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Merge branch 'ja_20190928_rationalize_search_param_extractor' of github.com:jamesagnew/hapi-fhir into ja_20190928_rationalize_search_param_extractor

This commit is contained in:
jamesagnew 2019-10-30 13:46:42 -04:00
parent 541fbf3ec1 43e91315cb
commit b13de41e9f
47 changed files with 1007 additions and 481 deletions
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1
hapi-fhir-base/src/main/resources/ca/uhn/fhir/i18n/hapi-messages.properties
View File

@ -1,4 +1,5 @@
ca.uhn.fhir.jpa.term.BaseTermReadSvcImpl.expansionRefersToUnknownCs=Unknown CodeSystem URI "{0}" referenced from ValueSet
# Core Library Messages
ca.uhn.fhir.context.FhirContext.unknownResourceName=Unknown resource name "{0}" (this name is not known in FHIR version "{1}")

1
hapi-fhir-cli/hapi-fhir-cli-jpaserver/pom.xml
View File

@ -45,7 +45,6 @@
<artifactId>hapi-fhir-testpage-overlay</artifactId>
<version>${project.version}</version>
<classifier>classes</classifier>
<scope>provided</scope>
</dependency>
<!-- HAPI-FHIR uses Logback for logging support. The logback library is included automatically by Maven as a part of the hapi-fhir-base dependency, but you also need to include a logging library. Logback

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

@ -979,7 +979,7 @@ public abstract class BaseHapiFhirDao<T extends IBaseResource> implements IDao,
if (thePerformIndexing) {
newParams = new ResourceIndexedSearchParams();
mySearchParamWithInlineReferencesExtractor.populateFromResource(newParams, this, theUpdateTime, theEntity, theResource, existingParams, theRequest);
mySearchParamWithInlineReferencesExtractor.populateFromResource(newParams, theUpdateTime, theEntity, theResource, existingParams, theRequest);
changed = populateResourceIntoEntity(theRequest, theResource, theEntity, true);
if (changed.isChanged()) {

11
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/dstu3/FhirResourceDaoCodeSystemDstu3.java
View File

@ -132,13 +132,16 @@ public class FhirResourceDaoCodeSystemDstu3 extends BaseHapiFhirResourceDao<Code
public ResourceTable updateEntity(RequestDetails theRequest, IBaseResource theResource, ResourceTable theEntity, Date theDeletedTimestampOrNull, boolean thePerformIndexing,
boolean theUpdateVersion, Date theUpdateTime, boolean theForceUpdate, boolean theCreateNewHistoryEntry) {
ResourceTable retVal = super.updateEntity(theRequest, theResource, theEntity, theDeletedTimestampOrNull, thePerformIndexing, theUpdateVersion, theUpdateTime, theForceUpdate, theCreateNewHistoryEntry);
if (!retVal.isUnchangedInCurrentOperation()) {
CodeSystem csDstu3 = (CodeSystem) theResource;
CodeSystem csDstu3 = (CodeSystem) theResource;
org.hl7.fhir.r4.model.CodeSystem cs = VersionConvertor_30_40.convertCodeSystem(csDstu3);
addPidToResource(theEntity, cs);
org.hl7.fhir.r4.model.CodeSystem cs = VersionConvertor_30_40.convertCodeSystem(csDstu3);
addPidToResource(theEntity, cs);
myTerminologyCodeSystemStorageSvc.storeNewCodeSystemVersionIfNeeded(cs, theEntity);
myTerminologyCodeSystemStorageSvc.storeNewCodeSystemVersionIfNeeded(cs, theEntity);
}
return retVal;
}

20
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/dstu3/FhirResourceDaoConceptMapDstu3.java
View File

@ -161,16 +161,18 @@ public class FhirResourceDaoConceptMapDstu3 extends BaseHapiFhirResourceDao<Conc
boolean theUpdateVersion, Date theUpdateTime, boolean theForceUpdate, boolean theCreateNewHistoryEntry) {
ResourceTable retVal = super.updateEntity(theRequestDetails, theResource, theEntity, theDeletedTimestampOrNull, thePerformIndexing, theUpdateVersion, theUpdateTime, theForceUpdate, theCreateNewHistoryEntry);
if (retVal.getDeleted() == null) {
try {
ConceptMap conceptMap = (ConceptMap) theResource;
org.hl7.fhir.r4.model.ConceptMap converted = VersionConvertor_30_40.convertConceptMap(conceptMap);
myHapiTerminologySvc.storeTermConceptMapAndChildren(retVal, converted);
} catch (FHIRException fe) {
throw new InternalErrorException(fe);
if (!retVal.isUnchangedInCurrentOperation()) {
if (retVal.getDeleted() == null) {
try {
ConceptMap conceptMap = (ConceptMap) theResource;
org.hl7.fhir.r4.model.ConceptMap converted = VersionConvertor_30_40.convertConceptMap(conceptMap);
myHapiTerminologySvc.storeTermConceptMapAndChildren(retVal, converted);
} catch (FHIRException fe) {
throw new InternalErrorException(fe);
}
} else {
myHapiTerminologySvc.deleteConceptMapAndChildren(retVal);
}
} else {
myHapiTerminologySvc.deleteConceptMapAndChildren(retVal);
}
return retVal;

2
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/dstu3/FhirResourceDaoValueSetDstu3.java
View File

@ -415,7 +415,7 @@ public class FhirResourceDaoValueSetDstu3 extends BaseHapiFhirResourceDao<ValueS
boolean theUpdateVersion, Date theUpdateTime, boolean theForceUpdate, boolean theCreateNewHistoryEntry) {
ResourceTable retVal = super.updateEntity(theRequestDetails, theResource, theEntity, theDeletedTimestampOrNull, thePerformIndexing, theUpdateVersion, theUpdateTime, theForceUpdate, theCreateNewHistoryEntry);
if (myDaoConfig.isPreExpandValueSets()) {
if (myDaoConfig.isPreExpandValueSets() && !retVal.isUnchangedInCurrentOperation()) {
if (retVal.getDeleted() == null) {
try {
ValueSet valueSet = (ValueSet) theResource;

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

@ -88,8 +88,8 @@ public class SearchParamWithInlineReferencesExtractor {
@PersistenceContext(type = PersistenceContextType.TRANSACTION)
protected EntityManager myEntityManager;
public void populateFromResource(ResourceIndexedSearchParams theParams, IDao theCallingDao, Date theUpdateTime, ResourceTable theEntity, IBaseResource theResource, ResourceIndexedSearchParams theExistingParams, RequestDetails theRequest) {
mySearchParamExtractorService.extractFromResource(theParams, theEntity, theResource);
public void populateFromResource(ResourceIndexedSearchParams theParams, Date theUpdateTime, ResourceTable theEntity, IBaseResource theResource, ResourceIndexedSearchParams theExistingParams, RequestDetails theRequest) {
mySearchParamExtractorService.extractFromResource(theRequest, theParams, theEntity, theResource);
Set<Map.Entry<String, RuntimeSearchParam>> activeSearchParams = mySearchParamRegistry.getActiveSearchParams(theEntity.getResourceType()).entrySet();
if (myDaoConfig.getIndexMissingFields() == DaoConfig.IndexEnabledEnum.ENABLED) {

8
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/r4/FhirResourceDaoCodeSystemR4.java
View File

@ -136,10 +136,12 @@ public class FhirResourceDaoCodeSystemR4 extends BaseHapiFhirResourceDao<CodeSys
boolean theUpdateVersion, Date theUpdateTime, boolean theForceUpdate, boolean theCreateNewHistoryEntry) {
ResourceTable retVal = super.updateEntity(theRequest, theResource, theEntity, theDeletedTimestampOrNull, thePerformIndexing, theUpdateVersion, theUpdateTime, theForceUpdate, theCreateNewHistoryEntry);
CodeSystem cs = (CodeSystem) theResource;
addPidToResource(theEntity, theResource);
if (!retVal.isUnchangedInCurrentOperation()) {
CodeSystem cs = (CodeSystem) theResource;
addPidToResource(theEntity, theResource);
myTerminologyCodeSystemStorageSvc.storeNewCodeSystemVersionIfNeeded(cs, theEntity);
myTerminologyCodeSystemStorageSvc.storeNewCodeSystemVersionIfNeeded(cs, theEntity);
}
return retVal;
}

12
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/r4/FhirResourceDaoConceptMapR4.java
View File

@ -161,11 +161,13 @@ public class FhirResourceDaoConceptMapR4 extends BaseHapiFhirResourceDao<Concept
boolean theUpdateVersion, Date theUpdateTime, boolean theForceUpdate, boolean theCreateNewHistoryEntry) {
ResourceTable retVal = super.updateEntity(theRequestDetails, theResource, theEntity, theDeletedTimestampOrNull, thePerformIndexing, theUpdateVersion, theUpdateTime, theForceUpdate, theCreateNewHistoryEntry);
if (retVal.getDeleted() == null) {
ConceptMap conceptMap = (ConceptMap) theResource;
myHapiTerminologySvc.storeTermConceptMapAndChildren(retVal, conceptMap);
} else {
myHapiTerminologySvc.deleteConceptMapAndChildren(retVal);
if (!retVal.isUnchangedInCurrentOperation()) {
if (retVal.getDeleted() == null) {
ConceptMap conceptMap = (ConceptMap) theResource;
myHapiTerminologySvc.storeTermConceptMapAndChildren(retVal, conceptMap);
} else {
myHapiTerminologySvc.deleteConceptMapAndChildren(retVal);
}
}
return retVal;

2
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/r4/FhirResourceDaoValueSetR4.java
View File

@ -396,7 +396,7 @@ public class FhirResourceDaoValueSetR4 extends BaseHapiFhirResourceDao<ValueSet>
boolean theUpdateVersion, Date theUpdateTime, boolean theForceUpdate, boolean theCreateNewHistoryEntry) {
ResourceTable retVal = super.updateEntity(theRequestDetails, theResource, theEntity, theDeletedTimestampOrNull, thePerformIndexing, theUpdateVersion, theUpdateTime, theForceUpdate, theCreateNewHistoryEntry);
if (myDaoConfig.isPreExpandValueSets()) {
if (myDaoConfig.isPreExpandValueSets() && !retVal.isUnchangedInCurrentOperation()) {
if (retVal.getDeleted() == null) {
ValueSet valueSet = (ValueSet) theResource;
myHapiTerminologySvc.storeTermValueSet(retVal, valueSet);

8
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/r5/FhirResourceDaoCodeSystemR5.java
View File

@ -135,11 +135,13 @@ public class FhirResourceDaoCodeSystemR5 extends BaseHapiFhirResourceDao<CodeSys
public ResourceTable updateEntity(RequestDetails theRequest, IBaseResource theResource, ResourceTable theEntity, Date theDeletedTimestampOrNull, boolean thePerformIndexing,
boolean theUpdateVersion, Date theUpdateTime, boolean theForceUpdate, boolean theCreateNewHistoryEntry) {
ResourceTable retVal = super.updateEntity(theRequest, theResource, theEntity, theDeletedTimestampOrNull, thePerformIndexing, theUpdateVersion, theUpdateTime, theForceUpdate, theCreateNewHistoryEntry);
if (!retVal.isUnchangedInCurrentOperation()) {
CodeSystem cs = (CodeSystem) theResource;
addPidToResource(theEntity, theResource);
CodeSystem cs = (CodeSystem) theResource;
addPidToResource(theEntity, theResource);
myTerminologyCodeSystemStorageSvc.storeNewCodeSystemVersionIfNeeded(org.hl7.fhir.convertors.conv40_50.CodeSystem.convertCodeSystem(cs), theEntity);
myTerminologyCodeSystemStorageSvc.storeNewCodeSystemVersionIfNeeded(org.hl7.fhir.convertors.conv40_50.CodeSystem.convertCodeSystem(cs), theEntity);
}
return retVal;
}

14
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/r5/FhirResourceDaoConceptMapR5.java
View File

@ -161,14 +161,16 @@ public class FhirResourceDaoConceptMapR5 extends BaseHapiFhirResourceDao<Concept
public ResourceTable updateEntity(RequestDetails theRequestDetails, IBaseResource theResource, ResourceTable theEntity, Date theDeletedTimestampOrNull, boolean thePerformIndexing,
boolean theUpdateVersion, Date theUpdateTime, boolean theForceUpdate, boolean theCreateNewHistoryEntry) {
ResourceTable retVal = super.updateEntity(theRequestDetails, theResource, theEntity, theDeletedTimestampOrNull, thePerformIndexing, theUpdateVersion, theUpdateTime, theForceUpdate, theCreateNewHistoryEntry);
if (!retVal.isUnchangedInCurrentOperation()) {
if (retVal.getDeleted() == null) {
ConceptMap conceptMap = (ConceptMap) theResource;
myHapiTerminologySvc.storeTermConceptMapAndChildren(retVal, org.hl7.fhir.convertors.conv40_50.ConceptMap.convertConceptMap(conceptMap));
} else {
myHapiTerminologySvc.deleteConceptMapAndChildren(retVal);
if (retVal.getDeleted() == null) {
ConceptMap conceptMap = (ConceptMap) theResource;
myHapiTerminologySvc.storeTermConceptMapAndChildren(retVal, org.hl7.fhir.convertors.conv40_50.ConceptMap.convertConceptMap(conceptMap));
} else {
myHapiTerminologySvc.deleteConceptMapAndChildren(retVal);
}
}
return retVal;
}
}

2
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/r5/FhirResourceDaoValueSetR5.java
View File

@ -408,7 +408,7 @@ public class FhirResourceDaoValueSetR5 extends BaseHapiFhirResourceDao<ValueSet>
boolean theUpdateVersion, Date theUpdateTime, boolean theForceUpdate, boolean theCreateNewHistoryEntry) {
ResourceTable retVal = super.updateEntity(theRequestDetails, theResource, theEntity, theDeletedTimestampOrNull, thePerformIndexing, theUpdateVersion, theUpdateTime, theForceUpdate, theCreateNewHistoryEntry);
if (myDaoConfig.isPreExpandValueSets()) {
if (myDaoConfig.isPreExpandValueSets() && !retVal.isUnchangedInCurrentOperation()) {
if (retVal.getDeleted() == null) {
ValueSet valueSet = (ValueSet) theResource;
myHapiTerminologySvc.storeTermValueSet(retVal, org.hl7.fhir.convertors.conv40_50.ValueSet.convertValueSet(valueSet));

104
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/provider/r4/JpaConformanceProviderR4.java
View File

