchParamRegistry;
@ -88,7 +89,6 @@ import java.util.stream.Collectors;
import static org.apache.commons.lang3.StringUtils.isBlank;
import static org.apache.commons.lang3.StringUtils.isNotBlank;
import static org.apache.commons.lang3.StringUtils.strip;
import static org.apache.commons.lang3.StringUtils.trim;
public abstract class BaseSearchParamExtractor implements ISearchParamExtractor {
@ -642,20 +642,35 @@ public abstract class BaseSearchParamExtractor implements ISearchParamExtractor
high.ifPresent(theIBase -> addQuantity_QuantityNormalized(theResourceType, theParams, theSearchParam, theIBase));
}
@SuppressWarnings("unchecked")
private void addToken_Identifier(String theResourceType, Set<BaseResourceIndexedSearchParam> theParams, RuntimeSearchParam theSearchParam, IBase theValue) {
String system = extractValueAsString(myIdentifierSystemValueChild, theValue);
String value = extractValueAsString(myIdentifierValueValueChild, theValue);
if (isNotBlank(value)) {
createTokenIndexIfNotBlank(theResourceType, theParams, theSearchParam, system, value);
}
createTokenIndexIfNotBlankAndAdd(theResourceType, theParams, theSearchParam, system, value);
if (shouldIndexTextComponentOfToken(theSearchParam)) {
Optional<IBase> type = myIdentifierTypeValueChild.getAccessor().getFirstValueOrNull(theValue);
if (type.isPresent()) {
String text = extractValueAsString(myIdentifierTypeTextValueChild, type.get());
createStringIndexIfNotBlank(theResourceType, theParams, theSearchParam, text);
boolean indexIdentifierType = myModelConfig.isIndexIdentifierOfType();
if (indexIdentifierType) {
Optional<IBase> type = myIdentifierTypeValueChild.getAccessor().getFirstValueOrNull(theValue);
if (type.isPresent()) {
List<IBase> codings = myCodeableConceptCodingValueChild.getAccessor().getValues(type.get());
for (IBase nextCoding : codings) {
String typeSystem = myCodingSystemValueChild.getAccessor().getFirstValueOrNull(nextCoding).map(t -> ((IPrimitiveType<String>) t).getValue()).orElse(null);
String typeValue = myCodingCodeValueChild.getAccessor().getFirstValueOrNull(nextCoding).map(t -> ((IPrimitiveType<String>) t).getValue()).orElse(null);
if (isNotBlank(typeSystem) && isNotBlank(typeValue)) {
String paramName = theSearchParam.getName() + Constants.PARAMQUALIFIER_TOKEN_OF_TYPE;
ResourceIndexedSearchParamToken token = createTokenIndexIfNotBlank(theResourceType, typeSystem, typeValue + "|" + value, paramName);
if (token != null) {
theParams.add(token);
}
}
}
}
}
}
}
protected boolean shouldIndexTextComponentOfToken(RuntimeSearchParam theSearchParam) {
@ -733,7 +748,7 @@ public abstract class BaseSearchParamExtractor implements ISearchParamExtractor
private void addToken_ContactPoint(String theResourceType, Set<BaseResourceIndexedSearchParam> theParams, RuntimeSearchParam theSearchParam, IBase theValue) {
String system = extractValueAsString(myContactPointSystemValueChild, theValue);
String value = extractValueAsString(myContactPointValueValueChild, theValue);
createTokenIndexIfNotBlank(theResourceType, theParams, theSearchParam, system, value);
createTokenIndexIfNotBlankAndAdd(theResourceType, theParams, theSearchParam, system, value);
}
private void addToken_PatientCommunication(String theResourceType, Set<BaseResourceIndexedSearchParam> theParams, RuntimeSearchParam theSearchParam, IBase theValue) {
@ -1062,7 +1077,7 @@ public abstract class BaseSearchParamExtractor implements ISearchParamExtractor
}
}
private void createTokenIndexIfNotBlank(String theResourceType, Set<BaseResourceIndexedSearchParam> theParams, RuntimeSearchParam theSearchParam, String theSystem, String theValue) {
private void createTokenIndexIfNotBlankAndAdd(String theResourceType, Set<BaseResourceIndexedSearchParam> theParams, RuntimeSearchParam theSearchParam, String theSystem, String theValue) {
