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hapi-fhir
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Merge branch 'master' into jpa_migration

This commit is contained in:
James Agnew 2018-09-02 06:05:11 +08:00
parent 07cfed14b8 e20924dd09
commit 0f7c4219cb
34 changed files with 678 additions and 245 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

15
hapi-fhir-base/src/main/java/ca/uhn/fhir/rest/api/Constants.java
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@ -9,9 +9,9 @@ package ca.uhn.fhir.rest.api;
* Licensed under the Apache License, Version 2.0 (the "License");
* you may not use this file except in compliance with the License.
* You may obtain a copy of the License at
*
*
* http://www.apache.org/licenses/LICENSE-2.0
*
*
* Unless required by applicable law or agreed to in writing, software
* distributed under the License is distributed on an "AS IS" BASIS,
* WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
@ -21,12 +21,7 @@ package ca.uhn.fhir.rest.api;
*/
import java.nio.charset.Charset;
import java.util.Arrays;
import java.util.Collections;
import java.util.HashMap;
import java.util.HashSet;
import java.util.Map;
import java.util.Set;
import java.util.*;
public class Constants {
@ -197,6 +192,10 @@ public class Constants {
public static final String POWERED_BY_HEADER = "X-Powered-By";
public static final Charset CHARSET_US_ASCII;
public static final String PARAM_PAGEID = "_pageId";
/**
* This is provided for testing only! Use with caution as this property may change.
*/
public static final String TEST_SYSTEM_PROP_VALIDATION_RESOURCE_CACHES_MS = "TEST_SYSTEM_PROP_VALIDATION_RESOURCE_CACHES_MS";
static {
CHARSET_UTF8 = Charset.forName(CHARSET_NAME_UTF8);

4
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/dstu3/FhirResourceDaoConceptMapDstu3.java
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@ -87,7 +87,9 @@ public class FhirResourceDaoConceptMapDstu3 extends FhirResourceDaoDstu3<Concept
if (targetsToReturn.add(target)) {
translationMatch = new TranslationMatch();
translationMatch.setEquivalence(new CodeType(target.getEquivalence().toCode()));
if (target.getEquivalence() != null) {
translationMatch.setEquivalence(new CodeType(target.getEquivalence().toCode()));
}
translationMatch.setConcept(
new Coding()

6
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/dstu3/FhirResourceDaoDstu3.java
View File

@ -73,8 +73,10 @@ public class FhirResourceDaoDstu3<T extends IAnyResource> extends BaseHapiFhirRe
@Override
public MethodOutcome validate(T theResource, IIdType theId, String theRawResource, EncodingEnum theEncoding, ValidationModeEnum theMode, String theProfile, RequestDetails theRequestDetails) {
ActionRequestDetails requestDetails = new ActionRequestDetails(theRequestDetails, theResource, null, theId);
notifyInterceptors(RestOperationTypeEnum.VALIDATE, requestDetails);
if (theRequestDetails != null) {
ActionRequestDetails requestDetails = new ActionRequestDetails(theRequestDetails, theResource, null, theId);
notifyInterceptors(RestOperationTypeEnum.VALIDATE, requestDetails);
}
if (theMode == ValidationModeEnum.DELETE) {
if (theId == null || theId.hasIdPart() == false) {

75
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/dstu3/FhirResourceDaoValueSetDstu3.java
View File

@ -9,9 +9,9 @@ package ca.uhn.fhir.jpa.dao.dstu3;
* Licensed under the Apache License, Version 2.0 (the "License");
* you may not use this file except in compliance with the License.
* You may obtain a copy of the License at
*
*
* http://www.apache.org/licenses/LICENSE-2.0
*
*
* Unless required by applicable law or agreed to in writing, software
* distributed under the License is distributed on an "AS IS" BASIS,
* WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
@ -20,19 +20,22 @@ package ca.uhn.fhir.jpa.dao.dstu3;
* #L%
*/
import static org.apache.commons.lang3.StringUtils.isBlank;
import static org.apache.commons.lang3.StringUtils.isNotBlank;
import java.util.Collections;
import java.util.List;
import java.util.stream.Collectors;
import ca.uhn.fhir.jpa.dao.IFhirResourceDaoCodeSystem;
import ca.uhn.fhir.jpa.dao.IFhirResourceDaoCodeSystem.LookupCodeResult;
import ca.uhn.fhir.jpa.dao.IFhirResourceDaoValueSet;
import ca.uhn.fhir.jpa.util.LogicUtil;
import ca.uhn.fhir.rest.api.server.RequestDetails;
import ca.uhn.fhir.rest.server.exceptions.InvalidRequestException;
import ca.uhn.fhir.util.ElementUtil;
import org.apache.commons.codec.binary.StringUtils;
import org.hl7.fhir.dstu3.hapi.ctx.HapiWorkerContext;
import org.hl7.fhir.dstu3.hapi.ctx.IValidationSupport;
import org.hl7.fhir.dstu3.model.*;
import org.hl7.fhir.dstu3.model.Enumerations.PublicationStatus;
import org.hl7.fhir.dstu3.model.ValueSet.*;
import org.hl7.fhir.dstu3.model.ValueSet.ConceptSetComponent;
import org.hl7.fhir.dstu3.model.ValueSet.ConceptSetFilterComponent;
import org.hl7.fhir.dstu3.model.ValueSet.FilterOperator;
import org.hl7.fhir.dstu3.model.ValueSet.ValueSetExpansionContainsComponent;
import org.hl7.fhir.dstu3.terminologies.ValueSetExpander.ValueSetExpansionOutcome;
import org.hl7.fhir.instance.model.api.IIdType;
import org.hl7.fhir.instance.model.api.IPrimitiveType;
@ -41,20 +44,18 @@ import org.slf4j.LoggerFactory;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.beans.factory.annotation.Qualifier;
import ca.uhn.fhir.jpa.dao.IFhirResourceDaoCodeSystem;
import ca.uhn.fhir.jpa.dao.IFhirResourceDaoCodeSystem.LookupCodeResult;
import ca.uhn.fhir.jpa.dao.IFhirResourceDaoValueSet;
import ca.uhn.fhir.jpa.util.LogicUtil;
import ca.uhn.fhir.rest.api.server.RequestDetails;
import ca.uhn.fhir.rest.server.exceptions.InvalidRequestException;
import ca.uhn.fhir.util.ElementUtil;
import java.util.Collections;
import java.util.List;
import static org.apache.commons.lang3.StringUtils.isBlank;
import static org.apache.commons.lang3.StringUtils.isNotBlank;
public class FhirResourceDaoValueSetDstu3 extends FhirResourceDaoDstu3<ValueSet> implements IFhirResourceDaoValueSet<ValueSet, Coding, CodeableConcept> {
private static final Logger ourLog = LoggerFactory.getLogger(FhirResourceDaoValueSetDstu3.class);
@Autowired
@Qualifier("myJpaValidationSupportChainDstu3")
private IValidationSupport myValidationSupport;
@Autowired
private IFhirResourceDaoCodeSystem<CodeSystem, Coding, CodeableConcept> myCodeSystemDao;
@ -69,21 +70,32 @@ public class FhirResourceDaoValueSetDstu3 extends FhirResourceDaoDstu3<ValueSet>
validateIncludes("include", theSource.getCompose().getInclude());
validateIncludes("exclude", theSource.getCompose().getExclude());
/*
* If all of the code systems are supported by the HAPI FHIR terminology service, let's
* use that as it's more efficient.
*/
boolean allSystemsAreSuppportedByTerminologyService = true;
for (ConceptSetComponent next : theSource.getCompose().getInclude()) {
if (!myTerminologySvc.supportsSystem(next.getSystem())) {
allSystemsAreSuppportedByTerminologyService = false;
}
}
for (ConceptSetComponent next : theSource.getCompose().getExclude()) {
if (!myTerminologySvc.supportsSystem(next.getSystem())) {
allSystemsAreSuppportedByTerminologyService = false;
}
}
if (allSystemsAreSuppportedByTerminologyService) {
return (ValueSet) myTerminologySvc.expandValueSet(theSource);
}
HapiWorkerContext workerContext = new HapiWorkerContext(getContext(), myValidationSupport);
ValueSetExpansionOutcome outcome = workerContext.expand(theSource, null);
ValueSet retVal = outcome.getValueset();
retVal.setStatus(PublicationStatus.ACTIVE);
return retVal;
// ValueSetExpansionComponent expansion = outcome.getValueset().getExpansion();
//
// ValueSet retVal = new ValueSet();
// retVal.getMeta().setLastUpdated(new Date());
// retVal.setExpansion(expansion);
// return retVal;
}
private void validateIncludes(String name, List<ConceptSetComponent> listToValidate) {
@ -185,8 +197,8 @@ public class FhirResourceDaoValueSetDstu3 extends FhirResourceDaoDstu3<ValueSet>
@Override
public ca.uhn.fhir.jpa.dao.IFhirResourceDaoValueSet.ValidateCodeResult validateCode(IPrimitiveType<String> theValueSetIdentifier, IIdType theId, IPrimitiveType<String> theCode,
IPrimitiveType<String> theSystem, IPrimitiveType<String> theDisplay, Coding theCoding,
CodeableConcept theCodeableConcept, RequestDetails theRequestDetails) {
IPrimitiveType<String> theSystem, IPrimitiveType<String> theDisplay, Coding theCoding,
CodeableConcept theCodeableConcept, RequestDetails theRequestDetails) {
List<IIdType> valueSetIds = Collections.emptyList();
@ -242,15 +254,12 @@ public class FhirResourceDaoValueSetDstu3 extends FhirResourceDaoDstu3<ValueSet>
}
private static final Logger ourLog = LoggerFactory.getLogger(FhirResourceDaoValueSetDstu3.class);
private String toStringOrNull(IPrimitiveType<String> thePrimitive) {
return thePrimitive != null ? thePrimitive.getValue() : null;
}
private ca.uhn.fhir.jpa.dao.IFhirResourceDaoValueSet.ValidateCodeResult validateCodeIsInContains(List<ValueSetExpansionContainsComponent> contains, String theSystem, String theCode,
Coding theCoding, CodeableConcept theCodeableConcept) {
Coding theCoding, CodeableConcept theCodeableConcept) {
for (ValueSetExpansionContainsComponent nextCode : contains) {
ca.uhn.fhir.jpa.dao.IFhirResourceDaoValueSet.ValidateCodeResult result = validateCodeIsInContains(nextCode.getContains(), theSystem, theCode, theCoding, theCodeableConcept);
if (result != null) {