@ -19,24 +19,25 @@ package ca.uhn.fhir.jpa.provider.r4;
* limitations under the License.
* #L%
*/
import java.util.*;
import javax.servlet.http.HttpServletRequest;
import ca.uhn.fhir.jpa.searchparam.registry.ISearchParamRegistry;
import ca.uhn.fhir.rest.api.Constants;
import ca.uhn.fhir.rest.api.server.RequestDetails;
import org.hl7.fhir.r4.model.*;
import org.hl7.fhir.r4.model.CapabilityStatement.*;
import org.hl7.fhir.r4.model.Enumerations.SearchParamType;
import ca.uhn.fhir.context.RuntimeResourceDefinition;
import ca.uhn.fhir.context.RuntimeSearchParam;
import ca.uhn.fhir.jpa.dao.DaoConfig;
import ca.uhn.fhir.jpa.dao.IFhirSystemDao;
import ca.uhn.fhir.jpa.searchparam.registry.ISearchParamRegistry;
import ca.uhn.fhir.rest.api.Constants;
import ca.uhn.fhir.rest.api.server.RequestDetails;
import ca.uhn.fhir.rest.server.RestfulServer;
import ca.uhn.fhir.util.CoverageIgnore;
import ca.uhn.fhir.util.ExtensionConstants;
import org.hl7.fhir.r4.model.*;
import org.hl7.fhir.r4.model.CapabilityStatement.*;
import org.hl7.fhir.r4.model.Enumerations.SearchParamType;
import javax.servlet.http.HttpServletRequest;
import java.util.Collection;
import java.util.Collections;
import java.util.Map;
import static org.apache.commons.lang3.ObjectUtils.defaultIfNull;
import static org.apache.commons.lang3.StringUtils.isNotBlank;
@ -50,17 +51,17 @@ public class JpaConformanceProviderR4 extends org.hl7.fhir.r4.hapi.rest.server.S
private boolean myIncludeResourceCounts;
private RestfulServer myRestfulServer;
private IFhirSystemDao<Bundle, Meta> mySystemDao;
/**
* Constructor
*/
@CoverageIgnore
public JpaConformanceProviderR4(){
public JpaConformanceProviderR4() {
super();
super.setCache(false);
setIncludeResourceCounts(true);
}
/**
* Constructor
*/
@ -94,7 +95,7 @@ public class JpaConformanceProviderR4 extends org.hl7.fhir.r4.hapi.rest.server.S
for (CapabilityStatementRestResourceComponent nextResource : nextRest.getResource()) {
nextResource.setVersioning(ResourceVersionPolicy.VERSIONEDUPDATE);
ConditionalDeleteStatus conditionalDelete = nextResource.getConditionalDelete();
if (conditionalDelete == ConditionalDeleteStatus.MULTIPLE && myDaoConfig.isAllowMultipleDelete() == false) {
nextResource.setConditionalDelete(ConditionalDeleteStatus.SINGLE);
@ -109,7 +110,7 @@ public class JpaConformanceProviderR4 extends org.hl7.fhir.r4.hapi.rest.server.S
nextResource.getSearchParam().clear();
String resourceName = nextResource.getType();
RuntimeResourceDefinition resourceDef = myRestfulServer.getFhirContext().getResourceDefinition(resourceName);
Collection<RuntimeSearchParam> searchParams = mySearchParamRegistry.getSearchParamsByResourceType(resourceDef);
Collection<RuntimeSearchParam> searchParams = mySearchParamRegistry.getSearchParamsByResourceType(resourceDef);
for (RuntimeSearchParam runtimeSp : searchParams) {
CapabilityStatementRestResourceSearchParamComponent confSp = nextResource.addSearchParam();
@ -117,37 +118,40 @@ public class JpaConformanceProviderR4 extends org.hl7.fhir.r4.hapi.rest.server.S
confSp.setDocumentation(runtimeSp.getDescription());
confSp.setDefinition(runtimeSp.getUri());
switch (runtimeSp.getParamType()) {
case COMPOSITE:
confSp.setType(SearchParamType.COMPOSITE);
break;
case DATE:
confSp.setType(SearchParamType.DATE);
break;
case NUMBER:
confSp.setType(SearchParamType.NUMBER);
break;
case QUANTITY:
confSp.setType(SearchParamType.QUANTITY);
break;
case REFERENCE:
confSp.setType(SearchParamType.REFERENCE);
break;
case STRING:
confSp.setType(SearchParamType.STRING);
break;
case TOKEN:
confSp.setType(SearchParamType.TOKEN);
break;
case URI:
confSp.setType(SearchParamType.URI);
break;
case HAS:
// Shouldn't happen
break;
case COMPOSITE:
confSp.setType(SearchParamType.COMPOSITE);
break;
case DATE:
confSp.setType(SearchParamType.DATE);
break;
case NUMBER:
confSp.setType(SearchParamType.NUMBER);
break;
case QUANTITY:
confSp.setType(SearchParamType.QUANTITY);
break;
case REFERENCE:
confSp.setType(SearchParamType.REFERENCE);
break;
case STRING:
confSp.setType(SearchParamType.STRING);
break;
case TOKEN:
confSp.setType(SearchParamType.TOKEN);
break;
case URI:
confSp.setType(SearchParamType.URI);
break;
case SPECIAL:
confSp.setType(SearchParamType.SPECIAL);
break;
case HAS:
// Shouldn't happen
break;
}
}
}
}
@ -161,7 +165,7 @@ public class JpaConformanceProviderR4 extends org.hl7.fhir.r4.hapi.rest.server.S
}
massage(retVal);
retVal.getImplementation().setDescription(myImplementationDescription);
myCachedValue = retVal;
return retVal;
@ -170,7 +174,11 @@ public class JpaConformanceProviderR4 extends org.hl7.fhir.r4.hapi.rest.server.S
public boolean isIncludeResourceCounts() {
return myIncludeResourceCounts;
}
public void setIncludeResourceCounts(boolean theIncludeResourceCounts) {
myIncludeResourceCounts = theIncludeResourceCounts;
}
/**
* Subclasses may override
*/
@ -187,10 +195,6 @@ public class JpaConformanceProviderR4 extends org.hl7.fhir.r4.hapi.rest.server.S
myImplementationDescription = theImplDesc;
}
public void setIncludeResourceCounts(boolean theIncludeResourceCounts) {
myIncludeResourceCounts = theIncludeResourceCounts;
}
@Override
public void setRestfulServer(RestfulServer theRestfulServer) {
this.myRestfulServer = theRestfulServer;

83
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/provider/r5/JpaConformanceProviderR5.java
View File

@ -51,16 +51,16 @@ public class JpaConformanceProviderR5 extends org.hl7.fhir.r5.hapi.rest.server.S
private boolean myIncludeResourceCounts;
private RestfulServer myRestfulServer;
private IFhirSystemDao<Bundle, Meta> mySystemDao;
/**
* Constructor
*/
@CoverageIgnore
public JpaConformanceProviderR5(){
public JpaConformanceProviderR5() {
super();
setIncludeResourceCounts(true);
}
/**
* Constructor
*/
@ -93,7 +93,7 @@ public class JpaConformanceProviderR5 extends org.hl7.fhir.r5.hapi.rest.server.S
for (CapabilityStatementRestResourceComponent nextResource : nextRest.getResource()) {
nextResource.setVersioning(ResourceVersionPolicy.VERSIONEDUPDATE);
ConditionalDeleteStatus conditionalDelete = nextResource.getConditionalDelete();
if (conditionalDelete == ConditionalDeleteStatus.MULTIPLE && myDaoConfig.isAllowMultipleDelete() == false) {
nextResource.setConditionalDelete(ConditionalDeleteStatus.SINGLE);
@ -108,7 +108,7 @@ public class JpaConformanceProviderR5 extends org.hl7.fhir.r5.hapi.rest.server.S
nextResource.getSearchParam().clear();
String resourceName = nextResource.getType();
RuntimeResourceDefinition resourceDef = myRestfulServer.getFhirContext().getResourceDefinition(resourceName);
Collection<RuntimeSearchParam> searchParams = mySearchParamRegistry.getSearchParamsByResourceType(resourceDef);
Collection<RuntimeSearchParam> searchParams = mySearchParamRegistry.getSearchParamsByResourceType(resourceDef);
for (RuntimeSearchParam runtimeSp : searchParams) {
CapabilityStatementRestResourceSearchParamComponent confSp = nextResource.addSearchParam();
@ -116,37 +116,40 @@ public class JpaConformanceProviderR5 extends org.hl7.fhir.r5.hapi.rest.server.S
confSp.setDocumentation(runtimeSp.getDescription());
confSp.setDefinition(runtimeSp.getUri());
switch (runtimeSp.getParamType()) {
case COMPOSITE:
confSp.setType(SearchParamType.COMPOSITE);
break;
case DATE:
confSp.setType(SearchParamType.DATE);
break;
case NUMBER:
confSp.setType(SearchParamType.NUMBER);
break;
case QUANTITY:
confSp.setType(SearchParamType.QUANTITY);
break;
case REFERENCE:
confSp.setType(SearchParamType.REFERENCE);
break;
case STRING:
confSp.setType(SearchParamType.STRING);
break;
case TOKEN:
confSp.setType(SearchParamType.TOKEN);
break;
case URI:
confSp.setType(SearchParamType.URI);
break;
case HAS:
// Shouldn't happen
break;
case COMPOSITE:
confSp.setType(SearchParamType.COMPOSITE);
break;
case DATE:
confSp.setType(SearchParamType.DATE);
break;
case NUMBER:
confSp.setType(SearchParamType.NUMBER);
break;
case QUANTITY:
confSp.setType(SearchParamType.QUANTITY);
break;
case REFERENCE:
confSp.setType(SearchParamType.REFERENCE);
break;
case STRING:
confSp.setType(SearchParamType.STRING);
break;
case TOKEN:
confSp.setType(SearchParamType.TOKEN);
break;
case URI:
confSp.setType(SearchParamType.URI);
break;
case SPECIAL:
confSp.setType(SearchParamType.SPECIAL);
break;
case HAS:
// Shouldn't happen
break;
}
}
}
}
@ -160,7 +163,7 @@ public class JpaConformanceProviderR5 extends org.hl7.fhir.r5.hapi.rest.server.S
}
massage(retVal);
retVal.getImplementation().setDescription(myImplementationDescription);
myCachedValue = retVal;
return retVal;
@ -169,7 +172,11 @@ public class JpaConformanceProviderR5 extends org.hl7.fhir.r5.hapi.rest.server.S
public boolean isIncludeResourceCounts() {
return myIncludeResourceCounts;
}
public void setIncludeResourceCounts(boolean theIncludeResourceCounts) {
myIncludeResourceCounts = theIncludeResourceCounts;
}
/**
* Subclasses may override
*/
@ -186,10 +193,6 @@ public class JpaConformanceProviderR5 extends org.hl7.fhir.r5.hapi.rest.server.S
myImplementationDescription = theImplDesc;
}
public void setIncludeResourceCounts(boolean theIncludeResourceCounts) {
myIncludeResourceCounts = theIncludeResourceCounts;
}
@Override
public void setRestfulServer(RestfulServer theRestfulServer) {
this.myRestfulServer = theRestfulServer;

5
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/search/reindex/ResourceReindexingSvcImpl.java
View File

@ -195,6 +195,11 @@ public class ResourceReindexingSvcImpl implements IResourceReindexingSvc {
mySchedulerService.scheduleFixedDelay(10 * DateUtils.MILLIS_PER_SECOND, true, jobDetail);
}
@VisibleForTesting
ReentrantLock getIndexingLockForUnitTest() {
return myIndexingLock;
}
@Override
@Transactional(Transactional.TxType.NEVER)
public Integer runReindexingPass() {

5
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/term/BaseTermReadSvcImpl.java
View File

@ -675,7 +675,10 @@ public abstract class BaseTermReadSvcImpl implements ITermReadSvc, ApplicationCo
CodeSystem codeSystemFromContext = getCodeSystemFromContext(system);
if (codeSystemFromContext == null) {
throw new InvalidRequestException("Unknown code system: " + system);
String msg = myContext.getLocalizer().getMessage(BaseTermReadSvcImpl.class, "expansionRefersToUnknownCs", system);
ourLog.warn(msg);
theValueSetCodeAccumulator.addMessage(msg);
return false;
}
if (!theIncludeOrExclude.getConcept().isEmpty()) {

2
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/term/IValueSetConceptAccumulator.java
View File

@ -27,6 +27,8 @@ import java.util.Collection;
public interface IValueSetConceptAccumulator {
void addMessage(String theMessage);
void includeConcept(String theSystem, String theCode, String theDisplay);
void includeConceptWithDesignations(String theSystem, String theCode, String theDisplay, Collection<TermConceptDesignation> theDesignations);

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

@ -57,6 +57,12 @@ public class ValueSetConceptAccumulator implements IValueSetConceptAccumulator {
myConceptsExcluded = 0;
}
@Override
public void addMessage(String theMessage) {
// ignore for now
}
@Override
public void includeConcept(String theSystem, String theCode, String theDisplay) {
saveConcept(theSystem, theCode, theDisplay);
@ -82,7 +88,7 @@ public class ValueSetConceptAccumulator implements IValueSetConceptAccumulator {
if (optionalConcept.isPresent()) {
TermValueSetConcept concept = optionalConcept.get();
ourLog.info("Excluding [{}|{}] from ValueSet[{}]", concept.getSystem(), concept.getCode(), myTermValueSet.getUrl());
ourLog.debug("Excluding [{}|{}] from ValueSet[{}]", concept.getSystem(), concept.getCode(), myTermValueSet.getUrl());
for (TermValueSetConceptDesignation designation : concept.getDesignations()) {
myValueSetConceptDesignationDao.deleteById(designation.getId());
myTermValueSet.decrementTotalConceptDesignations();
@ -90,7 +96,7 @@ public class ValueSetConceptAccumulator implements IValueSetConceptAccumulator {
myValueSetConceptDao.deleteById(concept.getId());
myTermValueSet.decrementTotalConcepts();
myValueSetDao.save(myTermValueSet);
ourLog.info("Done excluding [{}|{}] from ValueSet[{}]", concept.getSystem(), concept.getCode(), myTermValueSet.getUrl());
ourLog.debug("Done excluding [{}|{}] from ValueSet[{}]", concept.getSystem(), concept.getCode(), myTermValueSet.getUrl());
if (++myConceptsExcluded % 250 == 0) {
ourLog.info("Have excluded {} concepts from ValueSet[{}]", myConceptsExcluded, myTermValueSet.getUrl());

9
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/term/ValueSetExpansionComponentWithConceptAccumulator.java
View File

@ -22,9 +22,11 @@ package ca.uhn.fhir.jpa.term;
import ca.uhn.fhir.context.FhirContext;
import ca.uhn.fhir.jpa.entity.TermConceptDesignation;
import ca.uhn.fhir.jpa.model.util.JpaConstants;
import ca.uhn.fhir.jpa.term.ex.ExpansionTooCostlyException;
import ca.uhn.fhir.model.api.annotation.Block;
import ca.uhn.fhir.rest.server.exceptions.InternalErrorException;
import org.hl7.fhir.r4.model.StringType;
import org.hl7.fhir.r4.model.ValueSet;
import javax.annotation.Nullable;
@ -54,6 +56,13 @@ public class ValueSetExpansionComponentWithConceptAccumulator extends ValueSet.V
return myMaxCapacity - myConceptsCount;
}
@Override
public void addMessage(String theMessage) {
addExtension()
.setUrl(JpaConstants.EXT_VALUESET_EXPANSION_MESSAGE)
.setValue(new StringType(theMessage));
}
@Override
public void includeConcept(String theSystem, String theCode, String theDisplay) {
incrementConceptsCount();

39
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/r5/FhirResourceDaoR5SearchNoFtTest.java
View File

@ -1,5 +1,7 @@
package ca.uhn.fhir.jpa.dao.r5;
import ca.uhn.fhir.jpa.model.entity.ResourceHistoryTable;
import ca.uhn.fhir.jpa.model.entity.ResourceTable;
import ca.uhn.fhir.jpa.searchparam.SearchParameterMap;
import ca.uhn.fhir.jpa.util.TestUtil;
import ca.uhn.fhir.rest.api.Constants;
@ -9,11 +11,14 @@ import ca.uhn.fhir.rest.param.HasOrListParam;
import ca.uhn.fhir.rest.param.HasParam;
import ca.uhn.fhir.rest.param.StringParam;
import org.hl7.fhir.r5.model.Organization;
import org.hl7.fhir.r5.model.Patient;
import org.hl7.fhir.r5.model.Practitioner;
import org.hl7.fhir.r5.model.PractitionerRole;
import org.junit.AfterClass;
import org.junit.Test;
import java.util.Date;
import static org.junit.Assert.assertEquals;
@SuppressWarnings({"unchecked", "Duplicates"})
@ -98,6 +103,40 @@ public class FhirResourceDaoR5SearchNoFtTest extends BaseJpaR5Test {
assertEquals(1, outcome.getResources(0, 1).size());
}
@Test
public void testSearchDoesntFailIfResourcesAreDeleted() {
Patient p = new Patient();
p.addIdentifier().setValue("1");
myPatientDao.create(p);
p = new Patient();
p.addIdentifier().setValue("2");
myPatientDao.create(p);
p = new Patient();
p.addIdentifier().setValue("3");
Long id = myPatientDao.create(p).getId().getIdPartAsLong();
IBundleProvider outcome = myPatientDao.search(new SearchParameterMap());
assertEquals(3, outcome.size().intValue());
runInTransaction(()->{
ResourceTable table = myResourceTableDao.findById(id).orElseThrow(() -> new IllegalArgumentException());
table.setDeleted(new Date());
myResourceTableDao.save(table);
});
assertEquals(2, outcome.getResources(0, 3).size());
runInTransaction(()->{
myResourceHistoryTableDao.deleteAll();
});
assertEquals(0, outcome.getResources(0, 3).size());
}
@AfterClass
public static void afterClassClearContext() {
TestUtil.clearAllStaticFieldsForUnitTest();

10
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/provider/dstu3/ResourceProviderDstu3Test.java
View File