ResourceIndexedSearchParamToken nextEntity = createTokenIndexIfNotBlank(theResourceType, theSearchParam, theSystem, theValue);
if (nextEntity != null) {
theParams.add(nextEntity);
@ -1075,6 +1090,11 @@ public abstract class BaseSearchParamExtractor implements ISearchParamExtractor
}
private ResourceIndexedSearchParamToken createTokenIndexIfNotBlank(String theResourceType, RuntimeSearchParam theSearchParam, String theSystem, String theValue) {
String searchParamName = theSearchParam.getName();
return createTokenIndexIfNotBlank(theResourceType, theSystem, theValue, searchParamName);
}
private ResourceIndexedSearchParamToken createTokenIndexIfNotBlank(String theResourceType, String theSystem, String theValue, String searchParamName) {
String system = theSystem;
String value = theValue;
ResourceIndexedSearchParamToken nextEntity = null;
@ -1086,7 +1106,7 @@ public abstract class BaseSearchParamExtractor implements ISearchParamExtractor
value = value.substring(0, ResourceIndexedSearchParamToken.MAX_LENGTH);
}
nextEntity = new ResourceIndexedSearchParamToken(myPartitionSettings, theResourceType, theSearchParam.getName(), system, value);
nextEntity = new ResourceIndexedSearchParamToken(myPartitionSettings, theResourceType, searchParamName, system, value);
}
return nextEntity;
@ -1239,6 +1259,93 @@ public abstract class BaseSearchParamExtractor implements ISearchParamExtractor
}
/**
* Note that this should only be called for R4+ servers. Prior to
* R4 the paths could be separated by the word "or" or by a "|"
* character, so we used a slower splitting mechanism.
*/
@Nonnull
public static String[] splitPathsR4(@Nonnull String thePaths) {
StringTokenizer tok = new StringTokenizer(thePaths, " |");
tok.setTrimmerMatcher(new StringTrimmingTrimmerMatcher());
return tok.getTokenArray();
}
public static boolean tokenTextIndexingEnabledForSearchParam(ModelConfig theModelConfig, RuntimeSearchParam theSearchParam) {
Optional<Boolean> noSuppressForSearchParam = theSearchParam.getExtensions(HapiExtensions.EXT_SEARCHPARAM_TOKEN_SUPPRESS_TEXT_INDEXING).stream()
.map(IBaseExtension::getValue)
.map(val -> (IPrimitiveType<?>) val)
.map(IPrimitiveType::getValueAsString)
.map(Boolean::parseBoolean)
.findFirst();
//if the SP doesn't care, use the system default.
if (!noSuppressForSearchParam.isPresent()) {
return !theModelConfig.isSuppressStringIndexingInTokens();
//If the SP does care, use its value.
} else {
boolean suppressForSearchParam = noSuppressForSearchParam.get();
ourLog.trace("Text indexing for SearchParameter {}: {}", theSearchParam.getName(), suppressForSearchParam);
return !suppressForSearchParam;
}
}
private static void addIgnoredType(FhirContext theCtx, String theType, Set<String> theIgnoredTypes) {
BaseRuntimeElementDefinition<?> elementDefinition = theCtx.getElementDefinition(theType);
if (elementDefinition != null) {
theIgnoredTypes.add(elementDefinition.getName());
}
}
protected static String extractValueAsString(BaseRuntimeChildDefinition theChildDefinition, IBase theElement) {
return theChildDefinition
.getAccessor()
.<IPrimitiveType<?>>getFirstValueOrNull(theElement)
.map(IPrimitiveType::getValueAsString)
.orElse(null);
}
protected static Date extractValueAsDate(BaseRuntimeChildDefinition theChildDefinition, IBase theElement) {
return theChildDefinition
.getAccessor()
.<IPrimitiveType<Date>>getFirstValueOrNull(theElement)
.map(IPrimitiveType::getValue)
.orElse(null);
}
protected static BigDecimal extractValueAsBigDecimal(BaseRuntimeChildDefinition theChildDefinition, IBase theElement) {
return theChildDefinition
.getAccessor()
.<IPrimitiveType<BigDecimal>>getFirstValueOrNull(theElement)