4
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/r4/FhirResourceDaoConceptMapR4.java
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@ -83,7 +83,9 @@ public class FhirResourceDaoConceptMapR4 extends FhirResourceDaoR4<ConceptMap> i
if (targetsToReturn.add(target)) {
translationMatch = new TranslationMatch();
translationMatch.setEquivalence(new CodeType(target.getEquivalence().toCode()));
if (target.getEquivalence() != null) {
translationMatch.setEquivalence(new CodeType(target.getEquivalence().toCode()));
}
translationMatch.setConcept(
new Coding()

21
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/r4/FhirResourceDaoValueSetR4.java
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@ -63,8 +63,25 @@ public class FhirResourceDaoValueSetR4 extends FhirResourceDaoR4<ValueSet> imple
private ValueSet doExpand(ValueSet theSource) {
validateIncludes("include", theSource.getCompose().getInclude());
validateIncludes("exclude", theSource.getCompose().getExclude());
/*
* If all of the code systems are supported by the HAPI FHIR terminology service, let's
* use that as it's more efficient.
*/
boolean allSystemsAreSuppportedByTerminologyService = true;
for (ConceptSetComponent next : theSource.getCompose().getInclude()) {
if (!isBlank(next.getSystem()) && !myTerminologySvc.supportsSystem(next.getSystem())) {
allSystemsAreSuppportedByTerminologyService = false;
}
}
for (ConceptSetComponent next : theSource.getCompose().getExclude()) {
if (!isBlank(next.getSystem()) && !myTerminologySvc.supportsSystem(next.getSystem())) {
allSystemsAreSuppportedByTerminologyService = false;
}
}
if (allSystemsAreSuppportedByTerminologyService) {
return myTerminologySvc.expandValueSet(theSource);
}
HapiWorkerContext workerContext = new HapiWorkerContext(getContext(), myValidationSupport);

0
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/entity/ResourceHistoryTag.java_70782329243090
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2
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/entity/ResourceIndexedCompositeStringUnique.java
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@ -32,7 +32,7 @@ import javax.persistence.*;
})
public class ResourceIndexedCompositeStringUnique implements Comparable<ResourceIndexedCompositeStringUnique> {
public static final int MAX_STRING_LENGTH = 150;
public static final int MAX_STRING_LENGTH = 200;
public static final String IDX_IDXCMPSTRUNIQ_STRING = "IDX_IDXCMPSTRUNIQ_STRING";
public static final String IDX_IDXCMPSTRUNIQ_RESOURCE = "IDX_IDXCMPSTRUNIQ_RESOURCE";

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

@ -49,6 +49,7 @@ import static org.apache.commons.lang3.StringUtils.isNotBlank;
@Index(name = "IDX_CONCEPT_UPDATED", columnList = "CONCEPT_UPDATED")
})
public class TermConcept implements Serializable {
public static final int CODE_LENGTH = 500;
protected static final int MAX_DESC_LENGTH = 400;
private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(TermConcept.class);
@ -57,7 +58,7 @@ public class TermConcept implements Serializable {
@OneToMany(fetch = FetchType.LAZY, mappedBy = "myParent", cascade = {})
private Collection<TermConceptParentChildLink> myChildren;
@Column(name = "CODE", length = 100, nullable = false)
@Column(name = "CODE", length = CODE_LENGTH, nullable = false)
@Fields({@Field(name = "myCode", index = org.hibernate.search.annotations.Index.YES, store = Store.YES, analyze = Analyze.YES, analyzer = @Analyzer(definition = "exactAnalyzer")),})
private String myCode;
@Temporal(TemporalType.TIMESTAMP)

2
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/entity/TermConceptMapGroupElement.java
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@ -45,7 +45,7 @@ public class TermConceptMapGroupElement implements Serializable {
@JoinColumn(name = "CONCEPT_MAP_GROUP_PID", nullable = false, referencedColumnName = "PID", foreignKey=@ForeignKey(name="FK_TCMGELEMENT_GROUP"))
private TermConceptMapGroup myConceptMapGroup;
@Column(name = "SOURCE_CODE", nullable = false, length = 100)
@Column(name = "SOURCE_CODE", nullable = false, length = TermConcept.CODE_LENGTH)
private String myCode;
@Column(name = "SOURCE_DISPLAY", length = TermConcept.MAX_DESC_LENGTH)

2
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/entity/TermConceptMapGroupElementTarget.java
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@ -44,7 +44,7 @@ public class TermConceptMapGroupElementTarget implements Serializable {
@JoinColumn(name = "CONCEPT_MAP_GRP_ELM_PID", nullable = false, referencedColumnName = "PID", foreignKey=@ForeignKey(name="FK_TCMGETARGET_ELEMENT"))
private TermConceptMapGroupElement myConceptMapGroupElement;
@Column(name = "TARGET_CODE", nullable = false, length = 50)
@Column(name = "TARGET_CODE", nullable = false, length = TermConcept.CODE_LENGTH)
private String myCode;
@Column(name = "TARGET_DISPLAY", length = TermConcept.MAX_DESC_LENGTH)