@ -4080,22 +4080,16 @@ public class ResourceProviderDstu3Test extends BaseResourceProviderDstu3Test {
Patient patient = new Patient();
patient.addName().addGiven("James");
patient.setBirthDateElement(new DateType("2011-02-02"));
patient.addContact().setGender(AdministrativeGender.MALE);
String inputStr = myFhirCtx.newXmlParser().encodeResourceToString(patient);
HttpPost post = new HttpPost(ourServerBase + "/Patient/$validate");
post.setEntity(new StringEntity(inputStr, ContentType.create(Constants.CT_FHIR_XML, "UTF-8")));
CloseableHttpResponse response = ourHttpClient.execute(post);
try {
try (CloseableHttpResponse response = ourHttpClient.execute(post)) {
String resp = IOUtils.toString(response.getEntity().getContent(), StandardCharsets.UTF_8);
ourLog.info(resp);
assertEquals(412, response.getStatusLine().getStatusCode());
assertEquals(200, response.getStatusLine().getStatusCode());
assertThat(resp, not(containsString("Resource has no id")));
assertThat(resp, containsString("<issue><severity value=\"error\"/><code value=\"processing\"/><diagnostics value=\"SHALL at least contain a contact's details or a reference to an organization [name.exists() or telecom.exists() or address.exists() or organization.exists()]\"/><location value=\"Patient.contact[0]\"/><location value=\"Line 0, Col 0\"/></issue>"));
} finally {
IOUtils.closeQuietly(response.getEntity().getContent());
response.close();
}
}

4
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/provider/r4/BaseResourceProviderR4Test.java
View File

@ -68,7 +68,7 @@ public abstract class BaseResourceProviderR4Test extends BaseJpaR4Test {
private static SubscriptionMatcherInterceptor ourSubscriptionMatcherInterceptor;
protected static Server ourServer;
protected IGenericClient ourClient;
ResourceCountCache ourResourceCountsCache;
ResourceCountCache myResourceCountsCache;
private TerminologyUploaderProvider myTerminologyUploaderProvider;
private boolean ourRestHookSubscriptionInterceptorRequested;
@ -93,6 +93,7 @@ public abstract class BaseResourceProviderR4Test extends BaseJpaR4Test {
myFhirCtx.getRestfulClientFactory().setServerValidationMode(ServerValidationModeEnum.NEVER);
myFhirCtx.getRestfulClientFactory().setSocketTimeout(1200 * 1000);
myFhirCtx.setParserErrorHandler(new StrictErrorHandler());
myResourceCountsCache = (ResourceCountCache) myAppCtx.getBean("myResourceCountsCache");
if (ourServer == null) {
ourRestServer = new RestfulServer(myFhirCtx);
@ -113,7 +114,6 @@ public abstract class BaseResourceProviderR4Test extends BaseJpaR4Test {
ourRestServer.setServerConformanceProvider(confProvider);
ourPagingProvider = myAppCtx.getBean(DatabaseBackedPagingProvider.class);
ourResourceCountsCache = (ResourceCountCache) myAppCtx.getBean("myResourceCountsCache");
Server server = new Server(0);

4
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/provider/r4/ResourceProviderR4Test.java
View File

@ -5308,7 +5308,6 @@ public class ResourceProviderR4Test extends BaseResourceProviderR4Test {
Patient patient = new Patient();
patient.addName().addGiven("James");
patient.setBirthDateElement(new DateType("2011-02-02"));
patient.addContact().setGender(AdministrativeGender.MALE);
String inputStr = myFhirCtx.newXmlParser().encodeResourceToString(patient);
HttpPost post = new HttpPost(ourServerBase + "/Patient/$validate");
@ -5317,9 +5316,8 @@ public class ResourceProviderR4Test extends BaseResourceProviderR4Test {
try (CloseableHttpResponse response = ourHttpClient.execute(post)) {
String resp = IOUtils.toString(response.getEntity().getContent(), StandardCharsets.UTF_8);
ourLog.info(resp);
assertEquals(412, response.getStatusLine().getStatusCode());
assertEquals(200, response.getStatusLine().getStatusCode());
assertThat(resp, not(containsString("Resource has no id")));
assertThat(resp, containsString("<issue><severity value=\"error\"/><code value=\"processing\"/><diagnostics value=\"SHALL at least contain a contact's details or a reference to an organization [name.exists() or telecom.exists() or address.exists() or organization.exists()]\"/><location value=\"Patient.contact[0]\"/><location value=\"Line 0, Col 0\"/></issue>"));
}
}

31
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/provider/r4/ServerR4Test.java
View File

@ -1,6 +1,9 @@
package ca.uhn.fhir.jpa.provider.r4;
import ca.uhn.fhir.jpa.dao.IFhirResourceDao;
import ca.uhn.fhir.rest.api.EncodingEnum;
import ca.uhn.fhir.rest.server.exceptions.InternalErrorException;
import ca.uhn.fhir.rest.server.exceptions.PreconditionFailedException;
import ca.uhn.fhir.util.ExtensionConstants;
import ca.uhn.fhir.util.TestUtil;
import org.apache.commons.io.IOUtils;
@ -13,6 +16,7 @@ import org.hl7.fhir.r4.model.Extension;
import org.hl7.fhir.r4.model.Patient;
import org.junit.AfterClass;
import org.junit.Test;
import org.springframework.beans.factory.annotation.Autowired;
import java.io.IOException;
import java.nio.charset.StandardCharsets;
@ -25,6 +29,29 @@ public class ServerR4Test extends BaseResourceProviderR4Test {
private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(ServerR4Test.class);
@Autowired
private IFhirResourceDao<CapabilityStatement> myCapabilityStatementDao;
@Test
public void testCapabilityStatementValidates() throws IOException {
HttpGet get = new HttpGet(ourServerBase + "/metadata?_pretty=true&_format=json");
try (CloseableHttpResponse resp = ourHttpClient.execute(get)) {
assertEquals(200, resp.getStatusLine().getStatusCode());
String respString = IOUtils.toString(resp.getEntity().getContent(), StandardCharsets.UTF_8);
ourLog.info(respString);
CapabilityStatement cs = myFhirCtx.newJsonParser().parseResource(CapabilityStatement.class, respString);
try {
myCapabilityStatementDao.validate(cs, null, respString, EncodingEnum.JSON, null, null, null);
} catch (PreconditionFailedException e) {
ourLog.info(myFhirCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(e.getOperationOutcome()));
fail();
}
}
}
/**
* See #519
@ -71,7 +98,7 @@ public class ServerR4Test extends BaseResourceProviderR4Test {
* Initial fetch after a clear should return
* no results
*/
ourResourceCountsCache.clear();
myResourceCountsCache.clear();
CapabilityStatement capabilityStatement = ourClient
.capabilities()
@ -93,7 +120,7 @@ public class ServerR4Test extends BaseResourceProviderR4Test {
* Now run a background pass (the update
* method is called by the scheduler normally)
*/
ourResourceCountsCache.update();
myResourceCountsCache.update();
capabilityStatement = ourClient
.capabilities()

151
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/provider/r5/ServerR5Test.java Normal file
View File

@ -0,0 +1,151 @@
package ca.uhn.fhir.jpa.provider.r5;
import ca.uhn.fhir.jpa.dao.IFhirResourceDao;
import ca.uhn.fhir.rest.api.EncodingEnum;
import ca.uhn.fhir.rest.server.exceptions.InternalErrorException;
import ca.uhn.fhir.rest.server.exceptions.PreconditionFailedException;
import ca.uhn.fhir.util.ExtensionConstants;
import ca.uhn.fhir.util.TestUtil;
import org.apache.commons.io.IOUtils;
import org.apache.http.client.methods.CloseableHttpResponse;
import org.apache.http.client.methods.HttpGet;
import org.hl7.fhir.r5.model.CapabilityStatement;
import org.hl7.fhir.r5.model.CapabilityStatement.CapabilityStatementRestResourceComponent;
import org.hl7.fhir.r5.model.CapabilityStatement.CapabilityStatementRestResourceSearchParamComponent;
import org.hl7.fhir.r5.model.Extension;
import org.hl7.fhir.r5.model.Patient;
import org.junit.AfterClass;
import org.junit.Ignore;
import org.junit.Test;
import org.springframework.beans.factory.annotation.Autowired;
import java.io.IOException;
import java.nio.charset.StandardCharsets;
import java.util.HashSet;
import java.util.Set;
import static org.junit.Assert.*;
public class ServerR5Test extends BaseResourceProviderR5Test {
private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(ServerR5Test.class);
@Autowired
private IFhirResourceDao<CapabilityStatement> myCapabilityStatementDao;
@Test
@Ignore
public void testCapabilityStatementValidates() throws IOException {
HttpGet get = new HttpGet(ourServerBase + "/metadata?_pretty=true&_format=json");
try (CloseableHttpResponse resp = ourHttpClient.execute(get)) {
assertEquals(200, resp.getStatusLine().getStatusCode());
String respString = IOUtils.toString(resp.getEntity().getContent(), StandardCharsets.UTF_8);
ourLog.info(respString);
CapabilityStatement cs = myFhirCtx.newJsonParser().parseResource(CapabilityStatement.class, respString);
try {
myCapabilityStatementDao.validate(cs, null, respString, EncodingEnum.JSON, null, null, null);
} catch (PreconditionFailedException e) {
ourLog.info(myFhirCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(e.getOperationOutcome()));
fail();
}
}
}
/**
* See #519
*/
@Test
public void saveIdParamOnlyAppearsOnce() throws IOException {
HttpGet get = new HttpGet(ourServerBase + "/metadata?_pretty=true&_format=xml");
CloseableHttpResponse resp = ourHttpClient.execute(get);
try {
ourLog.info(resp.toString());
assertEquals(200, resp.getStatusLine().getStatusCode());
String respString = IOUtils.toString(resp.getEntity().getContent(), StandardCharsets.UTF_8);
ourLog.info(respString);
CapabilityStatement cs = myFhirCtx.newXmlParser().parseResource(CapabilityStatement.class, respString);
for (CapabilityStatementRestResourceComponent nextResource : cs.getRest().get(0).getResource()) {
ourLog.info("Testing resource: " + nextResource.getType());
Set<String> sps = new HashSet<String>();
for (CapabilityStatementRestResourceSearchParamComponent nextSp : nextResource.getSearchParam()) {
if (sps.add(nextSp.getName()) == false) {
fail("Duplicate search parameter " + nextSp.getName() + " for resource " + nextResource.getType());
}
}
if (!sps.contains("_id")) {
fail("No search parameter _id for resource " + nextResource.getType());
}
}
} finally {
IOUtils.closeQuietly(resp.getEntity().getContent());
}
}
@Test
public void testMetadataIncludesResourceCounts() {
Patient p = new Patient();
p.setActive(true);
ourClient.create().resource(p).execute();
/*
* Initial fetch after a clear should return
* no results
*/
myResourceCountsCache.clear();
CapabilityStatement capabilityStatement = ourClient
.capabilities()
.ofType(CapabilityStatement.class)
.execute();
Extension patientCountExt = capabilityStatement
.getRest()
.get(0)
.getResource()
.stream()
.filter(t -> t.getType().equals("Patient"))
.findFirst()
.orElseThrow(() -> new InternalErrorException("No patient"))
.getExtensionByUrl(ExtensionConstants.CONF_RESOURCE_COUNT);
assertNull(patientCountExt);
/*
* Now run a background pass (the update
* method is called by the scheduler normally)
*/
myResourceCountsCache.update();
capabilityStatement = ourClient
.capabilities()
.ofType(CapabilityStatement.class)
.execute();
patientCountExt = capabilityStatement
.getRest()
.get(0)
.getResource()
.stream()
.filter(t -> t.getType().equals("Patient"))
.findFirst()
.orElseThrow(() -> new InternalErrorException("No patient"))
.getExtensionByUrl(ExtensionConstants.CONF_RESOURCE_COUNT);
assertEquals("1", patientCountExt.getValueAsPrimitive().getValueAsString());
}
@AfterClass
public static void afterClassClearContext() {
TestUtil.clearAllStaticFieldsForUnitTest();
}
}

13
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/search/reindex/ResourceReindexingSvcImplTest.java
View File

@ -26,6 +26,8 @@ import org.springframework.data.domain.SliceImpl;
import org.springframework.transaction.PlatformTransactionManager;
import java.util.*;
import java.util.concurrent.CountDownLatch;
import java.util.concurrent.TimeUnit;
import static org.junit.Assert.assertEquals;
import static org.mockito.ArgumentMatchers.any;
@ -94,6 +96,17 @@ public class ResourceReindexingSvcImplTest extends BaseJpaTest {
mySvc.start();
}
@Test
public void testNoParallelReindexing() throws InterruptedException {
CountDownLatch latch = new CountDownLatch(1);
new Thread(()->{
mySvc.getIndexingLockForUnitTest().lock();
latch.countDown();
}).start();
latch.await(10, TimeUnit.SECONDS);
mySvc.runReindexingPass();
}
@Test
public void testReindexPassOnlyReturnsValuesAtLowThreshold() {
mockNothingToExpunge();

75
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/term/ValueSetConceptAccumulatorTest.java Normal file
View File

@ -0,0 +1,75 @@
package ca.uhn.fhir.jpa.term;
import ca.uhn.fhir.jpa.dao.data.ITermValueSetConceptDao;
import ca.uhn.fhir.jpa.dao.data.ITermValueSetConceptDesignationDao;
import ca.uhn.fhir.jpa.dao.data.ITermValueSetDao;
import ca.uhn.fhir.jpa.entity.TermValueSet;
import ca.uhn.fhir.jpa.entity.TermValueSetConcept;
import ca.uhn.fhir.jpa.entity.TermValueSetConceptDesignation;
import org.hl7.fhir.r4.model.ValueSet;
import org.junit.Before;
import org.junit.Test;
import org.junit.runner.RunWith;
import org.mockito.Mock;
import org.mockito.junit.MockitoJUnitRunner;
import java.util.Optional;
import static org.junit.Assert.*;
import static org.mockito.ArgumentMatchers.any;
import static org.mockito.Mockito.*;
@RunWith(MockitoJUnitRunner.class)
public class ValueSetConceptAccumulatorTest {
private ValueSetConceptAccumulator myAccumulator;
private TermValueSet myValueSet;
@Mock
private ITermValueSetDao myValueSetDao;
@Mock
private ITermValueSetConceptDesignationDao myValueSetDesignationDao;
@Mock
private ITermValueSetConceptDao myValueSetConceptDao;
@Before
public void before() {
myValueSet = new TermValueSet();
myAccumulator = new ValueSetConceptAccumulator(myValueSet, myValueSetDao, myValueSetConceptDao, myValueSetDesignationDao);
}
@Test
public void testIncludeConcept() {
for (int i = 0; i < 1000; i++) {
myAccumulator.includeConcept("sys", "code", "display");
}
verify(myValueSetConceptDao, times(1000)).save(any());
}
@Test
public void testExcludeBlankConcept() {
myAccumulator.excludeConcept("", "");
verifyNoInteractions(myValueSetConceptDao);
}
@Test
public void testAddMessage() {
myAccumulator.addMessage("foo");
verifyNoInteractions(myValueSetConceptDao);
}
@Test
public void testExcludeConceptWithDesignations() {
for (int i = 0; i <1000; i++) {
TermValueSetConcept value = new TermValueSetConcept();
value.setCode("code");
value.getDesignations().add(new TermValueSetConceptDesignation().setValue("foo"));
when(myValueSetConceptDao.findByTermValueSetIdSystemAndCode(any(), eq("sys"), eq("code"+i))).thenReturn(Optional.of(value));
myAccumulator.excludeConcept("sys", "code"+i);
}
}
}

17
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/term/ValueSetExpansionR4Test.java
View File