.map(IPrimitiveType::getValue)
.orElse(null);
}
@SuppressWarnings("unchecked")
protected static List<IPrimitiveType<Date>> extractValuesAsFhirDates(BaseRuntimeChildDefinition theChildDefinition, IBase theElement) {
return (List) theChildDefinition
.getAccessor()
.getValues(theElement);
}
protected static List<String> extractValuesAsStrings(BaseRuntimeChildDefinition theChildDefinition, IBase theValue) {
return theChildDefinition
.getAccessor()
.getValues(theValue)
.stream()
.map(t -> (IPrimitiveType) t)
.map(IPrimitiveType::getValueAsString)
.filter(StringUtils::isNotBlank)
.collect(Collectors.toList());
}
protected static <T extends Enum<?>> String extractSystem(IBaseEnumeration<T> theBoundCode) {
if (theBoundCode.getValue() != null) {
return theBoundCode.getEnumFactory().toSystem(theBoundCode.getValue());
}
return null;
}
private class ResourceLinkExtractor implements IExtractor<PathAndRef> {
private PathAndRef myPathAndRef = null;
@ -1313,7 +1420,7 @@ public abstract class BaseSearchParamExtractor implements ISearchParamExtractor
}
private boolean isOrCanBeTreatedAsLocal(IIdType theId) {
boolean acceptableAsLocalReference = !theId.isAbsolute() || myModelConfig.getTreatBaseUrlsAsLocal().contains(theId.getBaseUrl());
boolean acceptableAsLocalReference = !theId.isAbsolute() || myModelConfig.getTreatBaseUrlsAsLocal().contains(theId.getBaseUrl());
return acceptableAsLocalReference;
}
@ -1459,7 +1566,7 @@ public abstract class BaseSearchParamExtractor implements ISearchParamExtractor
IBaseEnumeration<?> obj = (IBaseEnumeration<?>) value;
String system = extractSystem(obj);
String code = obj.getValueAsString();
BaseSearchParamExtractor.this.createTokenIndexIfNotBlank(myResourceTypeName, params, searchParam, system, code);
BaseSearchParamExtractor.this.createTokenIndexIfNotBlankAndAdd(myResourceTypeName, params, searchParam, system, code);
return;
}
@ -1473,7 +1580,7 @@ public abstract class BaseSearchParamExtractor implements ISearchParamExtractor
system = boundCode.getBinder().toSystemString(valueAsEnum);
}
String code = boundCode.getValueAsString();
BaseSearchParamExtractor.this.createTokenIndexIfNotBlank(myResourceTypeName, params, searchParam, system, code);
BaseSearchParamExtractor.this.createTokenIndexIfNotBlankAndAdd(myResourceTypeName, params, searchParam, system, code);
return;
}
@ -1491,7 +1598,7 @@ public abstract class BaseSearchParamExtractor implements ISearchParamExtractor
valueAsString = ((IIdType) value).getIdPart();
}
BaseSearchParamExtractor.this.createTokenIndexIfNotBlank(myResourceTypeName, params, searchParam, systemAsString, valueAsString);
BaseSearchParamExtractor.this.createTokenIndexIfNotBlankAndAdd(myResourceTypeName, params, searchParam, systemAsString, valueAsString);
return;
}
@ -1552,87 +1659,4 @@ public abstract class BaseSearchParamExtractor implements ISearchParamExtractor
}
}
@Nonnull
public static String[] splitPathsR4(@Nonnull String thePaths) {
StringTokenizer tok = new StringTokenizer(thePaths, " |");
tok.setTrimmerMatcher(new StringTrimmingTrimmerMatcher());
return tok.getTokenArray();
}
public static boolean tokenTextIndexingEnabledForSearchParam(ModelConfig theModelConfig, RuntimeSearchParam theSearchParam) {
Optional<Boolean> noSuppressForSearchParam = theSearchParam.getExtensions(HapiExtensions.EXT_SEARCHPARAM_TOKEN_SUPPRESS_TEXT_INDEXING).stream()
.map(IBaseExtension::getValue)
.map(val -> (IPrimitiveType<?>) val)
.map(IPrimitiveType::getValueAsString)
.map(Boolean::parseBoolean)
.findFirst();
//if the SP doesn't care, use the system default.
if (!noSuppressForSearchParam.isPresent()) {
return !theModelConfig.isSuppressStringIndexingInTokens();
//If the SP does care, use its value.