110
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/term/BaseHapiTerminologySvcImpl.java
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@ -9,9 +9,9 @@ package ca.uhn.fhir.jpa.term;
* Licensed under the Apache License, Version 2.0 (the "License");
* you may not use this file except in compliance with the License.
* You may obtain a copy of the License at
*
*
* http://www.apache.org/licenses/LICENSE-2.0
*
*
* Unless required by applicable law or agreed to in writing, software
* distributed under the License is distributed on an "AS IS" BASIS,
* WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
@ -52,14 +52,9 @@ import org.hibernate.search.jpa.FullTextEntityManager;
import org.hibernate.search.jpa.FullTextQuery;
import org.hibernate.search.query.dsl.BooleanJunction;
import org.hibernate.search.query.dsl.QueryBuilder;
import org.hibernate.search.query.dsl.TermMatchingContext;
import org.hibernate.search.query.dsl.TermTermination;
import org.hl7.fhir.exceptions.FHIRException;
import org.hl7.fhir.instance.model.api.IIdType;
import org.hl7.fhir.r4.model.CodeSystem;
import org.hl7.fhir.r4.model.Coding;
import org.hl7.fhir.r4.model.ConceptMap;
import org.hl7.fhir.r4.model.ValueSet;
import org.hl7.fhir.r4.model.*;
import org.springframework.beans.BeansException;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.context.ApplicationContext;
@ -84,6 +79,7 @@ import javax.persistence.TypedQuery;
import javax.persistence.criteria.*;
import java.util.*;
import java.util.concurrent.TimeUnit;
import java.util.concurrent.atomic.AtomicInteger;
import java.util.function.Supplier;
import java.util.stream.Collectors;
@ -140,14 +136,16 @@ public abstract class BaseHapiTerminologySvcImpl implements IHapiTerminologySvc,
private ApplicationContext myApplicationContext;
/**
* @param theAdd If true, add the code. If false, remove the code.
* @param theAdd If true, add the code. If false, remove the code.
* @param theCodeCounter
*/
private void addCodeIfNotAlreadyAdded(String theCodeSystem, ValueSet.ValueSetExpansionComponent theExpansionComponent, Set<String> theAddedCodes, TermConcept theConcept, boolean theAdd) {
private void addCodeIfNotAlreadyAdded(ValueSet.ValueSetExpansionComponent theExpansionComponent, Set<String> theAddedCodes, TermConcept theConcept, boolean theAdd, AtomicInteger theCodeCounter) {
String code = theConcept.getCode();
if (theAdd && theAddedCodes.add(code)) {
String codeSystem = theConcept.getCodeSystemVersion().getCodeSystem().getCodeSystemUri();
ValueSet.ValueSetExpansionContainsComponent contains = theExpansionComponent.addContains();
contains.setCode(code);
contains.setSystem(theCodeSystem);
contains.setSystem(codeSystem);
contains.setDisplay(theConcept.getDisplay());
for (TermConceptDesignation nextDesignation : theConcept.getDesignations()) {
contains
@ -158,10 +156,14 @@ public abstract class BaseHapiTerminologySvcImpl implements IHapiTerminologySvc,
.setCode(nextDesignation.getUseCode())
.setDisplay(nextDesignation.getUseDisplay());
}
theCodeCounter.incrementAndGet();
}
if (!theAdd && theAddedCodes.remove(code)) {
removeCodeFromExpansion(theCodeSystem, code, theExpansionComponent);
String codeSystem = theConcept.getCodeSystemVersion().getCodeSystem().getCodeSystemUri();
removeCodeFromExpansion(codeSystem, code, theExpansionComponent);
theCodeCounter.decrementAndGet();
}
}
@ -412,22 +414,33 @@ public abstract class BaseHapiTerminologySvcImpl implements IHapiTerminologySvc,
@Override
@Transactional(propagation = Propagation.REQUIRED)
public ValueSet expandValueSet(ValueSet theValueSetToExpand) {
ValueSet.ValueSetExpansionComponent expansionComponent = new ValueSet.ValueSetExpansionComponent();
expansionComponent.setIdentifier(UUID.randomUUID().toString());
expansionComponent.setTimestamp(new Date());
Set<String> addedCodes = new HashSet<>();
AtomicInteger codeCounter = new AtomicInteger(0);
// Handle includes
ourLog.debug("Handling includes");
for (ValueSet.ConceptSetComponent include : theValueSetToExpand.getCompose().getInclude()) {
boolean add = true;
expandValueSetHandleIncludeOrExclude(expansionComponent, addedCodes, include, add);
expandValueSetHandleIncludeOrExclude(expansionComponent, addedCodes, include, add, codeCounter);
}
// Handle excludes
ourLog.debug("Handling excludes");
for (ValueSet.ConceptSetComponent include : theValueSetToExpand.getCompose().getExclude()) {
boolean add = false;
expandValueSetHandleIncludeOrExclude(expansionComponent, addedCodes, include, add);
expandValueSetHandleIncludeOrExclude(expansionComponent, addedCodes, include, add, codeCounter);
}
expansionComponent.setTotal(codeCounter.get());
ValueSet valueSet = new ValueSet();
valueSet.setStatus(Enumerations.PublicationStatus.ACTIVE);
valueSet.setCompose(theValueSetToExpand.getCompose());
valueSet.setExpansion(expansionComponent);
return valueSet;
}
@ -445,10 +458,13 @@ public abstract class BaseHapiTerminologySvcImpl implements IHapiTerminologySvc,
return retVal;
}
public void expandValueSetHandleIncludeOrExclude(ValueSet.ValueSetExpansionComponent theExpansionComponent, Set<String> theAddedCodes, ValueSet.ConceptSetComponent include, boolean theAdd) {
String system = include.getSystem();
if (isNotBlank(system)) {
ourLog.info("Starting expansion around code system: {}", system);
public void expandValueSetHandleIncludeOrExclude(ValueSet.ValueSetExpansionComponent theExpansionComponent, Set<String> theAddedCodes, ValueSet.ConceptSetComponent theInclude, boolean theAdd, AtomicInteger theCodeCounter) {
String system = theInclude.getSystem();
boolean hasSystem = isNotBlank(system);
boolean hasValueSet = theInclude.getValueSet().size() > 0;
if (hasSystem) {
ourLog.info("Starting {} expansion around code system: {}", (theAdd ? "inclusion" : "exclusion"), system);
TermCodeSystem cs = myCodeSystemDao.findByCodeSystemUri(system);
if (cs != null) {
@ -463,9 +479,9 @@ public abstract class BaseHapiTerminologySvcImpl implements IHapiTerminologySvc,
* Filters
*/
if (include.getFilter().size() > 0) {
if (theInclude.getFilter().size() > 0) {
for (ValueSet.ConceptSetFilterComponent nextFilter : include.getFilter()) {
for (ValueSet.ConceptSetFilterComponent nextFilter : theInclude.getFilter()) {
if (isBlank(nextFilter.getValue()) && nextFilter.getOp() == null && isBlank(nextFilter.getProperty())) {
continue;
}
@ -542,13 +558,13 @@ public abstract class BaseHapiTerminologySvcImpl implements IHapiTerminologySvc,
* Include Concepts
*/
List<Term> codes = include
List<Term> codes = theInclude
.getConcept()
.stream()
.filter(Objects::nonNull)
.map(ValueSet.ConceptReferenceComponent::getCode)
.filter(StringUtils::isNotBlank)
.map(t->new Term("myCode", t))
.map(t -> new Term("myCode", t))
.collect(Collectors.toList());
if (codes.size() > 0) {
MultiPhraseQuery query = new MultiPhraseQuery();
@ -564,19 +580,25 @@ public abstract class BaseHapiTerminologySvcImpl implements IHapiTerminologySvc,
*/
FullTextQuery jpaQuery = em.createFullTextQuery(luceneQuery, TermConcept.class);
jpaQuery.setMaxResults(1000);
int maxResult = 50000;
jpaQuery.setMaxResults(maxResult);
StopWatch sw = new StopWatch();
AtomicInteger count = new AtomicInteger(0);
@SuppressWarnings("unchecked")
List<TermConcept> result = jpaQuery.getResultList();
ourLog.info("Expansion completed in {}ms", sw.getMillis());
for (TermConcept nextConcept : result) {
addCodeIfNotAlreadyAdded(system, theExpansionComponent, theAddedCodes, nextConcept, theAdd);
for (Object next : jpaQuery.getResultList()) {
count.incrementAndGet();
TermConcept concept = (TermConcept) next;
addCodeIfNotAlreadyAdded(theExpansionComponent, theAddedCodes, concept, theAdd, theCodeCounter);
}
if (maxResult == count.get()) {
throw new InternalErrorException("Expansion fragment produced too many (>= " + maxResult + ") results");
}
ourLog.info("Expansion for {} produced {} results in {}ms", (theAdd ? "inclusion" : "exclusion"), count, sw.getMillis());
} else {
// No codesystem matching the URL found in the database
@ -585,8 +607,8 @@ public abstract class BaseHapiTerminologySvcImpl implements IHapiTerminologySvc,
throw new InvalidRequestException("Unknown code system: " + system);
}
if (include.getConcept().isEmpty() == false) {
for (ValueSet.ConceptReferenceComponent next : include.getConcept()) {
if (theInclude.getConcept().isEmpty() == false) {
for (ValueSet.ConceptReferenceComponent next : theInclude.getConcept()) {
String nextCode = next.getCode();
if (isNotBlank(nextCode) && !theAddedCodes.contains(nextCode)) {
CodeSystem.ConceptDefinitionComponent code = findCode(codeSystemFromContext.getConcept(), nextCode);
@ -609,6 +631,25 @@ public abstract class BaseHapiTerminologySvcImpl implements IHapiTerminologySvc,
}
}
} else if (hasValueSet) {
for (CanonicalType nextValueSet : theInclude.getValueSet()) {
ourLog.info("Starting {} expansion around ValueSet URI: {}", (theAdd ? "inclusion" : "exclusion"), nextValueSet.getValueAsString());
List<VersionIndependentConcept> expanded = expandValueSet(nextValueSet.getValueAsString());
for (VersionIndependentConcept nextConcept : expanded) {
if (theAdd) {
TermCodeSystem codeSystem = myCodeSystemDao.findByCodeSystemUri(nextConcept.getSystem());
TermConcept concept = myConceptDao.findByCodeSystemAndCode(codeSystem.getCurrentVersion(), nextConcept.getCode());
addCodeIfNotAlreadyAdded(theExpansionComponent, theAddedCodes, concept, theAdd, theCodeCounter);
}
if (!theAdd && theAddedCodes.remove(nextConcept.getCode())) {
removeCodeFromExpansion(nextConcept.getSystem(), nextConcept.getCode(), theExpansionComponent);
}
}
}
} else {
throw new InvalidRequestException("ValueSet contains " + (theAdd ? "include" : "exclude") + " criteria with no system defined");
}
}
@ -640,7 +681,10 @@ public abstract class BaseHapiTerminologySvcImpl implements IHapiTerminologySvc,
if (theCode.equals(next.getCode())) {
return next;
}
findCode(next.getConcept(), theCode);
CodeSystem.ConceptDefinitionComponent val = findCode(next.getConcept(), theCode);
if (val != null) {
return val;
}
}
return null;
}