@ -2,11 +2,13 @@ package ca.uhn.fhir.jpa.term;
import ca.uhn.fhir.jpa.entity.*;
import ca.uhn.fhir.jpa.model.entity.ResourceTable;
import ca.uhn.fhir.jpa.model.util.JpaConstants;
import ca.uhn.fhir.jpa.term.custom.CustomTerminologySet;
import ca.uhn.fhir.rest.server.exceptions.InternalErrorException;
import com.google.common.collect.Lists;
import org.hl7.fhir.instance.model.api.IIdType;
import org.hl7.fhir.r4.model.CodeSystem;
import org.hl7.fhir.r4.model.Extension;
import org.hl7.fhir.r4.model.ValueSet;
import org.hl7.fhir.r4.model.codesystems.HttpVerb;
import org.junit.Test;
@ -688,6 +690,21 @@ public class ValueSetExpansionR4Test extends BaseTermR4Test {
assertEquals("Systolische bloeddruk minimaal 1 uur", designationComponent.getValue());
}
@Test
public void testExpandValueSetWithUnknownCodeSystem() {
ValueSet vs = new ValueSet();
ValueSet.ConceptSetComponent include = vs.getCompose().addInclude();
include.setSystem("http://unknown-system");
ValueSet outcome = myTermSvc.expandValueSetInMemory(vs, null);
assertEquals(0, outcome.getExpansion().getContains().size());
String encoded = myFhirCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(outcome);
ourLog.info(encoded);
Extension extensionByUrl = outcome.getExpansion().getExtensionByUrl(JpaConstants.EXT_VALUESET_EXPANSION_MESSAGE);
assertEquals("Unknown CodeSystem URI \"http://unknown-system\" referenced from ValueSet", extensionByUrl.getValueAsPrimitive().getValueAsString());
}
@Test
public void testExpandTermValueSetAndChildrenWithOffsetAndCountWithClientAssignedId() throws Exception {
myDaoConfig.setPreExpandValueSets(true);

13
hapi-fhir-jpaserver-model/src/main/java/ca/uhn/fhir/jpa/model/util/JpaConstants.java
View File

@ -24,6 +24,13 @@ import ca.uhn.fhir.rest.api.Constants;
public class JpaConstants {
/**
* Non-instantiable
*/
private JpaConstants() {
// nothing
}
/**
* Operation name for the $apply-codesystem-delta-add operation
*/
@ -243,6 +250,12 @@ public class JpaConstants {
*/
public static final String EXTENSION_EXT_SYSTEMDEFINED = JpaConstants.class.getName() + "_EXTENSION_EXT_SYSTEMDEFINED";
/**
* Message added to expansion valueset
*/
public static final String EXT_VALUESET_EXPANSION_MESSAGE = "http://hapifhir.io/fhir/StructureDefinition/valueset-expansion-message";
/**
* Parameter for the $export operation
*/

5
hapi-fhir-jpaserver-searchparam/pom.xml
View File

@ -122,6 +122,11 @@
<artifactId>spring-boot-test</artifactId>
<scope>test</scope>
</dependency>
<dependency>
<groupId>javax.servlet</groupId>
<artifactId>javax.servlet-api</artifactId>
<scope>test</scope>
</dependency>
</dependencies>

396
hapi-fhir-jpaserver-searchparam/src/main/java/ca/uhn/fhir/jpa/searchparam/extractor/BaseSearchParamExtractor.java
View File