} else {
boolean suppressForSearchParam = noSuppressForSearchParam.get();
ourLog.trace("Text indexing for SearchParameter {}: {}", theSearchParam.getName(), suppressForSearchParam);
return !suppressForSearchParam;
}
}
private static void addIgnoredType(FhirContext theCtx, String theType, Set<String> theIgnoredTypes) {
BaseRuntimeElementDefinition<?> elementDefinition = theCtx.getElementDefinition(theType);
if (elementDefinition != null) {
theIgnoredTypes.add(elementDefinition.getName());
}
}
private static String extractValueAsString(BaseRuntimeChildDefinition theChildDefinition, IBase theElement) {
return theChildDefinition
.getAccessor()
.<IPrimitiveType<?>>getFirstValueOrNull(theElement)
.map(IPrimitiveType::getValueAsString)
.orElse(null);
}
private static Date extractValueAsDate(BaseRuntimeChildDefinition theChildDefinition, IBase theElement) {
return theChildDefinition
.getAccessor()
.<IPrimitiveType<Date>>getFirstValueOrNull(theElement)
.map(IPrimitiveType::getValue)
.orElse(null);
}
private static BigDecimal extractValueAsBigDecimal(BaseRuntimeChildDefinition theChildDefinition, IBase theElement) {
return theChildDefinition
.getAccessor()
.<IPrimitiveType<BigDecimal>>getFirstValueOrNull(theElement)
.map(IPrimitiveType::getValue)
.orElse(null);
}
@SuppressWarnings("unchecked")
private static List<IPrimitiveType<Date>> extractValuesAsFhirDates(BaseRuntimeChildDefinition theChildDefinition, IBase theElement) {
return (List) theChildDefinition
.getAccessor()
.getValues(theElement);
}
private static List<String> extractValuesAsStrings(BaseRuntimeChildDefinition theChildDefinition, IBase theValue) {
return theChildDefinition
.getAccessor()
.getValues(theValue)
.stream()
.map(t -> (IPrimitiveType) t)
.map(IPrimitiveType::getValueAsString)
.filter(StringUtils::isNotBlank)
.collect(Collectors.toList());
}
private static <T extends Enum<?>> String extractSystem(IBaseEnumeration<T> theBoundCode) {
if (theBoundCode.getValue() != null) {
return theBoundCode.getEnumFactory().toSystem(theBoundCode.getValue());
}
return null;
}
}

5
hapi-fhir-jpaserver-searchparam/src/main/java/ca/uhn/fhir/jpa/searchparam/extractor/ISearchParamExtractor.java
View File

@ -22,17 +22,16 @@ package ca.uhn.fhir.jpa.searchparam.extractor;
*/
import ca.uhn.fhir.context.RuntimeSearchParam;
import ca.uhn.fhir.jpa.model.entity.*;
import org.hl7.fhir.instance.model.api.IBase;
import ca.uhn.fhir.jpa.model.entity.BaseResourceIndexedSearchParam;
import ca.uhn.fhir.jpa.model.entity.ResourceIndexedSearchParamDate;
import ca.uhn.fhir.jpa.model.entity.ResourceIndexedSearchParamNumber;
import ca.uhn.fhir.jpa.model.entity.ResourceIndexedSearchParamQuantity;
import ca.uhn.fhir.jpa.model.entity.ResourceIndexedSearchParamQuantityNormalized;
import ca.uhn.fhir.jpa.model.entity.ResourceIndexedSearchParamString;
import ca.uhn.fhir.jpa.model.entity.ResourceIndexedSearchParamToken;
import ca.uhn.fhir.jpa.model.entity.ResourceIndexedSearchParamUri;
import org.hl7.fhir.instance.model.api.IBase;
import org.hl7.fhir.instance.model.api.IBaseResource;
import org.hl7.fhir.r4.utils.FHIRPathEngine;
import java.util.ArrayList;
import java.util.Collections;

25
hapi-fhir-jpaserver-searchparam/src/main/java/ca/uhn/fhir/jpa/searchparam/extractor/ResourceIndexedSearchParams.java
View File

@ -147,15 +147,15 @@ public final class ResourceIndexedSearchParams {
theEntity.setResourceLinks(myLinks);
}
public void updateSpnamePrefixForIndexedOnContainedResource(String theSpnamePrefix) {
updateSpnamePrefixForIndexedOnContainedResource(myNumberParams, theSpnamePrefix);
updateSpnamePrefixForIndexedOnContainedResource(myQuantityParams, theSpnamePrefix);
updateSpnamePrefixForIndexedOnContainedResource(myQuantityNormalizedParams, theSpnamePrefix);
updateSpnamePrefixForIndexedOnContainedResource(myDateParams, theSpnamePrefix);
updateSpnamePrefixForIndexedOnContainedResource(myUriParams, theSpnamePrefix);