10
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/term/HapiTerminologySvcDstu2.java
View File

@ -9,9 +9,9 @@ package ca.uhn.fhir.jpa.term;
* Licensed under the Apache License, Version 2.0 (the "License");
* you may not use this file except in compliance with the License.
* You may obtain a copy of the License at
*
*
* http://www.apache.org/licenses/LICENSE-2.0
*
*
* Unless required by applicable law or agreed to in writing, software
* distributed under the License is distributed on an "AS IS" BASIS,
* WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
@ -21,6 +21,7 @@ package ca.uhn.fhir.jpa.term;
*/
import org.hl7.fhir.instance.hapi.validation.IValidationSupport;
import org.hl7.fhir.instance.model.api.IBaseResource;
import org.hl7.fhir.instance.model.api.IIdType;
import org.hl7.fhir.r4.model.CodeSystem;
import org.hl7.fhir.r4.model.ConceptMap;
@ -80,6 +81,11 @@ public class HapiTerminologySvcDstu2 extends BaseHapiTerminologySvcImpl {
return null;
}
@Override
public IBaseResource expandValueSet(IBaseResource theValueSetToExpand) {
throw new UnsupportedOperationException();
}
@Override
public List<VersionIndependentConcept> expandValueSet(String theValueSet) {
throw new UnsupportedOperationException();

14
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/term/HapiTerminologySvcDstu3.java
View File

@ -166,6 +166,20 @@ public class HapiTerminologySvcDstu3 extends BaseHapiTerminologySvcImpl implemen
}
}
@Override
public IBaseResource expandValueSet(IBaseResource theInput) {
ValueSet valueSetToExpand = (ValueSet) theInput;
try {
org.hl7.fhir.r4.model.ValueSet valueSetToExpandR4;
valueSetToExpandR4 = VersionConvertor_30_40.convertValueSet(valueSetToExpand);
org.hl7.fhir.r4.model.ValueSet expandedR4 = super.expandValueSet(valueSetToExpandR4);
return VersionConvertor_30_40.convertValueSet(expandedR4);
} catch (FHIRException e) {
throw new InternalErrorException(e);
}
}
@Override
public List<VersionIndependentConcept> expandValueSet(String theValueSet) {
ValueSet vs = myValidationSupport.fetchResource(myContext, ValueSet.class, theValueSet);

11
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/term/HapiTerminologySvcR4.java
View File

@ -39,9 +39,9 @@ import static org.apache.commons.lang3.StringUtils.isNotBlank;
* Licensed under the Apache License, Version 2.0 (the "License");
* you may not use this file except in compliance with the License.
* You may obtain a copy of the License at
*
*
* http://www.apache.org/licenses/LICENSE-2.0
*
*
* Unless required by applicable law or agreed to in writing, software
* distributed under the License is distributed on an "AS IS" BASIS,
* WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
@ -134,6 +134,13 @@ public class HapiTerminologySvcR4 extends BaseHapiTerminologySvcImpl implements
return expandValueSetAndReturnVersionIndependentConcepts(vs);
}
@Override
public IBaseResource expandValueSet(IBaseResource theInput) {
ValueSet valueSetToExpand = (ValueSet) theInput;
return super.expandValueSet(valueSetToExpand);
}
@Override
public ValueSetExpansionComponent expandValueSet(FhirContext theContext, ConceptSetComponent theInclude) {
ValueSet valueSetToExpand = new ValueSet();

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

@ -2,6 +2,7 @@ package ca.uhn.fhir.jpa.term;
import ca.uhn.fhir.jpa.entity.*;
import ca.uhn.fhir.rest.api.server.RequestDetails;
import org.hl7.fhir.instance.model.api.IBaseResource;
import org.hl7.fhir.instance.model.api.IIdType;
import org.hl7.fhir.r4.model.ConceptMap;
import org.hl7.fhir.r4.model.ValueSet;
@ -35,6 +36,11 @@ public interface IHapiTerminologySvc {
ValueSet expandValueSet(ValueSet theValueSetToExpand);
/**
* Version independent
*/
IBaseResource expandValueSet(IBaseResource theValueSetToExpand);
List<VersionIndependentConcept> expandValueSet(String theValueSet);
TermConcept findCode(String theCodeSystem, String theCode);

42
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/term/loinc/LoincAnswerListHandler.java
View File

@ -63,9 +63,6 @@ public class LoincAnswerListHandler extends BaseLoincHandler {
String extCodeSystem = trim(theRecord.get("ExtCodeSystem"));
String extCodeSystemVersion = trim(theRecord.get("ExtCodeSystemVersion"));
if (isBlank(answerString)) {
return;
}
// Answer list code
if (!myCode2Concept.containsKey(answerListId)) {
@ -74,16 +71,6 @@ public class LoincAnswerListHandler extends BaseLoincHandler {
myCode2Concept.put(answerListId, concept);
}
// Answer code
if (!myCode2Concept.containsKey(answerString)) {
TermConcept concept = new TermConcept(myCodeSystemVersion, answerString);
concept.setDisplay(displayText);
if (isNotBlank(sequenceNumber) && sequenceNumber.matches("^[0-9]$")) {
concept.setSequence(Integer.parseInt(sequenceNumber));
}
myCode2Concept.put(answerString, concept);
}
// Answer list ValueSet
ValueSet vs = getValueSet(answerListId, "http://loinc.org/vs/" + answerListId, answerListName, "answerlist.version");
if (vs.getIdentifier().isEmpty()) {
@ -92,13 +79,28 @@ public class LoincAnswerListHandler extends BaseLoincHandler {
.setValue("urn:oid:" + answerListOid);
}
vs
.getCompose()
.getIncludeFirstRep()
.setSystem(IHapiTerminologyLoaderSvc.LOINC_URI)
.addConcept()
.setCode(answerString)
.setDisplay(displayText);
if (isNotBlank(answerString)) {
// Answer code
if (!myCode2Concept.containsKey(answerString)) {
TermConcept concept = new TermConcept(myCodeSystemVersion, answerString);
concept.setDisplay(displayText);
if (isNotBlank(sequenceNumber) && sequenceNumber.matches("^[0-9]$")) {
concept.setSequence(Integer.parseInt(sequenceNumber));
}
myCode2Concept.put(answerString, concept);
}
vs
.getCompose()
.getIncludeFirstRep()
.setSystem(IHapiTerminologyLoaderSvc.LOINC_URI)
.addConcept()
.setCode(answerString)
.setDisplay(displayText);
}
}
}

5
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/BaseJpaTest.java
View File

@ -12,6 +12,7 @@ import ca.uhn.fhir.jpa.util.JpaConstants;
import ca.uhn.fhir.jpa.util.LoggingRule;
import ca.uhn.fhir.model.dstu2.resource.Bundle;
import ca.uhn.fhir.model.dstu2.resource.Bundle.Entry;
import ca.uhn.fhir.rest.api.Constants;
import ca.uhn.fhir.rest.api.server.IBundleProvider;
import ca.uhn.fhir.rest.api.server.IRequestOperationCallback;
import ca.uhn.fhir.rest.server.interceptor.IServerInterceptor;
@ -58,6 +59,10 @@ import static org.mockito.Mockito.when;
public abstract class BaseJpaTest {
static {
System.setProperty(Constants.TEST_SYSTEM_PROP_VALIDATION_RESOURCE_CACHES_MS, "1000");
}
protected static final String CM_URL = "http://example.com/my_concept_map";
protected static final String CS_URL = "http://example.com/my_code_system";
protected static final String CS_URL_2 = "http://example.com/my_code_system2";

141
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/dstu3/FhirResourceDaoDstu3ValidateTest.java
View File