@ -59,6 +59,43 @@ public abstract class BaseSearchParamExtractor implements ISearchParamExtractor
@Autowired
private ModelConfig myModelConfig;
private Set<String> myIgnoredForSearchDatatypes;
private BaseRuntimeChildDefinition myQuantityValueValueChild;
private BaseRuntimeChildDefinition myQuantitySystemValueChild;
private BaseRuntimeChildDefinition myQuantityCodeValueChild;
private BaseRuntimeChildDefinition myMoneyValueChild;
private BaseRuntimeChildDefinition myMoneyCurrencyChild;
private BaseRuntimeElementCompositeDefinition<?> myLocationPositionDefinition;
private BaseRuntimeChildDefinition myCodeSystemUrlValueChild;
private BaseRuntimeChildDefinition myRangeLowValueChild;
private BaseRuntimeChildDefinition myRangeHighValueChild;
private BaseRuntimeChildDefinition myAddressLineValueChild;
private BaseRuntimeChildDefinition myAddressCityValueChild;
private BaseRuntimeChildDefinition myAddressStateValueChild;
private BaseRuntimeChildDefinition myAddressCountryValueChild;
private BaseRuntimeChildDefinition myAddressPostalCodeValueChild;
private BaseRuntimeChildDefinition myCapabilityStatementRestSecurityServiceValueChild;
private BaseRuntimeChildDefinition myPeriodStartValueChild;
private BaseRuntimeChildDefinition myPeriodEndValueChild;
private BaseRuntimeChildDefinition myTimingEventValueChild;
private BaseRuntimeChildDefinition myTimingRepeatValueChild;
private BaseRuntimeChildDefinition myTimingRepeatBoundsValueChild;
private BaseRuntimeChildDefinition myDurationSystemValueChild;
private BaseRuntimeChildDefinition myDurationCodeValueChild;
private BaseRuntimeChildDefinition myDurationValueValueChild;
private BaseRuntimeChildDefinition myHumanNameFamilyValueChild;
private BaseRuntimeChildDefinition myHumanNameGivenValueChild;
private BaseRuntimeChildDefinition myContactPointValueValueChild;
private BaseRuntimeChildDefinition myIdentifierSystemValueChild;
private BaseRuntimeChildDefinition myIdentifierValueValueChild;
private BaseRuntimeChildDefinition myIdentifierTypeValueChild;
private BaseRuntimeChildDefinition myIdentifierTypeTextValueChild;
private BaseRuntimeChildDefinition myCodeableConceptCodingValueChild;
private BaseRuntimeChildDefinition myCodeableConceptTextValueChild;
private BaseRuntimeChildDefinition myCodingSystemValueChild;
private BaseRuntimeChildDefinition myCodingCodeValueChild;
private BaseRuntimeChildDefinition myCodingDisplayValueChild;
private BaseRuntimeChildDefinition myContactPointSystemValueChild;
private BaseRuntimeChildDefinition myPatientCommunicationLanguageValueChild;
/**
* Constructor
@ -77,27 +114,20 @@ public abstract class BaseSearchParamExtractor implements ISearchParamExtractor
}
@Override
public Set<BaseResourceIndexedSearchParam> extractSearchParamTokens(IBaseResource theResource) {
BaseRuntimeElementCompositeDefinition<?> codeSystemDefinition;
BaseRuntimeChildDefinition codeSystemUrlValueChild = null;
if (getContext().getVersion().getVersion().isEqualOrNewerThan(FhirVersionEnum.DSTU3)) {
codeSystemDefinition = getContext().getResourceDefinition("CodeSystem");
assert codeSystemDefinition != null;
codeSystemUrlValueChild = codeSystemDefinition.getChildByName("url");
}
public SearchParamSet<BaseResourceIndexedSearchParam> extractSearchParamTokens(IBaseResource theResource) {
String resourceTypeName = toRootTypeName(theResource);
String useSystem;
if (getContext().getVersion().getVersion().equals(FhirVersionEnum.DSTU2)) {
if (resourceTypeName.equals("ValueSet")) {
ca.uhn.fhir.model.dstu2.resource.ValueSet dstu2ValueSet = (ca.uhn.fhir.model.dstu2.resource.ValueSet)theResource;
ca.uhn.fhir.model.dstu2.resource.ValueSet dstu2ValueSet = (ca.uhn.fhir.model.dstu2.resource.ValueSet) theResource;
useSystem = dstu2ValueSet.getCodeSystem().getSystem();
} else {
useSystem = null;
}
} else {
if (resourceTypeName.equals("CodeSystem")) {
useSystem = extractValueAsString(codeSystemUrlValueChild, theResource);
useSystem = extractValueAsString(myCodeSystemUrlValueChild, theResource);
} else {
useSystem = null;
}
@ -176,15 +206,20 @@ public abstract class BaseSearchParamExtractor implements ISearchParamExtractor
addToken_ContactPoint(resourceTypeName, params, searchParam, value);
break;
default:
throw new ConfigurationException("Search param " + searchParam.getName() + " is of unexpected datatype: " + value.getClass());
addUnexpectedDatatypeWarning(params, searchParam, value);
break;
}
};
return extractSearchParams(theResource, extractor, RestSearchParameterTypeEnum.TOKEN);
}
private void addUnexpectedDatatypeWarning(SearchParamSet<? extends BaseResourceIndexedSearchParam> params, RuntimeSearchParam searchParam, IBase value) {
params.addWarning("Search param " + searchParam.getName() + " is of unexpected datatype: " + value.getClass());
}
@Override
public Set<ResourceIndexedSearchParamUri> extractSearchParamUri(IBaseResource theResource) {
public SearchParamSet<ResourceIndexedSearchParamUri> extractSearchParamUri(IBaseResource theResource) {
IExtractor<ResourceIndexedSearchParamUri> extractor = (params, searchParam, value, path) -> {
String nextType = toRootTypeName(value);
String resourceType = toRootTypeName(theResource);
@ -197,7 +232,8 @@ public abstract class BaseSearchParamExtractor implements ISearchParamExtractor
addUri_Uri(resourceType, params, searchParam, value);
break;
default:
throw new ConfigurationException("Search param " + searchParam.getName() + " is of unexpected datatype: " + value.getClass());
addUnexpectedDatatypeWarning(params, searchParam, value);
break;
}
};
@ -205,13 +241,12 @@ public abstract class BaseSearchParamExtractor implements ISearchParamExtractor
}
@Override
public Set<ResourceIndexedSearchParamCoords> extractSearchParamCoords(IBaseResource theResource) {
// TODO: implement
return Collections.emptySet();
public SearchParamSet<ResourceIndexedSearchParamCoords> extractSearchParamCoords(IBaseResource theResource) {
return new SearchParamSet<>();
}
@Override
public Set<ResourceIndexedSearchParamDate> extractSearchParamDates(IBaseResource theResource) {
public SearchParamSet<ResourceIndexedSearchParamDate> extractSearchParamDates(IBaseResource theResource) {
IExtractor<ResourceIndexedSearchParamDate> extractor = (params, searchParam, value, path) -> {
String nextType = toRootTypeName(value);
String resourceType = toRootTypeName(theResource);
@ -231,7 +266,8 @@ public abstract class BaseSearchParamExtractor implements ISearchParamExtractor
// CarePlan.activitydate can be a string - ignored for now
break;
default:
throw new ConfigurationException("Search param " + searchParam.getName() + " is of unexpected datatype: " + value.getClass());
addUnexpectedDatatypeWarning(params, searchParam, value);
break;
}
};
@ -239,7 +275,7 @@ public abstract class BaseSearchParamExtractor implements ISearchParamExtractor
}
@Override
public Set<ResourceIndexedSearchParamNumber> extractSearchParamNumber(IBaseResource theResource) {
public SearchParamSet<ResourceIndexedSearchParamNumber> extractSearchParamNumber(IBaseResource theResource) {
IExtractor<ResourceIndexedSearchParamNumber> extractor = (params, searchParam, value, path) -> {
String nextType = toRootTypeName(value);
@ -260,7 +296,8 @@ public abstract class BaseSearchParamExtractor implements ISearchParamExtractor
addNumber_Decimal(resourceType, params, searchParam, value);
break;
default:
throw new ConfigurationException("Search param " + searchParam.getName() + " is of unexpected datatype: " + value.getClass());
addUnexpectedDatatypeWarning(params, searchParam, value);
break;
}
};
@ -268,14 +305,10 @@ public abstract class BaseSearchParamExtractor implements ISearchParamExtractor
}
@Override
public Set<ResourceIndexedSearchParamQuantity> extractSearchParamQuantity(IBaseResource theResource) {
BaseRuntimeElementCompositeDefinition<?> locationDefinition = (BaseRuntimeElementCompositeDefinition<?>) getContext().getResourceDefinition("Location");
BaseRuntimeChildDefinition locationPositionValueChild = locationDefinition.getChildByName("position");
BaseRuntimeElementCompositeDefinition<?> locationPositionDefinition = (BaseRuntimeElementCompositeDefinition<?>) locationPositionValueChild.getChildByName("position");
public SearchParamSet<ResourceIndexedSearchParamQuantity> extractSearchParamQuantity(IBaseResource theResource) {
IExtractor<ResourceIndexedSearchParamQuantity> extractor = (params, searchParam, value, path) -> {
if (value.getClass().equals(locationPositionDefinition.getImplementingClass())) {
if (value.getClass().equals(myLocationPositionDefinition.getImplementingClass())) {
ourLog.warn("Position search not currently supported, not indexing location");
return;
}
@ -293,7 +326,8 @@ public abstract class BaseSearchParamExtractor implements ISearchParamExtractor
addQuantity_Range(resourceType, params, searchParam, value);
break;
default:
throw new ConfigurationException("Search param " + searchParam.getName() + " is of unexpected datatype: " + value.getClass());
addUnexpectedDatatypeWarning(params, searchParam, value);
break;
}
};
@ -301,7 +335,7 @@ public abstract class BaseSearchParamExtractor implements ISearchParamExtractor
}
@Override
public Set<ResourceIndexedSearchParamString> extractSearchParamStrings(IBaseResource theResource) {
public SearchParamSet<ResourceIndexedSearchParamString> extractSearchParamStrings(IBaseResource theResource) {
IExtractor<ResourceIndexedSearchParamString> extractor = (params, searchParam, value, path) -> {
String resourceType = toRootTypeName(theResource);
@ -330,7 +364,8 @@ public abstract class BaseSearchParamExtractor implements ISearchParamExtractor
addString_Range(resourceType, params, searchParam, value);
break;
default:
throw new ConfigurationException("Search param " + searchParam.getName() + " is of unexpected datatype: " + value.getClass());
addUnexpectedDatatypeWarning(params, searchParam, value);
break;
}
};
@ -356,7 +391,6 @@ public abstract class BaseSearchParamExtractor implements ISearchParamExtractor
}
/**
* [
* Override parent because we're using FHIRPath here
*/
private List<IBase> extractValues(String thePaths, IBaseResource theResource) {
@ -401,7 +435,7 @@ public abstract class BaseSearchParamExtractor implements ISearchParamExtractor
return myModelConfig;
}
public Collection<RuntimeSearchParam> getSearchParams(IBaseResource theResource) {
private Collection<RuntimeSearchParam> getSearchParams(IBaseResource theResource) {
RuntimeResourceDefinition def = getContext().getResourceDefinition(theResource);
Collection<RuntimeSearchParam> retVal = mySearchParamRegistry.getActiveSearchParams(def.getName()).values();
List<RuntimeSearchParam> defaultList = Collections.emptyList();
@ -409,29 +443,14 @@ public abstract class BaseSearchParamExtractor implements ISearchParamExtractor
return retVal;
}
@PostConstruct
public void start() {
myIgnoredForSearchDatatypes = new HashSet<>();
addIgnoredType(getContext(), "Annotation", myIgnoredForSearchDatatypes);
addIgnoredType(getContext(), "Attachment", myIgnoredForSearchDatatypes);
addIgnoredType(getContext(), "Count", myIgnoredForSearchDatatypes);
addIgnoredType(getContext(), "Distance", myIgnoredForSearchDatatypes);
addIgnoredType(getContext(), "Ratio", myIgnoredForSearchDatatypes);
addIgnoredType(getContext(), "SampledData", myIgnoredForSearchDatatypes);
addIgnoredType(getContext(), "Signature", myIgnoredForSearchDatatypes);
}
private void addQuantity_Quantity(String theResourceType, Set<ResourceIndexedSearchParamQuantity> theParams, RuntimeSearchParam theSearchParam, IBase theValue) {
BaseRuntimeElementCompositeDefinition<?> quantityDefinition = (BaseRuntimeElementCompositeDefinition<?>) getContext().getElementDefinition("Quantity");
BaseRuntimeChildDefinition quantityValueChild = quantityDefinition.getChildByName("value");
BaseRuntimeChildDefinition quantitySystemChild = quantityDefinition.getChildByName("system");
BaseRuntimeChildDefinition quantityCodeChild = quantityDefinition.getChildByName("code");
Optional<IPrimitiveType<BigDecimal>> valueField = quantityValueChild.getAccessor().getFirstValueOrNull(theValue);
Optional<IPrimitiveType<BigDecimal>> valueField = myQuantityValueValueChild.getAccessor().getFirstValueOrNull(theValue);
if (valueField.isPresent() && valueField.get().getValue() != null) {
BigDecimal nextValueValue = valueField.get().getValue();
String system = extractValueAsString(quantitySystemChild, theValue);
String code = extractValueAsString(quantityCodeChild, theValue);
String system = extractValueAsString(myQuantitySystemValueChild, theValue);
String code = extractValueAsString(myQuantityCodeValueChild, theValue);
ResourceIndexedSearchParamQuantity nextEntity = new ResourceIndexedSearchParamQuantity(theResourceType, theSearchParam.getName(), nextValueValue, system, code);
theParams.add(nextEntity);
@ -440,16 +459,13 @@ public abstract class BaseSearchParamExtractor implements ISearchParamExtractor
}
private void addQuantity_Money(String theResourceType, Set<ResourceIndexedSearchParamQuantity> theParams, RuntimeSearchParam theSearchParam, IBase theValue) {
BaseRuntimeElementCompositeDefinition<?> moneyDefinition = (BaseRuntimeElementCompositeDefinition<?>) getContext().getElementDefinition("Money");
BaseRuntimeChildDefinition moneyValueChild = moneyDefinition.getChildByName("value");
BaseRuntimeChildDefinition moneyCurrencyChild = moneyDefinition.getChildByName("currency");
Optional<IPrimitiveType<BigDecimal>> valueField = moneyValueChild.getAccessor().getFirstValueOrNull(theValue);
Optional<IPrimitiveType<BigDecimal>> valueField = myMoneyValueChild.getAccessor().getFirstValueOrNull(theValue);
if (valueField.isPresent() && valueField.get().getValue() != null) {
BigDecimal nextValueValue = valueField.get().getValue();
String nextValueString = "urn:iso:std:iso:4217";
String nextValueCode = extractValueAsString(moneyCurrencyChild, theValue);
String nextValueCode = extractValueAsString(myMoneyCurrencyChild, theValue);
String searchParamName = theSearchParam.getName();
ResourceIndexedSearchParamQuantity nextEntity = new ResourceIndexedSearchParamQuantity(theResourceType, searchParamName, nextValueValue, nextValueString, nextValueCode);
theParams.add(nextEntity);
@ -458,102 +474,65 @@ public abstract class BaseSearchParamExtractor implements ISearchParamExtractor
}
private void addQuantity_Range(String theResourceType, Set<ResourceIndexedSearchParamQuantity> theParams, RuntimeSearchParam theSearchParam, IBase theValue) {
BaseRuntimeElementCompositeDefinition<?> rangeDefinition = (BaseRuntimeElementCompositeDefinition<?>) getContext().getElementDefinition("Range");
BaseRuntimeChildDefinition rangeLowValueChild = rangeDefinition.getChildByName("low");
BaseRuntimeChildDefinition rangeHighValueChild = rangeDefinition.getChildByName("high");
Optional<IBase> low = rangeLowValueChild.getAccessor().getFirstValueOrNull(theValue);
Optional<IBase> low = myRangeLowValueChild.getAccessor().getFirstValueOrNull(theValue);
low.ifPresent(theIBase -> addQuantity_Quantity(theResourceType, theParams, theSearchParam, theIBase));
Optional<IBase> high = rangeHighValueChild.getAccessor().getFirstValueOrNull(theValue);
Optional<IBase> high = myRangeHighValueChild.getAccessor().getFirstValueOrNull(theValue);
high.ifPresent(theIBase -> addQuantity_Quantity(theResourceType, theParams, theSearchParam, theIBase));
}
private void addToken_Identifier(String theResourceType, Set<BaseResourceIndexedSearchParam> theParams, RuntimeSearchParam theSearchParam, IBase theValue) {
BaseRuntimeElementCompositeDefinition<?> identifierDefinition = (BaseRuntimeElementCompositeDefinition<?>) getContext().getElementDefinition("Identifier");
BaseRuntimeChildDefinition identifierSystemValueChild = identifierDefinition.getChildByName("system");
BaseRuntimeChildDefinition identifierValueValueChild = identifierDefinition.getChildByName("value");
BaseRuntimeChildDefinition identifierTypeValueChild = identifierDefinition.getChildByName("type");
BaseRuntimeElementCompositeDefinition<?> identifierTypeDefinition = (BaseRuntimeElementCompositeDefinition<?>) identifierTypeValueChild.getChildByName("type");
BaseRuntimeChildDefinition identifierTypeTextValueChild = identifierTypeDefinition.getChildByName("text");
String system = extractValueAsString(identifierSystemValueChild, theValue);
String value = extractValueAsString(identifierValueValueChild, theValue);
String system = extractValueAsString(myIdentifierSystemValueChild, theValue);
String value = extractValueAsString(myIdentifierValueValueChild, theValue);
if (isNotBlank(value)) {
createTokenIndexIfNotBlank(theResourceType, theParams, theSearchParam, system, value);
}
Optional<IBase> type = identifierTypeValueChild.getAccessor().getFirstValueOrNull(theValue);
Optional<IBase> type = myIdentifierTypeValueChild.getAccessor().getFirstValueOrNull(theValue);
if (type.isPresent()) {
String text = extractValueAsString(identifierTypeTextValueChild, type.get());
String text = extractValueAsString(myIdentifierTypeTextValueChild, type.get());
createStringIndexIfNotBlank(theResourceType, theParams, theSearchParam, text);
}
}
private void addToken_CodeableConcept(String theResourceType, Set<BaseResourceIndexedSearchParam> theParams, RuntimeSearchParam theSearchParam, IBase theValue) {
BaseRuntimeElementCompositeDefinition<?> codeableConceptDefinition = (BaseRuntimeElementCompositeDefinition<?>) getContext().getElementDefinition("CodeableConcept");
BaseRuntimeChildDefinition codeableConceptCodingValueChild = codeableConceptDefinition.getChildByName("coding");
BaseRuntimeChildDefinition codeableConceptTextValueChild = codeableConceptDefinition.getChildByName("text");
List<IBase> codings = codeableConceptCodingValueChild.getAccessor().getValues(theValue);
List<IBase> codings = myCodeableConceptCodingValueChild.getAccessor().getValues(theValue);
for (IBase nextCoding : codings) {
addToken_Coding(theResourceType, theParams, theSearchParam, nextCoding);
}
String text = extractValueAsString(codeableConceptTextValueChild, theValue);
String text = extractValueAsString(myCodeableConceptTextValueChild, theValue);
if (isNotBlank(text)) {
createStringIndexIfNotBlank(theResourceType, theParams, theSearchParam, text);
}
}
private void addToken_Coding(String theResourceType, Set<BaseResourceIndexedSearchParam> theParams, RuntimeSearchParam theSearchParam, IBase theValue) {
BaseRuntimeElementCompositeDefinition<?> codingDefinition = (BaseRuntimeElementCompositeDefinition<?>) getContext().getElementDefinition("Coding");
BaseRuntimeChildDefinition codingSystemValueChild = codingDefinition.getChildByName("system");
BaseRuntimeChildDefinition codingCodeValueChild = codingDefinition.getChildByName("code");
BaseRuntimeChildDefinition codingDisplayValueChild = codingDefinition.getChildByName("display");
String system = extractValueAsString(codingSystemValueChild, theValue);
String code = extractValueAsString(codingCodeValueChild, theValue);
String system = extractValueAsString(myCodingSystemValueChild, theValue);
String code = extractValueAsString(myCodingCodeValueChild, theValue);
createTokenIndexIfNotBlank(theResourceType, theParams, theSearchParam, system, code);
String text = extractValueAsString(codingDisplayValueChild, theValue);
String text = extractValueAsString(myCodingDisplayValueChild, theValue);
createStringIndexIfNotBlank(theResourceType, theParams, theSearchParam, text);
}
private void addToken_ContactPoint(String theResourceType, Set<BaseResourceIndexedSearchParam> theParams, RuntimeSearchParam theSearchParam, IBase theValue) {
BaseRuntimeElementCompositeDefinition<?> contactPointDefinition = (BaseRuntimeElementCompositeDefinition<?>) getContext().getElementDefinition("ContactPoint");
BaseRuntimeChildDefinition contactPointSystemValueChild = contactPointDefinition.getChildByName("system");
BaseRuntimeChildDefinition contactPointValueValueChild = contactPointDefinition.getChildByName("value");
String system = extractValueAsString(contactPointSystemValueChild, theValue);
String value = extractValueAsString(contactPointValueValueChild, theValue);
String system = extractValueAsString(myContactPointSystemValueChild, theValue);
String value = extractValueAsString(myContactPointValueValueChild, theValue);
createTokenIndexIfNotBlank(theResourceType, theParams, theSearchParam, system, value);
}
private void addToken_PatientCommunication(String theResourceType, Set<BaseResourceIndexedSearchParam> theParams, RuntimeSearchParam theSearchParam, IBase theValue) {
BaseRuntimeElementCompositeDefinition<?> patientDefinition = getContext().getResourceDefinition("Patient");
BaseRuntimeChildDefinition patientCommunicationValueChild = patientDefinition.getChildByName("communication");
BaseRuntimeElementCompositeDefinition<?> patientCommunicationDefinition = (BaseRuntimeElementCompositeDefinition<?>) patientCommunicationValueChild.getChildByName("communication");
BaseRuntimeChildDefinition patientCommunicationLanguageValueChild = patientCommunicationDefinition.getChildByName("language");
List<IBase> values = patientCommunicationLanguageValueChild.getAccessor().getValues(theValue);
List<IBase> values = myPatientCommunicationLanguageValueChild.getAccessor().getValues(theValue);
for (IBase next : values) {
addToken_CodeableConcept(theResourceType, theParams, theSearchParam, next);
}
}
private void addToken_CapabilityStatementRestSecurity(String theResourceType, Set<BaseResourceIndexedSearchParam> theParams, RuntimeSearchParam theSearchParam, IBase theValue) {