updateSpnamePrefixForIndexedOnContainedResource(myTokenParams, theSpnamePrefix);
updateSpnamePrefixForIndexedOnContainedResource(myStringParams, theSpnamePrefix);
updateSpnamePrefixForIndexedOnContainedResource(myCoordsParams, theSpnamePrefix);
public void updateSpnamePrefixForIndexedOnContainedResource(String theContainingType, String theSpnamePrefix) {
updateSpnamePrefixForIndexedOnContainedResource(theContainingType, myNumberParams, theSpnamePrefix);
updateSpnamePrefixForIndexedOnContainedResource(theContainingType, myQuantityParams, theSpnamePrefix);
updateSpnamePrefixForIndexedOnContainedResource(theContainingType, myQuantityNormalizedParams, theSpnamePrefix);
updateSpnamePrefixForIndexedOnContainedResource(theContainingType, myDateParams, theSpnamePrefix);
updateSpnamePrefixForIndexedOnContainedResource(theContainingType, myUriParams, theSpnamePrefix);
updateSpnamePrefixForIndexedOnContainedResource(theContainingType, myTokenParams, theSpnamePrefix);
updateSpnamePrefixForIndexedOnContainedResource(theContainingType, myStringParams, theSpnamePrefix);
updateSpnamePrefixForIndexedOnContainedResource(theContainingType, myCoordsParams, theSpnamePrefix);
}
public void updateSpnamePrefixForLinksOnContainedResource(String theSpNamePrefix) {
@ -190,11 +190,14 @@ public final class ResourceIndexedSearchParams {
}
}
private void updateSpnamePrefixForIndexedOnContainedResource(Collection<? extends BaseResourceIndexedSearchParam> theParams, @Nonnull String theSpnamePrefix) {
private void updateSpnamePrefixForIndexedOnContainedResource(String theContainingType, Collection<? extends BaseResourceIndexedSearchParam> theParams, @Nonnull String theSpnamePrefix) {
for (BaseResourceIndexedSearchParam param : theParams) {
param.setResourceType(theContainingType);
param.setParamName(theSpnamePrefix + "." + param.getParamName());
param.calculateHashes(); // re-calculuteHashes
// re-calculate hashes
param.calculateHashes();
}
}

36
hapi-fhir-jpaserver-searchparam/src/main/java/ca/uhn/fhir/jpa/searchparam/extractor/SearchParamExtractorService.java
View File

@ -43,16 +43,15 @@ import ca.uhn.fhir.jpa.model.entity.ResourceIndexedSearchParamUri;
import ca.uhn.fhir.jpa.model.entity.ResourceLink;
import ca.uhn.fhir.jpa.model.entity.ResourceTable;
import ca.uhn.fhir.jpa.model.search.StorageProcessingMessage;
import ca.uhn.fhir.rest.server.util.ISearchParamRegistry;
import ca.uhn.fhir.rest.server.util.CompositeInterceptorBroadcaster;
import ca.uhn.fhir.parser.DataFormatException;
import ca.uhn.fhir.rest.api.server.RequestDetails;
import ca.uhn.fhir.rest.api.server.storage.ResourcePersistentId;
import ca.uhn.fhir.rest.api.server.storage.TransactionDetails;
import ca.uhn.fhir.rest.server.exceptions.InvalidRequestException;
import ca.uhn.fhir.rest.server.servlet.ServletRequestDetails;
import ca.uhn.fhir.rest.server.util.CompositeInterceptorBroadcaster;
import ca.uhn.fhir.rest.server.util.ISearchParamRegistry;
import ca.uhn.fhir.util.FhirTerser;
import com.google.common.annotations.VisibleForTesting;
import org.apache.commons.lang3.StringUtils;
import org.hl7.fhir.instance.model.api.IBaseReference;
@ -107,10 +106,10 @@ public class SearchParamExtractorService {
extractSearchIndexParametersForContainedResources(theRequestDetails, containedParams, theResource, theEntity);
mergeParams(containedParams, theParams);
}
// Do this after, because we add to strings during both string and token processing, and contained resource if any
populateResourceTables(theParams, theEntity);
// Reference search parameters
extractResourceLinks(theRequestPartitionId, theParams, theEntity, theResource, theTransactionDetails, theFailOnInvalidReference, theRequestDetails);
@ -126,8 +125,8 @@ public class SearchParamExtractorService {
myModelConfig = theModelConfig;
}