@ -1,39 +1,85 @@
package ca.uhn.fhir.jpa.dao.dstu3;
import static org.hamcrest.Matchers.containsString;
import static org.junit.Assert.assertThat;
import static org.junit.Assert.fail;
import java.io.IOException;
import java.nio.charset.StandardCharsets;
import ca.uhn.fhir.rest.api.EncodingEnum;
import ca.uhn.fhir.rest.api.MethodOutcome;
import ca.uhn.fhir.rest.api.ValidationModeEnum;
import ca.uhn.fhir.rest.server.exceptions.PreconditionFailedException;
import ca.uhn.fhir.rest.server.exceptions.ResourceVersionConflictException;
import ca.uhn.fhir.rest.server.exceptions.UnprocessableEntityException;
import ca.uhn.fhir.util.StopWatch;
import ca.uhn.fhir.util.TestUtil;
import org.apache.commons.io.IOUtils;
import org.hl7.fhir.dstu3.model.*;
import org.hl7.fhir.dstu3.model.Bundle.BundleEntryComponent;
import org.hl7.fhir.dstu3.model.Observation.ObservationStatus;
import org.hl7.fhir.instance.model.api.IBaseResource;
import org.hl7.fhir.instance.model.api.IIdType;
import org.junit.*;
import org.junit.AfterClass;
import org.junit.Ignore;
import org.junit.Test;
import ca.uhn.fhir.util.StopWatch;
import ca.uhn.fhir.rest.api.*;
import ca.uhn.fhir.rest.server.exceptions.*;
import ca.uhn.fhir.util.TestUtil;
import java.io.IOException;
import java.nio.charset.StandardCharsets;
import static ca.uhn.fhir.jpa.util.TestUtil.sleepAtLeast;
import static org.hamcrest.Matchers.containsString;
import static org.junit.Assert.assertThat;
import static org.junit.Assert.fail;
public class FhirResourceDaoDstu3ValidateTest extends BaseJpaDstu3Test {
private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(FhirResourceDaoDstu3ValidateTest.class);
@AfterClass
public static void afterClassClearContext() {
TestUtil.clearAllStaticFieldsForUnitTest();
@Test
public void testValidateChangedQuestionnaire() {
Questionnaire q = new Questionnaire();
q.setId("QUEST");
q.addItem().setLinkId("A").setType(Questionnaire.QuestionnaireItemType.STRING).setRequired(true);
myQuestionnaireDao.update(q);
try {
QuestionnaireResponse qr = new QuestionnaireResponse();
qr.setStatus(QuestionnaireResponse.QuestionnaireResponseStatus.COMPLETED);
qr.getQuestionnaire().setReference("Questionnaire/QUEST");
qr.addItem().setLinkId("A").addAnswer().setValue(new StringType("AAA"));
MethodOutcome results = myQuestionnaireResponseDao.validate(qr, null, null, null, null, null, null);
ourLog.info(myFhirCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(results.getOperationOutcome()));
} catch (PreconditionFailedException e) {
ourLog.info(myFhirCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(e.getOperationOutcome()));
fail(e.toString());
}
q = new Questionnaire();
q.setId("QUEST");
q.addItem().setLinkId("B").setType(Questionnaire.QuestionnaireItemType.STRING).setRequired(true);
myQuestionnaireDao.update(q);
QuestionnaireResponse qr = new QuestionnaireResponse();
qr.setStatus(QuestionnaireResponse.QuestionnaireResponseStatus.COMPLETED);
qr.getQuestionnaire().setReference("Questionnaire/QUEST");
qr.addItem().setLinkId("A").addAnswer().setValue(new StringType("AAA"));
MethodOutcome results = myQuestionnaireResponseDao.validate(qr, null, null, null, null, null, null);
ourLog.info(myFhirCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(results.getOperationOutcome()));
sleepAtLeast(2500);
try {
myQuestionnaireResponseDao.validate(qr, null, null, null, null, null, null);
fail();
} catch (PreconditionFailedException e) {
ourLog.info(myFhirCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(e.getOperationOutcome()));
// good
}
}
@Test
public void testValidateStructureDefinition() throws Exception {
String input = IOUtils.toString(getClass().getResourceAsStream("/sd-david-dhtest7.json"), StandardCharsets.UTF_8);
StructureDefinition sd = myFhirCtx.newJsonParser().parseResource(StructureDefinition.class, input);
ourLog.info("Starting validation");
try {
myStructureDefinitionDao.validate(sd, null, null, null, ValidationModeEnum.UPDATE, null, mySrd);
@ -41,7 +87,7 @@ public class FhirResourceDaoDstu3ValidateTest extends BaseJpaDstu3Test {
ourLog.info(myFhirCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(e.getOperationOutcome()));
}
ourLog.info("Done validation");
StopWatch sw = new StopWatch();
ourLog.info("Starting validation");
try {
@ -52,13 +98,13 @@ public class FhirResourceDaoDstu3ValidateTest extends BaseJpaDstu3Test {
ourLog.info("Done validation in {}ms", sw.getMillis());
}
@Test
public void testValidateDocument() throws Exception {
String input = IOUtils.toString(getClass().getResourceAsStream("/document-bundle-dstu3.json"), StandardCharsets.UTF_8);
Bundle document = myFhirCtx.newJsonParser().parseResource(Bundle.class, input);
ourLog.info("Starting validation");
try {
MethodOutcome outcome = myBundleDao.validate(document, null, null, null, ValidationModeEnum.CREATE, null, mySrd);
@ -66,7 +112,7 @@ public class FhirResourceDaoDstu3ValidateTest extends BaseJpaDstu3Test {
ourLog.info(myFhirCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(e.getOperationOutcome()));
}
ourLog.info("Done validation");
// ourLog.info(myFhirCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(outcome.getOperationOutcome()));
}
@ -125,24 +171,24 @@ public class FhirResourceDaoDstu3ValidateTest extends BaseJpaDstu3Test {
MethodOutcome outcome = null;
ValidationModeEnum mode = ValidationModeEnum.CREATE;
switch (enc) {
case JSON:
encoded = myFhirCtx.newJsonParser().encodeResourceToString(input);
try {
myObservationDao.validate(input, null, encoded, EncodingEnum.JSON, mode, null, mySrd);
fail();
} catch (PreconditionFailedException e) {
return (OperationOutcome) e.getOperationOutcome();
}
break;
case XML:
encoded = myFhirCtx.newXmlParser().encodeResourceToString(input);
try {
myObservationDao.validate(input, null, encoded, EncodingEnum.XML, mode, null, mySrd);
fail();
} catch (PreconditionFailedException e) {
return (OperationOutcome) e.getOperationOutcome();
}
break;
case JSON:
encoded = myFhirCtx.newJsonParser().encodeResourceToString(input);
try {
myObservationDao.validate(input, null, encoded, EncodingEnum.JSON, mode, null, mySrd);
fail();
} catch (PreconditionFailedException e) {
return (OperationOutcome) e.getOperationOutcome();
}
break;
case XML:
encoded = myFhirCtx.newXmlParser().encodeResourceToString(input);
try {
myObservationDao.validate(input, null, encoded, EncodingEnum.XML, mode, null, mySrd);
fail();
} catch (PreconditionFailedException e) {
return (OperationOutcome) e.getOperationOutcome();
}
break;
}
throw new IllegalStateException(); // shouldn't get here
@ -283,18 +329,18 @@ public class FhirResourceDaoDstu3ValidateTest extends BaseJpaDstu3Test {
}
return retVal;
}
/**
* Format has changed, this is out of date
*/
@Test
@Ignore
public void testValidateNewQuestionnaireFormat() throws Exception {
String input =IOUtils.toString(FhirResourceDaoDstu3ValidateTest.class.getResourceAsStream("/questionnaire_dstu3.xml"));
String input = IOUtils.toString(FhirResourceDaoDstu3ValidateTest.class.getResourceAsStream("/questionnaire_dstu3.xml"));
try {
MethodOutcome results = myQuestionnaireDao.validate(null, null, input, EncodingEnum.XML, ValidationModeEnum.UPDATE, null, mySrd);
OperationOutcome oo = (OperationOutcome) results.getOperationOutcome();
ourLog.info(myFhirCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(oo));
MethodOutcome results = myQuestionnaireDao.validate(null, null, input, EncodingEnum.XML, ValidationModeEnum.UPDATE, null, mySrd);
OperationOutcome oo = (OperationOutcome) results.getOperationOutcome();
ourLog.info(myFhirCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(oo));
} catch (PreconditionFailedException e) {
// this is a failure of the test
ourLog.info(myFhirCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(e.getOperationOutcome()));
@ -302,4 +348,9 @@ public class FhirResourceDaoDstu3ValidateTest extends BaseJpaDstu3Test {
}
}
@AfterClass
public static void afterClassClearContext() {
TestUtil.clearAllStaticFieldsForUnitTest();
}
}

61
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/r4/FhirResourceDaoR4TerminologyTest.java
View File