BaseRuntimeElementCompositeDefinition<?> capabilityStatementDefinition = getContext().getResourceDefinition("CapabilityStatement");
BaseRuntimeChildDefinition capabilityStatementRestChild = capabilityStatementDefinition.getChildByName("rest");
BaseRuntimeElementCompositeDefinition<?> capabilityStatementRestDefinition = (BaseRuntimeElementCompositeDefinition<?>) capabilityStatementRestChild.getChildByName("rest");
BaseRuntimeChildDefinition capabilityStatementRestSecurityValueChild = capabilityStatementRestDefinition.getChildByName("security");
BaseRuntimeElementCompositeDefinition<?> capabilityStatementRestSecurityDefinition = (BaseRuntimeElementCompositeDefinition<?>) capabilityStatementRestSecurityValueChild.getChildByName("security");
BaseRuntimeChildDefinition capabilityStatementRestSecurityServiceValueChild = capabilityStatementRestSecurityDefinition.getChildByName("service");
List<IBase> values = capabilityStatementRestSecurityServiceValueChild.getAccessor().getValues(theValue);
List<IBase> values = myCapabilityStatementRestSecurityServiceValueChild.getAccessor().getValues(theValue);
for (IBase nextValue : values) {
addToken_CodeableConcept(theResourceType, theParams, theSearchParam, nextValue);
}
@ -561,13 +540,9 @@ public abstract class BaseSearchParamExtractor implements ISearchParamExtractor
}
private void addDate_Period(String theResourceType, Set<ResourceIndexedSearchParamDate> theParams, RuntimeSearchParam theSearchParam, IBase theValue) {
BaseRuntimeElementCompositeDefinition<?> periodDefinition = (BaseRuntimeElementCompositeDefinition<?>) getContext().getElementDefinition("Period");
BaseRuntimeChildDefinition periodStartValueChild = periodDefinition.getChildByName("start");
BaseRuntimeChildDefinition periodEndValueChild = periodDefinition.getChildByName("end");
Date start = extractValueAsDate(periodStartValueChild, theValue);
String startAsString = extractValueAsString(periodStartValueChild, theValue);
Date end = extractValueAsDate(periodEndValueChild, theValue);
Date start = extractValueAsDate(myPeriodStartValueChild, theValue);
String startAsString = extractValueAsString(myPeriodStartValueChild, theValue);
Date end = extractValueAsDate(myPeriodEndValueChild, theValue);
if (start != null || end != null) {
ResourceIndexedSearchParamDate nextEntity = new ResourceIndexedSearchParamDate(theResourceType, theSearchParam.getName(), start, end, startAsString);
@ -576,13 +551,7 @@ public abstract class BaseSearchParamExtractor implements ISearchParamExtractor
}
private void addDate_Timing(String theResourceType, Set<ResourceIndexedSearchParamDate> theParams, RuntimeSearchParam theSearchParam, IBase theValue) {
BaseRuntimeElementCompositeDefinition<?> timingDefinition = (BaseRuntimeElementCompositeDefinition<?>) getContext().getElementDefinition("Timing");
BaseRuntimeChildDefinition timingEventValueChild = timingDefinition.getChildByName("event");
BaseRuntimeChildDefinition timingRepeatValueChild = timingDefinition.getChildByName("repeat");
BaseRuntimeElementCompositeDefinition<?> timingRepeatDefinition = (BaseRuntimeElementCompositeDefinition<?>) timingRepeatValueChild.getChildByName("repeat");
BaseRuntimeChildDefinition timingRepeatBoundsValueChild = timingRepeatDefinition.getChildByName("bounds[x]");
List<IPrimitiveType<Date>> values = extractValuesAsFhirDates(timingEventValueChild, theValue);
List<IPrimitiveType<Date>> values = extractValuesAsFhirDates(myTimingEventValueChild, theValue);
TreeSet<Date> dates = new TreeSet<>();
String firstValue = null;
@ -595,21 +564,16 @@ public abstract class BaseSearchParamExtractor implements ISearchParamExtractor
}
}
Optional<IBase> repeat = timingRepeatValueChild.getAccessor().getFirstValueOrNull(theValue);
Optional<IBase> repeat = myTimingRepeatValueChild.getAccessor().getFirstValueOrNull(theValue);
if (repeat.isPresent()) {
Optional<IBase> bounds = timingRepeatBoundsValueChild.getAccessor().getFirstValueOrNull(repeat.get());
Optional<IBase> bounds = myTimingRepeatBoundsValueChild.getAccessor().getFirstValueOrNull(repeat.get());
if (bounds.isPresent()) {
String boundsType = toRootTypeName(bounds.get());
switch (boundsType) {
case "Period":
BaseRuntimeElementCompositeDefinition<?> periodDefinition = (BaseRuntimeElementCompositeDefinition<?>) getContext().getElementDefinition("Period");
BaseRuntimeChildDefinition periodStartValueChild = periodDefinition.getChildByName("start");
BaseRuntimeChildDefinition periodEndValueChild = periodDefinition.getChildByName("end");
Date start = extractValueAsDate(periodStartValueChild, bounds.get());
Date end = extractValueAsDate(periodEndValueChild, bounds.get());
dates.add(start);
dates.add(end);
break;
if ("Period".equals(boundsType)) {
Date start = extractValueAsDate(myPeriodStartValueChild, bounds.get());
Date end = extractValueAsDate(myPeriodEndValueChild, bounds.get());
dates.add(start);
dates.add(end);
}
}
}
@ -621,14 +585,9 @@ public abstract class BaseSearchParamExtractor implements ISearchParamExtractor
}
private void addNumber_Duration(String theResourceType, Set<ResourceIndexedSearchParamNumber> theParams, RuntimeSearchParam theSearchParam, IBase theValue) {
BaseRuntimeElementCompositeDefinition<?> durationDefinition = (BaseRuntimeElementCompositeDefinition<?>) getContext().getElementDefinition("Duration");
BaseRuntimeChildDefinition durationSystemValueChild = durationDefinition.getChildByName("system");
BaseRuntimeChildDefinition durationCodeValueChild = durationDefinition.getChildByName("code");
BaseRuntimeChildDefinition durationValueValueChild = durationDefinition.getChildByName("value");
String system = extractValueAsString(durationSystemValueChild, theValue);
String code = extractValueAsString(durationCodeValueChild, theValue);
BigDecimal value = extractValueAsBigDecimal(durationValueValueChild, theValue);
String system = extractValueAsString(myDurationSystemValueChild, theValue);
String code = extractValueAsString(myDurationCodeValueChild, theValue);
BigDecimal value = extractValueAsBigDecimal(myDurationValueValueChild, theValue);
if (value != null) {
value = normalizeQuantityContainingTimeUnitsIntoDaysForNumberParam(system, code, value);
ResourceIndexedSearchParamNumber nextEntity = new ResourceIndexedSearchParamNumber(theResourceType, theSearchParam.getName(), value);
@ -637,15 +596,10 @@ public abstract class BaseSearchParamExtractor implements ISearchParamExtractor
}
private void addNumber_Quantity(String theResourceType, Set<ResourceIndexedSearchParamNumber> theParams, RuntimeSearchParam theSearchParam, IBase theValue) {
BaseRuntimeElementCompositeDefinition<?> quantityDefinition = (BaseRuntimeElementCompositeDefinition<?>) getContext().getElementDefinition("Duration");
BaseRuntimeChildDefinition quantityValueValueChild = quantityDefinition.getChildByName("value");
BaseRuntimeChildDefinition quantitySystemChild = quantityDefinition.getChildByName("system");
BaseRuntimeChildDefinition quantityCodeChild = quantityDefinition.getChildByName("code");
BigDecimal value = extractValueAsBigDecimal(quantityValueValueChild, theValue);
BigDecimal value = extractValueAsBigDecimal(myQuantityValueValueChild, theValue);
if (value != null) {
String system = extractValueAsString(quantitySystemChild, theValue);
String code = extractValueAsString(quantityCodeChild, theValue);
String system = extractValueAsString(myQuantitySystemValueChild, theValue);
String code = extractValueAsString(myQuantityCodeValueChild, theValue);
value = normalizeQuantityContainingTimeUnitsIntoDaysForNumberParam(system, code, value);
ResourceIndexedSearchParamNumber nextEntity = new ResourceIndexedSearchParamNumber(theResourceType, theSearchParam.getName(), value);
theParams.add(nextEntity);
@ -675,16 +629,12 @@ public abstract class BaseSearchParamExtractor implements ISearchParamExtractor
}
private void addString_HumanName(String theResourceType, Set<ResourceIndexedSearchParamString> theParams, RuntimeSearchParam theSearchParam, IBase theValue) {
BaseRuntimeElementCompositeDefinition<?> humanNameDefinition = (BaseRuntimeElementCompositeDefinition<?>) getContext().getElementDefinition("HumanName");
BaseRuntimeChildDefinition humanNameFamilyValueChild = humanNameDefinition.getChildByName("family");
BaseRuntimeChildDefinition humanNameGivenValueChild = humanNameDefinition.getChildByName("given");
List<String> families = extractValuesAsStrings(humanNameFamilyValueChild, theValue);
List<String> families = extractValuesAsStrings(myHumanNameFamilyValueChild, theValue);
for (String next : families) {
createStringIndexIfNotBlank(theResourceType, theParams, theSearchParam, next);
}
List<String> givens = extractValuesAsStrings(humanNameGivenValueChild, theValue);
List<String> givens = extractValuesAsStrings(myHumanNameGivenValueChild, theValue);
for (String next : givens) {
createStringIndexIfNotBlank(theResourceType, theParams, theSearchParam, next);
}
@ -692,61 +642,48 @@ public abstract class BaseSearchParamExtractor implements ISearchParamExtractor
}
private void addString_Quantity(String theResourceType, Set<ResourceIndexedSearchParamString> theParams, RuntimeSearchParam theSearchParam, IBase theValue) {
BaseRuntimeElementCompositeDefinition<?> quantityDefinition = (BaseRuntimeElementCompositeDefinition<?>) getContext().getElementDefinition("Quantity");
BaseRuntimeChildDefinition quantityValueChild = quantityDefinition.getChildByName("value");
BigDecimal value = extractValueAsBigDecimal(quantityValueChild, theValue);
BigDecimal value = extractValueAsBigDecimal(myQuantityValueValueChild, theValue);
if (value != null) {
createStringIndexIfNotBlank(theResourceType, theParams, theSearchParam, value.toPlainString());
}
}
private void addString_Range(String theResourceType, Set<ResourceIndexedSearchParamString> theParams, RuntimeSearchParam theSearchParam, IBase theValue) {
BaseRuntimeElementCompositeDefinition<?> rangeDefinition = (BaseRuntimeElementCompositeDefinition<?>) getContext().getElementDefinition("Range");
BaseRuntimeChildDefinition rangeLowValueChild = rangeDefinition.getChildByName("low");
BigDecimal value = extractValueAsBigDecimal(rangeLowValueChild, theValue);
BigDecimal value = extractValueAsBigDecimal(myRangeLowValueChild, theValue);
if (value != null) {
createStringIndexIfNotBlank(theResourceType, theParams, theSearchParam, value.toPlainString());
}
}
private void addString_ContactPoint(String theResourceType, Set<ResourceIndexedSearchParamString> theParams, RuntimeSearchParam theSearchParam, IBase theValue) {
BaseRuntimeElementCompositeDefinition<?> contactPointDefinition = (BaseRuntimeElementCompositeDefinition<?>) getContext().getElementDefinition("ContactPoint");
BaseRuntimeChildDefinition contactPointValueValueChild = contactPointDefinition.getChildByName("value");
String value = extractValueAsString(contactPointValueValueChild, theValue);
String value = extractValueAsString(myContactPointValueValueChild, theValue);
if (isNotBlank(value)) {
createStringIndexIfNotBlank(theResourceType, theParams, theSearchParam, value);
}
}
private void addString_Address(String theResourceType, Set<ResourceIndexedSearchParamString> theParams, RuntimeSearchParam theSearchParam, IBase theValue) {
BaseRuntimeElementCompositeDefinition<?> addressDefinition = (BaseRuntimeElementCompositeDefinition<?>) getContext().getElementDefinition("Address");
BaseRuntimeChildDefinition addressLineValueChild = addressDefinition.getChildByName("line");
BaseRuntimeChildDefinition addressCityValueChild = addressDefinition.getChildByName("city");
BaseRuntimeChildDefinition addressStateValueChild = addressDefinition.getChildByName("state");
BaseRuntimeChildDefinition addressCountryValueChild = addressDefinition.getChildByName("country");
BaseRuntimeChildDefinition addressPostalCodeValueChild = addressDefinition.getChildByName("postalCode");
List<String> allNames = new ArrayList<>(extractValuesAsStrings(addressLineValueChild, theValue));
List<String> allNames = new ArrayList<>(extractValuesAsStrings(myAddressLineValueChild, theValue));
String city = extractValueAsString(addressCityValueChild, theValue);
String city = extractValueAsString(myAddressCityValueChild, theValue);
if (isNotBlank(city)) {
allNames.add(city);
}
String state = extractValueAsString(addressStateValueChild, theValue);
String state = extractValueAsString(myAddressStateValueChild, theValue);
if (isNotBlank(state)) {
allNames.add(state);
}
String country = extractValueAsString(addressCountryValueChild, theValue);
String country = extractValueAsString(myAddressCountryValueChild, theValue);
if (isNotBlank(country)) {
allNames.add(country);
}
String postalCode = extractValueAsString(addressPostalCodeValueChild, theValue);
String postalCode = extractValueAsString(myAddressPostalCodeValueChild, theValue);
if (isNotBlank(postalCode)) {
allNames.add(postalCode);
}
@ -758,8 +695,8 @@ public abstract class BaseSearchParamExtractor implements ISearchParamExtractor
}
private <T extends BaseResourceIndexedSearchParam> Set<T> extractSearchParams(IBaseResource theResource, IExtractor<T> theExtractor, RestSearchParameterTypeEnum theSearchParamType) {
Set<T> retVal = new HashSet<>();
private <T extends BaseResourceIndexedSearchParam> SearchParamSet<T> extractSearchParams(IBaseResource theResource, IExtractor<T> theExtractor, RestSearchParameterTypeEnum theSearchParamType) {
SearchParamSet<T> retVal = new SearchParamSet<>();
Collection<RuntimeSearchParam> searchParams = getSearchParams(theResource);
for (RuntimeSearchParam nextSpDef : searchParams) {
@ -874,19 +811,119 @@ public abstract class BaseSearchParamExtractor implements ISearchParamExtractor
return theValue;
}
@PostConstruct
public void start() {
myIgnoredForSearchDatatypes = new HashSet<>();
addIgnoredType(getContext(), "Annotation", myIgnoredForSearchDatatypes);
addIgnoredType(getContext(), "Attachment", myIgnoredForSearchDatatypes);
addIgnoredType(getContext(), "Count", myIgnoredForSearchDatatypes);
addIgnoredType(getContext(), "Distance", myIgnoredForSearchDatatypes);
addIgnoredType(getContext(), "Ratio", myIgnoredForSearchDatatypes);
addIgnoredType(getContext(), "SampledData", myIgnoredForSearchDatatypes);
addIgnoredType(getContext(), "Signature", myIgnoredForSearchDatatypes);
/*
* This is building up an internal map of all the various field accessors we'll need in order to work
* with the model. This is kind of ugly, but we want to be as efficient as possible since
* search param extraction happens a whole heck of a lot at runtime..
*/
BaseRuntimeElementCompositeDefinition<?> quantityDefinition = (BaseRuntimeElementCompositeDefinition<?>) getContext().getElementDefinition("Quantity");
myQuantityValueValueChild = quantityDefinition.getChildByName("value");
myQuantitySystemValueChild = quantityDefinition.getChildByName("system");
myQuantityCodeValueChild = quantityDefinition.getChildByName("code");
BaseRuntimeElementCompositeDefinition<?> moneyDefinition = (BaseRuntimeElementCompositeDefinition<?>) getContext().getElementDefinition("Money");
myMoneyValueChild = moneyDefinition.getChildByName("value");
myMoneyCurrencyChild = moneyDefinition.getChildByName("currency");
BaseRuntimeElementCompositeDefinition<?> locationDefinition = getContext().getResourceDefinition("Location");
BaseRuntimeChildDefinition locationPositionValueChild = locationDefinition.getChildByName("position");
myLocationPositionDefinition = (BaseRuntimeElementCompositeDefinition<?>) locationPositionValueChild.getChildByName("position");
BaseRuntimeElementCompositeDefinition<?> codeSystemDefinition;
if (getContext().getVersion().getVersion().isEqualOrNewerThan(FhirVersionEnum.DSTU3)) {
codeSystemDefinition = getContext().getResourceDefinition("CodeSystem");
assert codeSystemDefinition != null;
myCodeSystemUrlValueChild = codeSystemDefinition.getChildByName("url");
}
BaseRuntimeElementCompositeDefinition<?> rangeDefinition = (BaseRuntimeElementCompositeDefinition<?>) getContext().getElementDefinition("Range");
myRangeLowValueChild = rangeDefinition.getChildByName("low");
myRangeHighValueChild = rangeDefinition.getChildByName("high");
BaseRuntimeElementCompositeDefinition<?> addressDefinition = (BaseRuntimeElementCompositeDefinition<?>) getContext().getElementDefinition("Address");
myAddressLineValueChild = addressDefinition.getChildByName("line");
myAddressCityValueChild = addressDefinition.getChildByName("city");
myAddressStateValueChild = addressDefinition.getChildByName("state");
myAddressCountryValueChild = addressDefinition.getChildByName("country");
myAddressPostalCodeValueChild = addressDefinition.getChildByName("postalCode");
BaseRuntimeElementCompositeDefinition<?> capabilityStatementDefinition = getContext().getResourceDefinition("CapabilityStatement");
BaseRuntimeChildDefinition capabilityStatementRestChild = capabilityStatementDefinition.getChildByName("rest");
BaseRuntimeElementCompositeDefinition<?> capabilityStatementRestDefinition = (BaseRuntimeElementCompositeDefinition<?>) capabilityStatementRestChild.getChildByName("rest");
BaseRuntimeChildDefinition capabilityStatementRestSecurityValueChild = capabilityStatementRestDefinition.getChildByName("security");
BaseRuntimeElementCompositeDefinition<?> capabilityStatementRestSecurityDefinition = (BaseRuntimeElementCompositeDefinition<?>) capabilityStatementRestSecurityValueChild.getChildByName("security");
myCapabilityStatementRestSecurityServiceValueChild = capabilityStatementRestSecurityDefinition.getChildByName("service");
BaseRuntimeElementCompositeDefinition<?> periodDefinition = (BaseRuntimeElementCompositeDefinition<?>) getContext().getElementDefinition("Period");
myPeriodStartValueChild = periodDefinition.getChildByName("start");
myPeriodEndValueChild = periodDefinition.getChildByName("end");
BaseRuntimeElementCompositeDefinition<?> timingDefinition = (BaseRuntimeElementCompositeDefinition<?>) getContext().getElementDefinition("Timing");
myTimingEventValueChild = timingDefinition.getChildByName("event");
myTimingRepeatValueChild = timingDefinition.getChildByName("repeat");
BaseRuntimeElementCompositeDefinition<?> timingRepeatDefinition = (BaseRuntimeElementCompositeDefinition<?>) myTimingRepeatValueChild.getChildByName("repeat");
myTimingRepeatBoundsValueChild = timingRepeatDefinition.getChildByName("bounds[x]");
BaseRuntimeElementCompositeDefinition<?> durationDefinition = (BaseRuntimeElementCompositeDefinition<?>) getContext().getElementDefinition("Duration");
myDurationSystemValueChild = durationDefinition.getChildByName("system");
myDurationCodeValueChild = durationDefinition.getChildByName("code");
myDurationValueValueChild = durationDefinition.getChildByName("value");
BaseRuntimeElementCompositeDefinition<?> humanNameDefinition = (BaseRuntimeElementCompositeDefinition<?>) getContext().getElementDefinition("HumanName");
myHumanNameFamilyValueChild = humanNameDefinition.getChildByName("family");
myHumanNameGivenValueChild = humanNameDefinition.getChildByName("given");
BaseRuntimeElementCompositeDefinition<?> contactPointDefinition = (BaseRuntimeElementCompositeDefinition<?>) getContext().getElementDefinition("ContactPoint");
myContactPointValueValueChild = contactPointDefinition.getChildByName("value");
myContactPointSystemValueChild = contactPointDefinition.getChildByName("system");
BaseRuntimeElementCompositeDefinition<?> identifierDefinition = (BaseRuntimeElementCompositeDefinition<?>) getContext().getElementDefinition("Identifier");
myIdentifierSystemValueChild = identifierDefinition.getChildByName("system");
myIdentifierValueValueChild = identifierDefinition.getChildByName("value");
myIdentifierTypeValueChild = identifierDefinition.getChildByName("type");
BaseRuntimeElementCompositeDefinition<?> identifierTypeDefinition = (BaseRuntimeElementCompositeDefinition<?>) myIdentifierTypeValueChild.getChildByName("type");
myIdentifierTypeTextValueChild = identifierTypeDefinition.getChildByName("text");
BaseRuntimeElementCompositeDefinition<?> codeableConceptDefinition = (BaseRuntimeElementCompositeDefinition<?>) getContext().getElementDefinition("CodeableConcept");
myCodeableConceptCodingValueChild = codeableConceptDefinition.getChildByName("coding");
myCodeableConceptTextValueChild = codeableConceptDefinition.getChildByName("text");
BaseRuntimeElementCompositeDefinition<?> codingDefinition = (BaseRuntimeElementCompositeDefinition<?>) getContext().getElementDefinition("Coding");
myCodingSystemValueChild = codingDefinition.getChildByName("system");
myCodingCodeValueChild = codingDefinition.getChildByName("code");
myCodingDisplayValueChild = codingDefinition.getChildByName("display");
BaseRuntimeElementCompositeDefinition<?> patientDefinition = getContext().getResourceDefinition("Patient");
BaseRuntimeChildDefinition patientCommunicationValueChild = patientDefinition.getChildByName("communication");
BaseRuntimeElementCompositeDefinition<?> patientCommunicationDefinition = (BaseRuntimeElementCompositeDefinition<?>) patientCommunicationValueChild.getChildByName("communication");
myPatientCommunicationLanguageValueChild = patientCommunicationDefinition.getChildByName("language");
}
@FunctionalInterface
public interface IValueExtractor {
List<? extends IBase> get() throws FHIRException;
}
@FunctionalInterface
private interface IExtractor<T> {
void extract(Set<T> theParams, RuntimeSearchParam theSearchParam, IBase theValue, String thePath);
void extract(SearchParamSet<T> theParams, RuntimeSearchParam theSearchParam, IBase theValue, String thePath);
}
@ -946,5 +983,4 @@ public abstract class BaseSearchParamExtractor implements ISearchParamExtractor
return null;
}
}