private void extractSearchIndexParametersForContainedResources(RequestDetails theRequestDetails, ResourceIndexedSearchParams theParams, IBaseResource theResource, ResourceTable theEntity) {
private void extractSearchIndexParametersForContainedResources(RequestDetails theRequestDetails, ResourceIndexedSearchParams theParams, IBaseResource theResource, ResourceTable theEntity) {
FhirTerser terser = myContext.newTerser();
// 1. get all contained resources
@ -176,7 +175,7 @@ public class SearchParamExtractorService {
// 3.5 added reference name as a prefix for the contained resource if any
// e.g. for Observation.subject contained reference
// the SP_NAME = subject.family
currParams.updateSpnamePrefixForIndexedOnContainedResource(spnamePrefix);
currParams.updateSpnamePrefixForIndexedOnContainedResource(theEntity.getResourceType(), spnamePrefix);
// 3.6 merge to the mainParams
// NOTE: the spname prefix is different
@ -188,12 +187,12 @@ public class SearchParamExtractorService {
for (IBaseResource resource : resources) {
if (resource.getIdElement().equals(reference.getReferenceElement()))
return resource;
}
}
return null;
}
private void mergeParams(ResourceIndexedSearchParams theSrcParams, ResourceIndexedSearchParams theTargetParams) {
theTargetParams.myNumberParams.addAll(theSrcParams.myNumberParams);
theTargetParams.myQuantityParams.addAll(theSrcParams.myQuantityParams);
theTargetParams.myQuantityNormalizedParams.addAll(theSrcParams.myQuantityNormalizedParams);
@ -203,7 +202,7 @@ public class SearchParamExtractorService {
theTargetParams.myStringParams.addAll(theSrcParams.myStringParams);
theTargetParams.myCoordsParams.addAll(theSrcParams.myCoordsParams);
}
private void extractSearchIndexParameters(RequestDetails theRequestDetails, ResourceIndexedSearchParams theParams, IBaseResource theResource, ResourceTable theEntity) {
// Strings
@ -239,7 +238,8 @@ public class SearchParamExtractorService {
// Tokens (can result in both Token and String, as we index the display name for
// the types: Coding, CodeableConcept)
for (BaseResourceIndexedSearchParam next : extractSearchParamTokens(theResource)) {
ISearchParamExtractor.SearchParamSet<BaseResourceIndexedSearchParam> tokens = extractSearchParamTokens(theResource);
for (BaseResourceIndexedSearchParam next : tokens) {
if (next instanceof ResourceIndexedSearchParamToken) {
theParams.myTokenParams.add((ResourceIndexedSearchParamToken) next);
} else if (next instanceof ResourceIndexedSearchParamCoords) {
@ -250,16 +250,17 @@ public class SearchParamExtractorService {
}
// Specials
for (BaseResourceIndexedSearchParam next : extractSearchParamSpecial(theResource)) {
ISearchParamExtractor.SearchParamSet<BaseResourceIndexedSearchParam> specials = extractSearchParamSpecial(theResource);
for (BaseResourceIndexedSearchParam next : specials) {
if (next instanceof ResourceIndexedSearchParamCoords) {
theParams.myCoordsParams.add((ResourceIndexedSearchParamCoords) next);
}
}
}
private void populateResourceTables(ResourceIndexedSearchParams theParams, ResourceTable theEntity) {
populateResourceTable(theParams.myNumberParams, theEntity);
populateResourceTable(theParams.myQuantityParams, theEntity);
populateResourceTable(theParams.myQuantityNormalizedParams, theEntity);
@ -437,7 +438,7 @@ public class SearchParamExtractorService {
// 2. Find referenced search parameters
ISearchParamExtractor.SearchParamSet<PathAndRef> referencedSearchParamSet = mySearchParamExtractor.extractResourceLinks(theResource, true);
String spNamePrefix = null;
String spNamePrefix;
ResourceIndexedSearchParams currParams;
// 3. for each referenced search parameter, create an index
for (PathAndRef nextPathAndRef : referencedSearchParamSet) {
@ -482,6 +483,7 @@ public class SearchParamExtractorService {
}