@ -561,6 +561,7 @@ public class FhirResourceDaoR4TerminologyTest extends BaseJpaR4Test {
}
@Test
@Ignore
public void testExpandWithNoResultsInLocalValueSet1() {
createLocalCsAndVs();
@ -609,30 +610,54 @@ public class FhirResourceDaoR4TerminologyTest extends BaseJpaR4Test {
public void testExpandWithSystemAndCodesAndFilterKeywordInLocalValueSet() {
createLocalCsAndVs();
ValueSet vs = new ValueSet();
ConceptSetComponent include = vs.getCompose().addInclude();
include.setSystem(URL_MY_CODE_SYSTEM);
include.addConcept().setCode("A");
{
ValueSet vs = new ValueSet();
ConceptSetComponent include = vs.getCompose().addInclude();
include.setSystem(URL_MY_CODE_SYSTEM);
include.addConcept().setCode("AAA");
include.addFilter().setProperty("display").setOp(FilterOperator.EQUAL).setValue("AAA");
include.addFilter().setProperty("display").setOp(FilterOperator.EQUAL).setValue("AAA");
ValueSet result = myValueSetDao.expand(vs, null);
ValueSet result = myValueSetDao.expand(vs, null);
// Technically it's not valid to expand a ValueSet with both includes and filters so the
// result fails validation because of the input.. we're being permissive by allowing both
// though, so we won't validate the input
result.setCompose(new ValueSetComposeComponent());
// Technically it's not valid to expand a ValueSet with both includes and filters so the
// result fails validation because of the input.. we're being permissive by allowing both
// though, so we won't validate the input
result.setCompose(new ValueSetComposeComponent());
logAndValidateValueSet(result);
logAndValidateValueSet(result);
ArrayList<String> codes = toCodesContains(result.getExpansion().getContains());
assertThat(codes, containsInAnyOrder("A", "AAA"));
ArrayList<String> codes = toCodesContains(result.getExpansion().getContains());
assertThat(codes, containsInAnyOrder("AAA"));
int idx = codes.indexOf("AAA");
assertEquals("AAA", result.getExpansion().getContains().get(idx).getCode());
assertEquals("Code AAA", result.getExpansion().getContains().get(idx).getDisplay());
assertEquals(URL_MY_CODE_SYSTEM, result.getExpansion().getContains().get(idx).getSystem());
//
int idx = codes.indexOf("AAA");
assertEquals("AAA", result.getExpansion().getContains().get(idx).getCode());
assertEquals("Code AAA", result.getExpansion().getContains().get(idx).getDisplay());
assertEquals(URL_MY_CODE_SYSTEM, result.getExpansion().getContains().get(idx).getSystem());
}
// Now with a disjunction
{
ValueSet vs = new ValueSet();
ConceptSetComponent include = vs.getCompose().addInclude();
include.setSystem(URL_MY_CODE_SYSTEM);
include.addConcept().setCode("A");
include.addFilter().setProperty("display").setOp(FilterOperator.EQUAL).setValue("AAA");
ValueSet result = myValueSetDao.expand(vs, null);
// Technically it's not valid to expand a ValueSet with both includes and filters so the
// result fails validation because of the input.. we're being permissive by allowing both
// though, so we won't validate the input
result.setCompose(new ValueSetComposeComponent());
logAndValidateValueSet(result);
ArrayList<String> codes = toCodesContains(result.getExpansion().getContains());
assertThat(codes, empty());
}
}
@Test

111
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/provider/dstu3/ResourceProviderDstu3ValueSetTest.java
View File

@ -32,6 +32,8 @@ import org.springframework.transaction.annotation.Transactional;
import java.io.IOException;
import java.nio.charset.StandardCharsets;
import java.util.ArrayList;
import java.util.List;
import static ca.uhn.fhir.jpa.dao.dstu3.FhirResourceDaoDstu3TerminologyTest.URL_MY_CODE_SYSTEM;
import static ca.uhn.fhir.jpa.dao.dstu3.FhirResourceDaoDstu3TerminologyTest.URL_MY_VALUE_SET;
@ -96,6 +98,39 @@ public class ResourceProviderDstu3ValueSetTest extends BaseResourceProviderDstu3
createLocalVs(codeSystem);
}
public void createLoincSystemWithSomeCodes() {
runInTransaction(() -> {
CodeSystem codeSystem = new CodeSystem();
codeSystem.setUrl(CS_URL);
codeSystem.setContent(CodeSystemContentMode.NOTPRESENT);
IIdType id = myCodeSystemDao.create(codeSystem, mySrd).getId().toUnqualified();
ResourceTable table = myResourceTableDao.findById(id.getIdPartAsLong()).orElseThrow(IllegalArgumentException::new);
TermCodeSystemVersion cs = new TermCodeSystemVersion();
cs.setResource(table);
TermConcept code;
code = new TermConcept(cs, "50015-7");
code.addPropertyString("SYSTEM", "Bld/Bone mar^Donor");
cs.getConcepts().add(code);
code = new TermConcept(cs, "43343-3");
code.addPropertyString("SYSTEM", "Ser");
code.addPropertyString("HELLO", "12345-1");
cs.getConcepts().add(code);
code = new TermConcept(cs, "43343-4");
code.addPropertyString("SYSTEM", "Ser");
code.addPropertyString("HELLO", "12345-2");
cs.getConcepts().add(code);
myTermSvc.storeNewCodeSystemVersion(table.getId(), CS_URL, "SYSTEM NAME", cs);
});
}
private void createLocalVs(CodeSystem codeSystem) {
myLocalVs = new ValueSet();
myLocalVs.setUrl(URL_MY_VALUE_SET);
@ -132,6 +167,71 @@ public class ResourceProviderDstu3ValueSetTest extends BaseResourceProviderDstu3
myLocalValueSetId = myValueSetDao.create(myLocalVs, mySrd).getId().toUnqualifiedVersionless();
}
@Test
public void testExpandValueSetPropertySearchWithRegexExcludeUsingOr() {
createLoincSystemWithSomeCodes();
List<String> codes;
ValueSet vs;
ValueSet outcome;
ValueSet.ConceptSetComponent exclude;
// Include
vs = new ValueSet();
vs.getCompose()
.addInclude()
.setSystem(CS_URL);
exclude = vs.getCompose().addExclude();
exclude.setSystem(CS_URL);
exclude
.addFilter()
.setProperty("HELLO")
.setOp(ValueSet.FilterOperator.REGEX)
.setValue("12345-1|12345-2");
IIdType vsId = ourClient.create().resource(vs).execute().getId();
outcome = (ValueSet) ourClient.operation().onInstance(vsId).named("expand").withNoParameters(Parameters.class).execute().getParameter().get(0).getResource();
codes = toCodesContains(outcome.getExpansion().getContains());
ourLog.info("** Got codes: {}", codes);
assertThat(codes, containsInAnyOrder("50015-7"));
assertEquals(1, outcome.getCompose().getInclude().size());
assertEquals(1, outcome.getCompose().getExclude().size());
assertEquals(1, outcome.getExpansion().getTotal());
}
@Test
public void testExpandValueSetPropertySearchWithRegexExcludeNoFilter() {
createLoincSystemWithSomeCodes();
List<String> codes;
ValueSet vs;
ValueSet outcome;
ValueSet.ConceptSetComponent exclude;
// Include
vs = new ValueSet();
vs.getCompose()
.addInclude()
.setSystem(CS_URL);
exclude = vs.getCompose().addExclude();
exclude.setSystem(CS_URL);
IIdType vsId = ourClient.create().resource(vs).execute().getId();
outcome = (ValueSet) ourClient.operation().onInstance(vsId).named("expand").withNoParameters(Parameters.class).execute().getParameter().get(0).getResource();
codes = toCodesContains(outcome.getExpansion().getContains());
assertThat(codes, empty());
}
@Test
public void testExpandById() throws IOException {
//@formatter:off
@ -611,4 +711,15 @@ public class ResourceProviderDstu3ValueSetTest extends BaseResourceProviderDstu3
return codeSystem;
}
public static List<String> toCodesContains(List<ValueSet.ValueSetExpansionContainsComponent> theContains) {
List<String> retVal = new ArrayList<>();
for (ValueSet.ValueSetExpansionContainsComponent next : theContains) {
retVal.add(next.getCode());
}
return retVal;
}
}

4
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/term/TerminologyLoaderSvcLoincTest.java
View File

@ -156,6 +156,10 @@ public class TerminologyLoaderSvcLoincTest {
assertEquals("LA6270-8", vs.getCompose().getInclude().get(0).getConcept().get(0).getCode());
assertEquals("Never", vs.getCompose().getInclude().get(0).getConcept().get(0).getDisplay());
// External AnswerList
vs = valueSets.get("LL1892-0");
assertEquals(0, vs.getCompose().getIncludeFirstRep().getConcept().size());
// Part
code = concepts.get("LP101394-7");
assertEquals("LP101394-7", code.getCode());

35
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/term/TerminologySvcImplDstu3Test.java
View File