40
hapi-fhir-jpaserver-searchparam/src/main/java/ca/uhn/fhir/jpa/searchparam/extractor/ISearchParamExtractor.java
View File

@ -4,8 +4,7 @@ import ca.uhn.fhir.context.RuntimeSearchParam;
import ca.uhn.fhir.jpa.model.entity.*;
import org.hl7.fhir.instance.model.api.IBaseResource;
import java.util.List;
import java.util.Set;
import java.util.*;
/*
* #%L
@ -29,21 +28,44 @@ import java.util.Set;
public interface ISearchParamExtractor {
Set<ResourceIndexedSearchParamCoords> extractSearchParamCoords(IBaseResource theResource);
SearchParamSet<ResourceIndexedSearchParamCoords> extractSearchParamCoords(IBaseResource theResource);
Set<ResourceIndexedSearchParamDate> extractSearchParamDates(IBaseResource theResource);
SearchParamSet<ResourceIndexedSearchParamDate> extractSearchParamDates(IBaseResource theResource);
Set<ResourceIndexedSearchParamNumber> extractSearchParamNumber(IBaseResource theResource);
SearchParamSet<ResourceIndexedSearchParamNumber> extractSearchParamNumber(IBaseResource theResource);
Set<ResourceIndexedSearchParamQuantity> extractSearchParamQuantity(IBaseResource theResource);
SearchParamSet<ResourceIndexedSearchParamQuantity> extractSearchParamQuantity(IBaseResource theResource);
Set<ResourceIndexedSearchParamString> extractSearchParamStrings(IBaseResource theResource);
SearchParamSet<ResourceIndexedSearchParamString> extractSearchParamStrings(IBaseResource theResource);
Set<BaseResourceIndexedSearchParam> extractSearchParamTokens(IBaseResource theResource);
SearchParamSet<BaseResourceIndexedSearchParam> extractSearchParamTokens(IBaseResource theResource);
Set<ResourceIndexedSearchParamUri> extractSearchParamUri(IBaseResource theResource);
SearchParamSet<ResourceIndexedSearchParamUri> extractSearchParamUri(IBaseResource theResource);
List<PathAndRef> extractResourceLinks(IBaseResource theResource, RuntimeSearchParam theNextSpDef);
String[] split(String theExpression);
class SearchParamSet<T> extends HashSet<T> {
private List<String> myWarnings;
public void addWarning(String theWarning) {
if (myWarnings == null) {
myWarnings = new ArrayList<>();
}
myWarnings.add(theWarning);
}
List<String> getWarnings() {
if (myWarnings == null) {
return Collections.emptyList();
}
return myWarnings;
}
}
}

78
hapi-fhir-jpaserver-searchparam/src/main/java/ca/uhn/fhir/jpa/searchparam/extractor/SearchParamExtractorService.java
View File

@ -20,14 +20,21 @@ package ca.uhn.fhir.jpa.searchparam.extractor;
* #L%
*/
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.jpa.model.entity.*;
import ca.uhn.fhir.jpa.model.search.StorageProcessingMessage;
import ca.uhn.fhir.jpa.util.JpaInterceptorBroadcaster;
import ca.uhn.fhir.rest.api.server.RequestDetails;
import ca.uhn.fhir.rest.server.servlet.ServletRequestDetails;
import com.google.common.annotations.VisibleForTesting;
import org.hl7.fhir.instance.model.api.IBaseResource;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.context.annotation.Lazy;
import org.springframework.stereotype.Service;
import java.util.Collection;
import java.util.Set;
@Service
@Lazy
@ -36,14 +43,33 @@ public class SearchParamExtractorService {
@Autowired
private ISearchParamExtractor mySearchParamExtractor;
@Autowired
private IInterceptorBroadcaster myInterceptorBroadcaster;
public void extractFromResource(ResourceIndexedSearchParams theParams, ResourceTable theEntity, IBaseResource theResource) {
theParams.myStringParams.addAll(extractSearchParamStrings(theResource));
theParams.myNumberParams.addAll(extractSearchParamNumber(theResource));
theParams.myQuantityParams.addAll(extractSearchParamQuantity(theResource));
theParams.myDateParams.addAll(extractSearchParamDates(theResource));
theParams.myUriParams.addAll(extractSearchParamUri(theResource));
theParams.myCoordsParams.addAll(extractSearchParamCoords(theResource));
public void extractFromResource(RequestDetails theRequestDetails, ResourceIndexedSearchParams theParams, ResourceTable theEntity, IBaseResource theResource) {
ISearchParamExtractor.SearchParamSet<ResourceIndexedSearchParamString> strings = extractSearchParamStrings(theResource);
handleWarnings(theRequestDetails, strings);
theParams.myStringParams.addAll(strings);
ISearchParamExtractor.SearchParamSet<ResourceIndexedSearchParamNumber> numbers = extractSearchParamNumber(theResource);
handleWarnings(theRequestDetails, numbers);
theParams.myNumberParams.addAll(numbers);
ISearchParamExtractor.SearchParamSet<ResourceIndexedSearchParamQuantity> quantities = extractSearchParamQuantity(theResource);
handleWarnings(theRequestDetails, quantities);
theParams.myQuantityParams.addAll(quantities);
ISearchParamExtractor.SearchParamSet<ResourceIndexedSearchParamDate> dates = extractSearchParamDates(theResource);
handleWarnings(theRequestDetails, dates);
theParams.myDateParams.addAll(dates);
ISearchParamExtractor.SearchParamSet<ResourceIndexedSearchParamUri> uris = extractSearchParamUri(theResource);
handleWarnings(theRequestDetails, uris);
theParams.myUriParams.addAll(uris);
ISearchParamExtractor.SearchParamSet<ResourceIndexedSearchParamCoords> coords = extractSearchParamCoords(theResource);
handleWarnings(theRequestDetails, coords);
theParams.myCoordsParams.addAll(coords);
ourLog.trace("Storing date indexes: {}", theParams.myDateParams);
@ -64,40 +90,60 @@ public class SearchParamExtractorService {
populateResourceTable(theParams.myTokenParams, theEntity);
}
void handleWarnings(RequestDetails theRequestDetails, ISearchParamExtractor.SearchParamSet<?> theSearchParamSet) {
if (theSearchParamSet.getWarnings().isEmpty()) {
return;
}
// If extraction generated any warnings, broadcast an error
for (String next : theSearchParamSet.getWarnings()) {
StorageProcessingMessage messageHolder = new StorageProcessingMessage();
messageHolder.setMessage(next);
HookParams params = new HookParams()
.add(RequestDetails.class, theRequestDetails)
.addIfMatchesType(ServletRequestDetails.class, theRequestDetails)
.add(StorageProcessingMessage.class, messageHolder);
JpaInterceptorBroadcaster.doCallHooks(myInterceptorBroadcaster, theRequestDetails, Pointcut.JPA_PERFTRACE_WARNING, params);
}
}
private void populateResourceTable(Collection<? extends BaseResourceIndexedSearchParam> theParams, ResourceTable theResourceTable) {
for (BaseResourceIndexedSearchParam next : theParams) {
next.setResource(theResourceTable);
}
}
private Set<ResourceIndexedSearchParamCoords> extractSearchParamCoords(IBaseResource theResource) {
private ISearchParamExtractor.SearchParamSet<ResourceIndexedSearchParamCoords> extractSearchParamCoords(IBaseResource theResource) {
return mySearchParamExtractor.extractSearchParamCoords(theResource);
}
private Set<ResourceIndexedSearchParamDate> extractSearchParamDates(IBaseResource theResource) {
private ISearchParamExtractor.SearchParamSet<ResourceIndexedSearchParamDate> extractSearchParamDates(IBaseResource theResource) {
return mySearchParamExtractor.extractSearchParamDates(theResource);
}
private Set<ResourceIndexedSearchParamNumber> extractSearchParamNumber(IBaseResource theResource) {
private ISearchParamExtractor.SearchParamSet<ResourceIndexedSearchParamNumber> extractSearchParamNumber(IBaseResource theResource) {
return mySearchParamExtractor.extractSearchParamNumber(theResource);
}
private Set<ResourceIndexedSearchParamQuantity> extractSearchParamQuantity(IBaseResource theResource) {
private ISearchParamExtractor.SearchParamSet<ResourceIndexedSearchParamQuantity> extractSearchParamQuantity(IBaseResource theResource) {
return mySearchParamExtractor.extractSearchParamQuantity(theResource);
}
private Set<ResourceIndexedSearchParamString> extractSearchParamStrings(IBaseResource theResource) {
private ISearchParamExtractor.SearchParamSet<ResourceIndexedSearchParamString> extractSearchParamStrings(IBaseResource theResource) {
return mySearchParamExtractor.extractSearchParamStrings(theResource);
}
private Set<BaseResourceIndexedSearchParam> extractSearchParamTokens(IBaseResource theResource) {
private ISearchParamExtractor.SearchParamSet<BaseResourceIndexedSearchParam> extractSearchParamTokens(IBaseResource theResource) {
return mySearchParamExtractor.extractSearchParamTokens(theResource);
}
private Set<ResourceIndexedSearchParamUri> extractSearchParamUri(IBaseResource theResource) {
private ISearchParamExtractor.SearchParamSet<ResourceIndexedSearchParamUri> extractSearchParamUri(IBaseResource theResource) {
return mySearchParamExtractor.extractSearchParamUri(theResource);
}
@VisibleForTesting
void setInterceptorBroadcasterForUnitTest(IInterceptorBroadcaster theJpaInterceptorBroadcaster) {
myInterceptorBroadcaster = theJpaInterceptorBroadcaster;
}
}

2
hapi-fhir-jpaserver-searchparam/src/main/java/ca/uhn/fhir/jpa/searchparam/matcher/IndexedSearchParamExtractor.java
View File

@ -46,7 +46,7 @@ public class IndexedSearchParamExtractor {
String resourceType = myContext.getResourceDefinition(theResource).getName();
entity.setResourceType(resourceType);
ResourceIndexedSearchParams resourceIndexedSearchParams = new ResourceIndexedSearchParams();
mySearchParamExtractorService.extractFromResource(resourceIndexedSearchParams, entity, theResource);
mySearchParamExtractorService.extractFromResource(theRequest, resourceIndexedSearchParams, entity, theResource);
myResourceLinkExtractor.extractResourceLinks(resourceIndexedSearchParams, entity, theResource, theResource.getMeta().getLastUpdated(), myInlineResourceLinkResolver, false, theRequest);
return resourceIndexedSearchParams;
}

62
hapi-fhir-jpaserver-searchparam/src/test/java/ca/uhn/fhir/jpa/searchparam/extractor/SearchParamExtractorDstu3Test.java
View File

@ -12,10 +12,10 @@ import ca.uhn.fhir.jpa.searchparam.registry.ISearchParamRegistry;
import ca.uhn.fhir.rest.api.RestSearchParameterTypeEnum;
import ca.uhn.fhir.util.TestUtil;
import com.google.common.collect.Sets;
import org.hamcrest.Matchers;
import org.hl7.fhir.dstu3.hapi.ctx.DefaultProfileValidationSupport;
import org.hl7.fhir.dstu3.hapi.ctx.IValidationSupport;
import org.hl7.fhir.dstu3.model.*;
import org.hl7.fhir.instance.model.api.IBaseResource;
import org.junit.AfterClass;
import org.junit.BeforeClass;
import org.junit.Test;
@ -25,7 +25,8 @@ import java.util.*;
import java.util.stream.Collectors;
import java.util.stream.IntStream;
import static org.junit.Assert.assertEquals;
import static org.junit.Assert.*;
import static org.mockito.ArgumentMatchers.contains;
public class SearchParamExtractorDstu3Test {
@ -146,63 +147,42 @@ public class SearchParamExtractorDstu3Test {
SearchParamExtractorDstu3 extractor = new SearchParamExtractorDstu3(new ModelConfig(), ourCtx, ourValidationSupport, searchParamRegistry);
extractor.start();
try {
{
searchParamRegistry.addSearchParam(new RuntimeSearchParam("foo", "foo", "Patient", RestSearchParameterTypeEnum.STRING, Sets.newHashSet(), Sets.newHashSet(), RuntimeSearchParam.RuntimeSearchParamStatusEnum.ACTIVE));
Patient resource = new Patient();
extractor.extractSearchParamStrings(resource);
} catch (ConfigurationException e) {
assertEquals("Search param foo is of unexpected datatype: class org.hl7.fhir.dstu3.model.Patient", e.getMessage());
ISearchParamExtractor.SearchParamSet<ResourceIndexedSearchParamString> outcome = extractor.extractSearchParamStrings(resource);
assertThat(outcome.getWarnings(), Matchers.contains("Search param foo is of unexpected datatype: class org.hl7.fhir.dstu3.model.Patient"));
}
try {
{
searchParamRegistry.addSearchParam(new RuntimeSearchParam("foo", "foo", "Patient", RestSearchParameterTypeEnum.TOKEN, Sets.newHashSet(), Sets.newHashSet(), RuntimeSearchParam.RuntimeSearchParamStatusEnum.ACTIVE));
Patient resource = new Patient();
extractor.extractSearchParamTokens(resource);
} catch (ConfigurationException e) {
assertEquals("Search param foo is of unexpected datatype: class org.hl7.fhir.dstu3.model.Patient", e.getMessage());
ISearchParamExtractor.SearchParamSet<BaseResourceIndexedSearchParam> outcome = extractor.extractSearchParamTokens(resource);
assertThat(outcome.getWarnings(), Matchers.contains("Search param foo is of unexpected datatype: class org.hl7.fhir.dstu3.model.Patient"));
}
try {
{
searchParamRegistry.addSearchParam(new RuntimeSearchParam("foo", "foo", "Patient", RestSearchParameterTypeEnum.QUANTITY, Sets.newHashSet(), Sets.newHashSet(), RuntimeSearchParam.RuntimeSearchParamStatusEnum.ACTIVE));
Patient resource = new Patient();
extractor.extractSearchParamQuantity(resource);
} catch (ConfigurationException e) {
assertEquals("Search param foo is of unexpected datatype: class org.hl7.fhir.dstu3.model.Patient", e.getMessage());
ISearchParamExtractor.SearchParamSet<ResourceIndexedSearchParamQuantity> outcome = extractor.extractSearchParamQuantity(resource);
assertThat(outcome.getWarnings(), Matchers.contains("Search param foo is of unexpected datatype: class org.hl7.fhir.dstu3.model.Patient"));
}
try {
{
searchParamRegistry.addSearchParam(new RuntimeSearchParam("foo", "foo", "Patient", RestSearchParameterTypeEnum.DATE, Sets.newHashSet(), Sets.newHashSet(), RuntimeSearchParam.RuntimeSearchParamStatusEnum.ACTIVE));
Patient resource = new Patient();
extractor.extractSearchParamDates(resource);
} catch (ConfigurationException e) {
assertEquals("Search param foo is of unexpected datatype: class org.hl7.fhir.dstu3.model.Patient", e.getMessage());
ISearchParamExtractor.SearchParamSet<ResourceIndexedSearchParamDate> outcome = extractor.extractSearchParamDates(resource);
assertThat(outcome.getWarnings(), Matchers.contains("Search param foo is of unexpected datatype: class org.hl7.fhir.dstu3.model.Patient"));
}
try {
{
searchParamRegistry.addSearchParam(new RuntimeSearchParam("foo", "foo", "Patient", RestSearchParameterTypeEnum.NUMBER, Sets.newHashSet(), Sets.newHashSet(), RuntimeSearchParam.RuntimeSearchParamStatusEnum.ACTIVE));
Patient resource = new Patient();
extractor.extractSearchParamNumber(resource);
} catch (ConfigurationException e) {
assertEquals("Search param foo is of unexpected datatype: class org.hl7.fhir.dstu3.model.Patient", e.getMessage());
ISearchParamExtractor.SearchParamSet<ResourceIndexedSearchParamNumber> outcome = extractor.extractSearchParamNumber(resource);
assertThat(outcome.getWarnings(), Matchers.contains("Search param foo is of unexpected datatype: class org.hl7.fhir.dstu3.model.Patient"));
}
try {
{
searchParamRegistry.addSearchParam(new RuntimeSearchParam("foo", "foo", "Patient", RestSearchParameterTypeEnum.URI, Sets.newHashSet(), Sets.newHashSet(), RuntimeSearchParam.RuntimeSearchParamStatusEnum.ACTIVE));
Patient resource = new Patient();
extractor.extractSearchParamUri(resource);
} catch (ConfigurationException e) {
assertEquals("Search param foo is of unexpected datatype: class org.hl7.fhir.dstu3.model.Patient", e.getMessage());
ISearchParamExtractor.SearchParamSet<ResourceIndexedSearchParamUri> outcome = extractor.extractSearchParamUri(resource);
assertThat(outcome.getWarnings(), Matchers.contains("Search param foo is of unexpected datatype: class org.hl7.fhir.dstu3.model.Patient"));
}
try {
RuntimeSearchParam sp = new RuntimeSearchParam("foo", "foo", "Patient", RestSearchParameterTypeEnum.REFERENCE, Sets.newHashSet(), Sets.newHashSet(), RuntimeSearchParam.RuntimeSearchParamStatusEnum.ACTIVE);
searchParamRegistry.addSearchParam(sp);
Patient resource = new Patient();
extractor.extractResourceLinks(resource, sp);
} catch (ConfigurationException e) {
assertEquals("Search param foo is of unexpected datatype: class org.hl7.fhir.dstu3.model.Patient", e.getMessage());
}
}