private ResourceLink resolveTargetAndCreateResourceLinkOrReturnNull(@Nonnull RequestPartitionId theRequestPartitionId, ResourceTable theEntity, Date theUpdateTime, RuntimeSearchParam nextSpDef, String theNextPathsUnsplit, PathAndRef nextPathAndRef, IIdType theNextId, String theTypeString, Class<? extends IBaseResource> theType, IBaseReference theReference, RequestDetails theRequest, TransactionDetails theTransactionDetails) {
assert theRequestPartitionId != null;
ResourcePersistentId resolvedResourceId = theTransactionDetails.getResolvedResourceId(theNextId);
if (resolvedResourceId != null) {

24
hapi-fhir-storage/src/main/java/ca/uhn/fhir/jpa/api/dao/IJpaDao.java
View File

@ -30,10 +30,24 @@ import java.util.Date;
public interface IJpaDao<T extends IBaseResource> {
@SuppressWarnings("unchecked")
IBasePersistedResource updateEntity(RequestDetails theRequest, IBaseResource theResource, IBasePersistedResource
theEntity, Date theDeletedTimestampOrNull, boolean thePerformIndexing,
boolean theUpdateVersion, TransactionDetails theTransactionDetails, boolean theForceUpdate, boolean theCreateNewHistoryEntry);
IBasePersistedResource updateEntity(
RequestDetails theRequest,
IBaseResource theResource,
IBasePersistedResource theEntity,
Date theDeletedTimestampOrNull,
boolean thePerformIndexing,
boolean theUpdateVersion,
TransactionDetails theTransactionDetails,
boolean theForceUpdate,
boolean theCreateNewHistoryEntry);
IBasePersistedResource updateInternal(RequestDetails theRequestDetails, T theResource, boolean thePerformIndexing, boolean theForceUpdateVersion,
IBasePersistedResource theEntity, IIdType theResourceId, IBaseResource theOldResource, TransactionDetails theTransactionDetails);
IBasePersistedResource updateInternal(
RequestDetails theRequestDetails,
T theResource,
boolean thePerformIndexing,
boolean theForceUpdateVersion,
IBasePersistedResource theEntity,
IIdType theResourceId,
IBaseResource theOldResource,
TransactionDetails theTransactionDetails);
}

2
hapi-fhir-storage/src/main/java/ca/uhn/fhir/jpa/dao/BaseStorageDao.java
View File

@ -259,7 +259,7 @@ public abstract class BaseStorageDao {
* <p>
* We only do this if thePerformIndexing is true because if it's false, that means
* we're in a FHIR transaction during the first phase of write operation processing,
* meaning that the versions of other resources may not have need updated yet. For example
* meaning that the versions of other resources may not have need updatd yet. For example
* we're about to store an Observation with a reference to a Patient, and that Patient
* is also being updated in the same transaction, during the first "no index" phase,
* the Patient will not yet have its version number incremented, so it would be wrong

18
hapi-fhir-base/src/test/java/ca/uhn/fhir/rest/param/TokenParamTest.java → hapi-fhir-structures-r4/src/test/java/ca/uhn/fhir/rest/param/TokenParamTest.java
View File

@ -1,10 +1,17 @@
package ca.uhn.fhir.rest.param;
import ca.uhn.fhir.context.FhirContext;
import ca.uhn.fhir.rest.api.Constants;
import org.junit.jupiter.api.Test;
import static org.junit.jupiter.api.Assertions.*;
import static org.junit.jupiter.api.Assertions.assertEquals;
import static org.junit.jupiter.api.Assertions.assertFalse;
import static org.junit.jupiter.api.Assertions.assertNotEquals;
import static org.junit.jupiter.api.Assertions.assertTrue;
public class TokenParamTest {
private static final FhirContext ourCtx = FhirContext.forR4Cached();
@Test
public void testEquals() {
TokenParam tokenParam1 = new TokenParam("foo", "bar");
@ -32,4 +39,13 @@ public class TokenParamTest {
assertEquals("", new TokenParam().getValueNotNull());
}
@Test
public void testOfType() {
TokenParam param = new TokenParam();
param.setValueAsQueryToken(ourCtx, "identifier", Constants.PARAMQUALIFIER_TOKEN_OF_TYPE, "http://type-system|type-value|identifier-value");
assertEquals(TokenParamModifier.OF_TYPE, param.getModifier());
assertEquals("http://type-system", param.getSystem());
assertEquals("type-value|identifier-value", param.getValue());
}
}