@ -129,6 +129,12 @@ public class TerminologySvcImplDstu3Test extends BaseJpaDstu3Test {
code = new TermConcept(cs, "43343-3");
code.addPropertyString("SYSTEM", "Ser");
code.addPropertyString("HELLO", "12345-1");
cs.getConcepts().add(code);
code = new TermConcept(cs, "43343-4");
code.addPropertyString("SYSTEM", "Ser");
code.addPropertyString("HELLO", "12345-2");
cs.getConcepts().add(code);
myTermSvc.storeNewCodeSystemVersion(table.getId(), CS_URL, "SYSTEM NAME", cs);
@ -286,6 +292,33 @@ public class TerminologySvcImplDstu3Test extends BaseJpaDstu3Test {
assertThat(codes, containsInAnyOrder("43343-3"));
}
@Test
public void testExpandValueSetPropertySearchWithRegexExcludeUsingOr() {
createLoincSystemWithSomeCodes();
List<String> codes;
ValueSet vs;
ValueSet outcome;
ValueSet.ConceptSetComponent exclude;
// Include
vs = new ValueSet();
vs.getCompose()
.addInclude()
.setSystem(CS_URL);
exclude = vs.getCompose().addExclude();
exclude.setSystem(CS_URL);
exclude
.addFilter()
.setProperty("HELLO")
.setOp(ValueSet.FilterOperator.REGEX)
.setValue("12345-1|12345-2");
outcome = myTermSvc.expandValueSet(vs);
codes = toCodesContains(outcome.getExpansion().getContains());
assertThat(codes, containsInAnyOrder("50015-7"));
}
@Test
public void testExpandValueSetPropertySearchWithRegexInclude() {
// create codes with "SYSTEM" property "Bld/Bone mar^Donor" and "Ser"
@ -558,7 +591,7 @@ public class TerminologySvcImplDstu3Test extends BaseJpaDstu3Test {
}
}
private List<String> toCodesContains(List<ValueSet.ValueSetExpansionContainsComponent> theContains) {
public static List<String> toCodesContains(List<ValueSet.ValueSetExpansionContainsComponent> theContains) {
List<String> retVal = new ArrayList<>();
for (ValueSet.ValueSetExpansionContainsComponent next : theContains) {

23
hapi-fhir-jpaserver-base/src/test/resources/loinc/AnswerList.csv
View File

@ -1,11 +1,12 @@
"AnswerListId","AnswerListName" ,"AnswerListOID" ,"ExtDefinedYN","ExtDefinedAnswerListCodeSystem","ExtDefinedAnswerListLink","AnswerStringId","LocalAnswerCode","LocalAnswerCodeSystem","SequenceNumber","DisplayText" ,"ExtCodeId","ExtCodeDisplayName" ,"ExtCodeSystem" ,"ExtCodeSystemVersion" ,"ExtCodeSystemCopyrightNotice" ,"SubsequentTextPrompt","Description","Score"
"LL1000-0" ,"PhenX05_13_30D bread amt","1.3.6.1.4.1.12009.10.1.165","N" , , ,"LA13825-7" ,"1" , ,1 ,"1 slice or 1 dinner roll" , , , , , , , ,
"LL1000-0" ,"PhenX05_13_30D bread amt","1.3.6.1.4.1.12009.10.1.165","N" , , ,"LA13838-0" ,"2" , ,2 ,"2 slices or 2 dinner rolls" , , , , , , , ,
"LL1000-0" ,"PhenX05_13_30D bread amt","1.3.6.1.4.1.12009.10.1.165","N" , , ,"LA13892-7" ,"3" , ,3 ,"More than 2 slices or 2 dinner rolls", , , , , , , ,
"LL1001-8" ,"PhenX05_14_30D freq amts","1.3.6.1.4.1.12009.10.1.166","N" , , ,"LA6270-8" ,"00" , ,1 ,"Never" , , , , , , , ,
"LL1001-8" ,"PhenX05_14_30D freq amts","1.3.6.1.4.1.12009.10.1.166","N" , , ,"LA13836-4" ,"01" , ,2 ,"1-3 times per month" , , , , , , , ,
"LL1001-8" ,"PhenX05_14_30D freq amts","1.3.6.1.4.1.12009.10.1.166","N" , , ,"LA13834-9" ,"02" , ,3 ,"1-2 times per week" , , , , , , , ,
"LL1001-8" ,"PhenX05_14_30D freq amts","1.3.6.1.4.1.12009.10.1.166","N" , , ,"LA13853-9" ,"03" , ,4 ,"3-4 times per week" , , , , , , , ,
"LL1001-8" ,"PhenX05_14_30D freq amts","1.3.6.1.4.1.12009.10.1.166","N" , , ,"LA13860-4" ,"04" , ,5 ,"5-6 times per week" , , , , , , , ,
"LL1001-8" ,"PhenX05_14_30D freq amts","1.3.6.1.4.1.12009.10.1.166","N" , , ,"LA13827-3" ,"05" , ,6 ,"1 time per day" , , , , , , , ,
"LL1001-8" ,"PhenX05_14_30D freq amts","1.3.6.1.4.1.12009.10.1.166","N" , , ,"LA4389-8" ,"97" , ,11 ,"Refused" ,"443390004","Refused (qualifier value)","http://snomed.info/sct","http://snomed.info/sct/900000000000207008/version/20170731","This material includes SNOMED Clinical Terms® (SNOMED CT®) which is used by permission of the International Health Terminology Standards Development Organisation (IHTSDO) under license. All rights reserved. SNOMED CT® was originally created by The College", , ,
"AnswerListId","AnswerListName" ,"AnswerListOID" ,"ExtDefinedYN","ExtDefinedAnswerListCodeSystem","ExtDefinedAnswerListLink" ,"AnswerStringId","LocalAnswerCode","LocalAnswerCodeSystem","SequenceNumber","DisplayText" ,"ExtCodeId","ExtCodeDisplayName" ,"ExtCodeSystem" ,"ExtCodeSystemVersion" ,"ExtCodeSystemCopyrightNotice" ,"SubsequentTextPrompt","Description","Score"
"LL1000-0" ,"PhenX05_13_30D bread amt","1.3.6.1.4.1.12009.10.1.165" ,"N" , , ,"LA13825-7" ,"1" , ,1 ,"1 slice or 1 dinner roll" , , , , , , , ,
"LL1000-0" ,"PhenX05_13_30D bread amt","1.3.6.1.4.1.12009.10.1.165" ,"N" , , ,"LA13838-0" ,"2" , ,2 ,"2 slices or 2 dinner rolls" , , , , , , , ,
"LL1000-0" ,"PhenX05_13_30D bread amt","1.3.6.1.4.1.12009.10.1.165" ,"N" , , ,"LA13892-7" ,"3" , ,3 ,"More than 2 slices or 2 dinner rolls", , , , , , , ,
"LL1001-8" ,"PhenX05_14_30D freq amts","1.3.6.1.4.1.12009.10.1.166" ,"N" , , ,"LA6270-8" ,"00" , ,1 ,"Never" , , , , , , , ,
"LL1001-8" ,"PhenX05_14_30D freq amts","1.3.6.1.4.1.12009.10.1.166" ,"N" , , ,"LA13836-4" ,"01" , ,2 ,"1-3 times per month" , , , , , , , ,
"LL1001-8" ,"PhenX05_14_30D freq amts","1.3.6.1.4.1.12009.10.1.166" ,"N" , , ,"LA13834-9" ,"02" , ,3 ,"1-2 times per week" , , , , , , , ,
"LL1001-8" ,"PhenX05_14_30D freq amts","1.3.6.1.4.1.12009.10.1.166" ,"N" , , ,"LA13853-9" ,"03" , ,4 ,"3-4 times per week" , , , , , , , ,
"LL1001-8" ,"PhenX05_14_30D freq amts","1.3.6.1.4.1.12009.10.1.166" ,"N" , , ,"LA13860-4" ,"04" , ,5 ,"5-6 times per week" , , , , , , , ,
"LL1001-8" ,"PhenX05_14_30D freq amts","1.3.6.1.4.1.12009.10.1.166" ,"N" , , ,"LA13827-3" ,"05" , ,6 ,"1 time per day" , , , , , , , ,
"LL1001-8" ,"PhenX05_14_30D freq amts","1.3.6.1.4.1.12009.10.1.166" ,"N" , , ,"LA4389-8" ,"97" , ,11 ,"Refused" ,"443390004","Refused (qualifier value)","http://snomed.info/sct","http://snomed.info/sct/900000000000207008/version/20170731","This material includes SNOMED Clinical Terms® (SNOMED CT®) which is used by permission of the International Health Terminology Standards Development Organisation (IHTSDO) under license. All rights reserved. SNOMED CT® was originally created by The College", , ,
"LL1892-0" ,"ICD-9_ICD-10" ,"1.3.6.1.4.1.12009.10.1.1069","Y" , ,"http://www.cdc.gov/nchs/icd.htm", , , , , , , , , , , , ,

Can't render this file because it contains an unexpected character in line 1 and column 31.