46
hapi-fhir-jpaserver-searchparam/src/test/java/ca/uhn/fhir/jpa/searchparam/extractor/SearchParamExtractorServiceTest.java Normal file
View File

@ -0,0 +1,46 @@
package ca.uhn.fhir.jpa.searchparam.extractor;
import ca.uhn.fhir.interceptor.api.IInterceptorBroadcaster;
import ca.uhn.fhir.interceptor.api.Pointcut;
import ca.uhn.fhir.rest.server.servlet.ServletRequestDetails;
import org.junit.Before;
import org.junit.Test;
import org.junit.runner.RunWith;
import org.mockito.Mock;
import org.mockito.junit.MockitoJUnitRunner;
import org.springframework.beans.factory.annotation.Autowired;
import static org.mockito.ArgumentMatchers.any;
import static org.mockito.ArgumentMatchers.eq;
import static org.mockito.Mockito.*;
@RunWith(MockitoJUnitRunner.class)
public class SearchParamExtractorServiceTest {
private SearchParamExtractorService mySvc;
@Mock
private IInterceptorBroadcaster myRequestInterceptorBroadcaster;
@Mock
private IInterceptorBroadcaster myJpaInterceptorBroadcaster;
@Before
public void before() {
mySvc = new SearchParamExtractorService();
mySvc.setInterceptorBroadcasterForUnitTest(myJpaInterceptorBroadcaster);
}
@Test
public void testHandleWarnings() {
ISearchParamExtractor.SearchParamSet<Object> searchParamSet = new ISearchParamExtractor.SearchParamSet<>();
searchParamSet.addWarning("help i'm a bug");
searchParamSet.addWarning("Spiff");
when(myJpaInterceptorBroadcaster.callHooks(any(), any())).thenReturn(true);
mySvc.handleWarnings(new ServletRequestDetails(myRequestInterceptorBroadcaster), searchParamSet);
verify(myJpaInterceptorBroadcaster, times(2)).callHooks(eq(Pointcut.JPA_PERFTRACE_WARNING), any());
verify(myRequestInterceptorBroadcaster, times(2)).callHooks(eq(Pointcut.JPA_PERFTRACE_WARNING), any());
}
}

14
hapi-fhir-jpaserver-subscription/src/test/java/ca/uhn/fhir/jpa/subscription/module/cache/SubscriptionLoaderTest.java vendored
View File

@ -11,6 +11,8 @@ import org.springframework.beans.factory.annotation.Autowired;
import java.util.ArrayList;
import java.util.List;
import java.util.concurrent.CountDownLatch;
import java.util.concurrent.TimeUnit;
import static org.junit.Assert.assertEquals;
@ -50,7 +52,17 @@ public class SubscriptionLoaderTest extends BaseBlockingQueueSubscribableChannel
@Test
public void testMultipleThreadsDontBlock() throws InterruptedException {
SubscriptionLoader svc = new SubscriptionLoader();
svc.acquireSemaphoreForUnitTest();
CountDownLatch latch = new CountDownLatch(1);
new Thread(()->{
try {
svc.acquireSemaphoreForUnitTest();
latch.countDown();
} catch (InterruptedException theE) {
// ignore
}
}).start();
latch.await(10, TimeUnit.SECONDS);
svc.syncSubscriptions();
}

1
hapi-fhir-jpaserver-uhnfhirtest/pom.xml
View File

@ -51,7 +51,6 @@
<artifactId>hapi-fhir-testpage-overlay</artifactId>
<version>${project.version}</version>
<classifier>classes</classifier>
<scope>provided</scope>
</dependency>
<dependency>

3
hapi-fhir-server/src/main/java/ca/uhn/fhir/rest/server/method/ReadMethodBinding.java
View File

@ -140,8 +140,7 @@ public class ReadMethodBinding extends BaseResourceReturningMethodBinding {
if (Constants.PARAM_HISTORY.equals(theRequest.getOperation())) {
if (mySupportsVersion == false) {
return false;
}
if (theRequest.getId().hasVersionIdPart() == false) {
} else if (theRequest.getId().hasVersionIdPart() == false) {
return false;
}
} else if (!StringUtils.isBlank(theRequest.getOperation())) {

25
hapi-fhir-server/src/test/java/ca/uhn/fhir/rest/server/method/ReadMethodBindingTest.java
View File

@ -101,6 +101,31 @@ public class ReadMethodBindingTest {
when(myRequestDetails.getOperation()).thenReturn("$foo");
assertFalse(binding.incomingServerRequestMatchesMethod(myRequestDetails));
// History operation
when(myRequestDetails.getId()).thenReturn(new IdDt("Patient/123"));
when(myRequestDetails.getOperation()).thenReturn("_history");
assertFalse(binding.incomingServerRequestMatchesMethod(myRequestDetails));
}
@Test
public void testIncomingServerRequestNoMatch_HasCompartment() throws NoSuchMethodException {
class MyProvider {
@Read(version = false)
public IBaseResource read(@IdParam IIdType theIdType) {
return null;
}
}
when(myCtx.getResourceDefinition(any(Class.class))).thenReturn(definition);
when(definition.getName()).thenReturn("Patient");
when(myRequestDetails.getResourceName()).thenReturn("Patient");
when(myRequestDetails.getCompartmentName()).thenReturn("Patient");
when(myRequestDetails.getId()).thenReturn(new IdDt("Patient/123"));
ReadMethodBinding binding = createBinding(new MyProvider());
assertFalse(binding.incomingServerRequestMatchesMethod(myRequestDetails));
}
public ReadMethodBinding createBinding(Object theProvider) throws NoSuchMethodException {

131
hapi-fhir-structures-r4/src/main/java/org/hl7/fhir/r4/hapi/rest/server/ServerCapabilityStatementProvider.java
View File

@ -9,7 +9,10 @@ import ca.uhn.fhir.rest.annotation.Metadata;
import ca.uhn.fhir.rest.annotation.Read;
import ca.uhn.fhir.rest.api.Constants;
import ca.uhn.fhir.rest.api.server.RequestDetails;
import ca.uhn.fhir.rest.server.*;
import ca.uhn.fhir.rest.server.Bindings;
import ca.uhn.fhir.rest.server.IServerConformanceProvider;
import ca.uhn.fhir.rest.server.RestfulServer;
import ca.uhn.fhir.rest.server.RestfulServerConfiguration;
import ca.uhn.fhir.rest.server.exceptions.ResourceNotFoundException;
import ca.uhn.fhir.rest.server.method.*;
import ca.uhn.fhir.rest.server.method.SearchParameter;
@ -113,7 +116,6 @@ public class ServerCapabilityStatementProvider extends BaseServerCapabilityState
}
private DateTimeType conformanceDate(RequestDetails theRequestDetails) {
IPrimitiveType<Date> buildDate = getServerConfiguration(theRequestDetails).getConformanceDate();
if (buildDate != null && buildDate.getValue() != null) {
@ -127,7 +129,6 @@ public class ServerCapabilityStatementProvider extends BaseServerCapabilityState
}
/**
* Gets the value of the "publisher" that will be placed in the generated conformance statement. As this is a mandatory element, the value should not be null (although this is not enforced). The
* value defaults to "Not provided" but may be set to null, which will cause this element to be omitted.
@ -194,47 +195,46 @@ public class ServerCapabilityStatementProvider extends BaseServerCapabilityState
// Map<String, CapabilityStatement.RestResourceSearchParam> nameToSearchParam = new HashMap<String,
// CapabilityStatement.RestResourceSearchParam>();
for (BaseMethodBinding<?> nextMethodBinding : nextEntry.getValue()) {
if (nextMethodBinding.getRestOperationType() != null) {
String resOpCode = nextMethodBinding.getRestOperationType().getCode();
if (resOpCode != null) {
TypeRestfulInteraction resOp;
try {
resOp = TypeRestfulInteraction.fromCode(resOpCode);
} catch (Exception e) {
resOp = null;
nextMethodBinding.getRestOperationType();
String resOpCode = nextMethodBinding.getRestOperationType().getCode();
if (resOpCode != null) {
TypeRestfulInteraction resOp;
try {
resOp = TypeRestfulInteraction.fromCode(resOpCode);
} catch (Exception e) {
resOp = null;
}
if (resOp != null) {
if (resourceOps.contains(resOp) == false) {
resourceOps.add(resOp);
resource.addInteraction().setCode(resOp);
}
if (resOp != null) {
if ("vread".equals(resOpCode)) {
// vread implies read
resOp = TypeRestfulInteraction.READ;
if (resourceOps.contains(resOp) == false) {
resourceOps.add(resOp);
resource.addInteraction().setCode(resOp);
}
if ("vread".equals(resOpCode)) {
// vread implies read
resOp = TypeRestfulInteraction.READ;
if (resourceOps.contains(resOp) == false) {
resourceOps.add(resOp);
resource.addInteraction().setCode(resOp);
}
}
}
if (nextMethodBinding.isSupportsConditional()) {
switch (resOp) {
case CREATE:
resource.setConditionalCreate(true);
break;
case DELETE:
if (nextMethodBinding.isSupportsConditionalMultiple()) {
resource.setConditionalDelete(ConditionalDeleteStatus.MULTIPLE);
} else {
resource.setConditionalDelete(ConditionalDeleteStatus.SINGLE);
}
break;
case UPDATE:
resource.setConditionalUpdate(true);
break;
default:
break;
}
if (nextMethodBinding.isSupportsConditional()) {
switch (resOp) {
case CREATE:
resource.setConditionalCreate(true);
break;
case DELETE:
if (nextMethodBinding.isSupportsConditionalMultiple()) {
resource.setConditionalDelete(ConditionalDeleteStatus.MULTIPLE);
} else {
resource.setConditionalDelete(ConditionalDeleteStatus.SINGLE);
}
break;
case UPDATE:
resource.setConditionalUpdate(true);
break;
default:
break;
}
}
}
@ -315,28 +315,18 @@ public class ServerCapabilityStatementProvider extends BaseServerCapabilityState
}
sortSearchParameters(searchParameters);
if (!searchParameters.isEmpty()) {
// boolean allOptional = searchParameters.get(0).isRequired() == false;
//
// OperationDefinition query = null;
// if (!allOptional) {
// RestOperation operation = rest.addOperation();
// query = new OperationDefinition();
// operation.setDefinition(new ResourceReferenceDt(query));
// query.getDescriptionElement().setValue(searchMethodBinding.getDescription());
// query.addUndeclaredExtension(false, ExtensionConstants.QUERY_RETURN_TYPE, new CodeDt(resourceName));
// for (String nextInclude : searchMethodBinding.getIncludes()) {
// query.addUndeclaredExtension(false, ExtensionConstants.QUERY_ALLOWED_INCLUDE, new StringDt(nextInclude));
// }
// }
for (SearchParameter nextParameter : searchParameters) {
if (nextParameter.getParamType() == null) {
ourLog.warn("SearchParameter {}:{} does not declare a type - Not exporting in CapabilityStatement", def.getName(), nextParameter.getName());
continue;
}
String nextParamName = nextParameter.getName();
String chain = null;
String nextParamUnchainedName = nextParamName;
if (nextParamName.contains(".")) {
chain = nextParamName.substring(nextParamName.indexOf('.') + 1);
nextParamUnchainedName = nextParamName.substring(0, nextParamName.indexOf('.'));
}
@ -352,45 +342,18 @@ public class ServerCapabilityStatementProvider extends BaseServerCapabilityState
}
}
CapabilityStatementRestResourceSearchParamComponent param = resource.addSearchParam();
String typeCode = nextParameter.getParamType().getCode();
param.getTypeElement().setValueAsString(typeCode);
param.setName(nextParamUnchainedName);
// if (StringUtils.isNotBlank(chain)) {
// param.addChain(chain);
// }
//
// if (nextParameter.getParamType() == RestSearchParameterTypeEnum.REFERENCE) {
// for (String nextWhitelist : new TreeSet<String>(nextParameter.getQualifierWhitelist())) {
// if (nextWhitelist.startsWith(".")) {
// param.addChain(nextWhitelist.substring(1));
// }
// }
// }
param.setDocumentation(nextParamDescription);
if (nextParameter.getParamType() != null) {
param.getTypeElement().setValueAsString(nextParameter.getParamType().getCode());
}
for (Class<? extends IBaseResource> nextTarget : nextParameter.getDeclaredTypes()) {
RuntimeResourceDefinition targetDef = getServerConfiguration(theRequestDetails).getFhirContext().getResourceDefinition(nextTarget);
if (targetDef != null) {
ResourceType code;
try {
code = ResourceType.fromCode(targetDef.getName());
} catch (FHIRException e) {
code = null;
}
// if (code != null) {
// param.addTarget(targetDef.getName());
// }
}
}
}
}
}
@Read(type = OperationDefinition.class)
public OperationDefinition readOperationDefinition(@IdParam IdType theId, RequestDetails theRequestDetails) {
if (theId == null || theId.hasIdPart() == false) {

6
hapi-fhir-validation/src/main/java/org/hl7/fhir/common/hapi/validation/ValidatorWrapper.java
View File

@ -111,7 +111,11 @@ public class ValidatorWrapper {
profileSet.getCanonical().add(new ValidationProfileSet.ProfileRegistration(nextProfile, true));
}
v.validate(null, messages, document, profileSet);
String resourceAsString = theValidationContext.getResourceAsString();
InputStream inputStream = new ReaderInputStream(new StringReader(resourceAsString), Charsets.UTF_8);
Manager.FhirFormat format = Manager.FhirFormat.XML;
v.validate(null, messages, inputStream, format, profileSet);
} else if (encoding == EncodingEnum.JSON) {

2
hapi-fhir-validation/src/test/java/org/hl7/fhir/r4/validation/FhirInstanceValidatorR4Test.java
View File

@ -799,6 +799,8 @@ public class FhirInstanceValidatorR4Test extends BaseTest {
ourLog.info(output.getMessages().get(0).getMessage());
assertEquals("/f:Patient", output.getMessages().get(0).getLocationString());
assertEquals("Undefined element 'foo'", output.getMessages().get(0).getMessage());
assertEquals(28, output.getMessages().get(0).getLocationCol().intValue());
assertEquals(4, output.getMessages().get(0).getLocationLine().intValue());
}
@Test

4
src/changes/changes.xml
View File

@ -476,6 +476,10 @@
<action type="fix">
Search parameters of type URI did not work in the hapi-fhir-testpage-overlay. This has been corrected.
</action>
<action type="fix" issue="1568">
JPA servers accidentally stripped the type attribute from the server-exported CapabilityStatement
when search parameters of type "special" were found. This has been corrected.
</action>
</release>
<release version="4.0.3" date="2019-09-03" description="Igloo (Point Release)">
<action type="fix">

10
src/site/xdoc/download.xml.vm
View File

@ -262,6 +262,16 @@
<td style="background: #CEC;">4.0.0</td>
<td style="background: #EEB;">4.1.0-e0e3caf9ba</td>
</tr>
<tr>
<td>HAPI FHIR 4.1.0</td>
<td>JDK8</td>
<td style="background: #DDD;"></td>
<td style="background: #CEC;">1.0.2</td>
<td style="background: #EEB;">1.4.0</td>
<td style="background: #CEC;">3.0.1</td>
<td style="background: #CEC;">4.0.0</td>
<td style="background: #EEB;">4.1.0-1a7623d866</td>
</tr>
</tbody>
</table>

1
sync_ri5.sh
View File

@ -1,5 +1,6 @@
mkdir -p hapi-tinder-plugin/src/main/resources/res/r5/
rm hapi-tinder-plugin/src/main/resources/res/r5/*.xml; cp ~/git/fhir/source/*/*-spreadsheet.xml hapi-tinder-plugin/src/main/resources/res/r5/; rm hapi-tinder-plugin/src/main/resources/res/r5/*-*-*.xml