8
hapi-fhir-server/src/main/java/ca/uhn/fhir/rest/server/interceptor/IServerInterceptor.java
View File

@ -9,9 +9,9 @@ package ca.uhn.fhir.rest.server.interceptor;
* Licensed under the Apache License, Version 2.0 (the "License");
* you may not use this file except in compliance with the License.
* You may obtain a copy of the License at
*
*
* http://www.apache.org/licenses/LICENSE-2.0
*
*
* Unless required by applicable law or agreed to in writing, software
* distributed under the License is distributed on an "AS IS" BASIS,
* WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
@ -262,6 +262,10 @@ public interface IServerInterceptor {
* This method is called after all processing is completed for a request, but only if the
* request completes normally (i.e. no exception is thrown).
* <p>
* This method should not throw any exceptions. Any exception that is thrown by this
* method will be logged, but otherwise not acted upon.
* </p>
* <p>
* Note that this individual interceptors will have this method called in the reverse order from the order in
* which the interceptors were registered with the server.
* </p>

8
hapi-fhir-structures-dstu3/pom.xml
View File

@ -168,6 +168,14 @@
</dependency>
-->
<!-- Used by the validator -->
<dependency>
<groupId>com.github.ben-manes.caffeine</groupId>
<artifactId>caffeine</artifactId>
<optional>true</optional>
</dependency>
<!-- Testing -->
<dependency>
<groupId>org.xmlunit</groupId>

24
hapi-fhir-structures-dstu3/src/main/java/org/hl7/fhir/dstu3/hapi/ctx/HapiWorkerContext.java
View File

@ -1,10 +1,14 @@
package org.hl7.fhir.dstu3.hapi.ctx;
import ca.uhn.fhir.context.FhirContext;
import ca.uhn.fhir.rest.api.Constants;
import ca.uhn.fhir.rest.server.exceptions.InternalErrorException;
import ca.uhn.fhir.rest.server.exceptions.InvalidRequestException;
import ca.uhn.fhir.util.CoverageIgnore;
import com.github.benmanes.caffeine.cache.Cache;
import com.github.benmanes.caffeine.cache.Caffeine;
import org.apache.commons.lang3.Validate;
import org.apache.commons.lang3.time.DateUtils;
import org.hl7.fhir.dstu3.context.IWorkerContext;
import org.hl7.fhir.dstu3.formats.IParser;
import org.hl7.fhir.dstu3.formats.ParserType;
@ -22,13 +26,15 @@ import org.hl7.fhir.exceptions.FHIRException;
import org.hl7.fhir.utilities.validation.ValidationMessage.IssueSeverity;
import java.util.*;
import java.util.concurrent.TimeUnit;
import static org.apache.commons.lang3.StringUtils.isBlank;
import static org.apache.commons.lang3.StringUtils.isNotBlank;
public final class HapiWorkerContext implements IWorkerContext, ValueSetExpander, ValueSetExpanderFactory {
private final FhirContext myCtx;
private Map<String, Resource> myFetchedResourceCache = new HashMap<String, Resource>();
private final Cache<String, Resource> myFetchedResourceCache;
private IValidationSupport myValidationSupport;
private ExpansionProfile myExpansionProfile;
@ -37,6 +43,12 @@ public final class HapiWorkerContext implements IWorkerContext, ValueSetExpander
Validate.notNull(theValidationSupport, "theValidationSupport must not be null");
myCtx = theCtx;
myValidationSupport = theValidationSupport;
long timeoutMillis = 10 * DateUtils.MILLIS_PER_SECOND;
if (System.getProperties().containsKey(Constants.TEST_SYSTEM_PROP_VALIDATION_RESOURCE_CACHES_MS)) {
timeoutMillis = Long.parseLong(System.getProperty(Constants.TEST_SYSTEM_PROP_VALIDATION_RESOURCE_CACHES_MS));
}
myFetchedResourceCache = Caffeine.newBuilder().expireAfterWrite(timeoutMillis, TimeUnit.MILLISECONDS).build();
}
@Override
@ -92,13 +104,9 @@ public final class HapiWorkerContext implements IWorkerContext, ValueSetExpander
return null;
} else {
@SuppressWarnings("unchecked")
T retVal = (T) myFetchedResourceCache.get(theUri);
if (retVal == null) {
retVal = myValidationSupport.fetchResource(myCtx, theClass, theUri);
if (retVal != null) {
myFetchedResourceCache.put(theUri, retVal);
}
}
T retVal = (T) myFetchedResourceCache.get(theUri, t->{
return myValidationSupport.fetchResource(myCtx, theClass, theUri);
});
return retVal;
}
}

78
hapi-fhir-structures-dstu3/src/test/java/ca/uhn/fhir/rest/server/InterceptorDstu3Test.java
View File

@ -156,6 +156,28 @@ public class InterceptorDstu3Test {
assertNotNull(arTypeCapt.getValue().getResource());
}
@Test
public void testExceptionInProcessingCompletedNormally() throws Exception {
ourServlet.setInterceptors(myInterceptor1);
when(myInterceptor1.incomingRequestPreProcessed(nullable(HttpServletRequest.class), nullable(HttpServletResponse.class))).thenReturn(true);
when(myInterceptor1.incomingRequestPostProcessed(nullable(ServletRequestDetails.class), nullable(HttpServletRequest.class), nullable(HttpServletResponse.class))).thenReturn(true);
when(myInterceptor1.outgoingResponse(nullable(ServletRequestDetails.class), nullable(OperationOutcome.class))).thenReturn(true);
when(myInterceptor1.outgoingResponse(nullable(ServletRequestDetails.class), nullable(ResponseDetails.class), nullable(HttpServletRequest.class), nullable(HttpServletResponse.class))).thenReturn(true);
doThrow(new NullPointerException("FOO")).when(myInterceptor1).processingCompletedNormally(any());
String input = createInput();
HttpPost httpPost = new HttpPost("http://localhost:" + ourPort + "/Patient");
httpPost.setEntity(new StringEntity(input, ContentType.create(Constants.CT_FHIR_JSON, "UTF-8")));
HttpResponse status = ourClient.execute(httpPost);
try {
assertEquals(201, status.getStatusLine().getStatusCode());
} finally {
IOUtils.closeQuietly(status.getEntity().getContent());
}
}
@Test
public void testResponseWithNothing() throws Exception {
ourServlet.setInterceptors(myInterceptor1);
@ -229,34 +251,6 @@ public class InterceptorDstu3Test {
i.resourceUpdated(null, null, null);
}
@AfterClass
public static void afterClassClearContext() throws Exception {
ourServer.stop();
TestUtil.clearAllStaticFieldsForUnitTest();
}
@BeforeClass
public static void beforeClass() throws Exception {
ourPort = PortUtil.findFreePort();
ourServer = new Server(ourPort);
DummyPatientResourceProvider patientProvider = new DummyPatientResourceProvider();
ServletHandler proxyHandler = new ServletHandler();
ourServlet = new RestfulServer(ourCtx);
ourServlet.setResourceProviders(patientProvider);
ServletHolder servletHolder = new ServletHolder(ourServlet);
proxyHandler.addServletWithMapping(servletHolder, "/*");
ourServer.setHandler(proxyHandler);
ourServer.start();
PoolingHttpClientConnectionManager connectionManager = new PoolingHttpClientConnectionManager(5000, TimeUnit.MILLISECONDS);
HttpClientBuilder builder = HttpClientBuilder.create();
builder.setConnectionManager(connectionManager);
ourClient = builder.build();
}
public static class DummyPatientResourceProvider implements IResourceProvider {
@Create()
@ -285,4 +279,32 @@ public class InterceptorDstu3Test {
}
@AfterClass
public static void afterClassClearContext() throws Exception {
ourServer.stop();
TestUtil.clearAllStaticFieldsForUnitTest();
}
@BeforeClass
public static void beforeClass() throws Exception {
ourPort = PortUtil.findFreePort();
ourServer = new Server(ourPort);
DummyPatientResourceProvider patientProvider = new DummyPatientResourceProvider();
ServletHandler proxyHandler = new ServletHandler();
ourServlet = new RestfulServer(ourCtx);
ourServlet.setResourceProviders(patientProvider);
ServletHolder servletHolder = new ServletHolder(ourServlet);
proxyHandler.addServletWithMapping(servletHolder, "/*");
ourServer.setHandler(proxyHandler);
ourServer.start();
PoolingHttpClientConnectionManager connectionManager = new PoolingHttpClientConnectionManager(5000, TimeUnit.MILLISECONDS);
HttpClientBuilder builder = HttpClientBuilder.create();
builder.setConnectionManager(connectionManager);
ourClient = builder.build();
}
}

7
hapi-fhir-structures-r4/pom.xml
View File

@ -50,6 +50,13 @@
<optional>true</optional>
</dependency>
<!-- Used by the validator -->
<dependency>
<groupId>com.github.ben-manes.caffeine</groupId>
<artifactId>caffeine</artifactId>
<optional>true</optional>
</dependency>
<!--
Test dependencies on other optional parts of HAPI
-->

31
hapi-fhir-structures-r4/src/main/java/org/hl7/fhir/r4/hapi/ctx/HapiWorkerContext.java
View File

@ -1,11 +1,14 @@
package org.hl7.fhir.r4.hapi.ctx;
import ca.uhn.fhir.context.FhirContext;
import ca.uhn.fhir.context.RuntimeResourceDefinition;
import ca.uhn.fhir.rest.api.Constants;
import ca.uhn.fhir.rest.server.exceptions.InternalErrorException;
import ca.uhn.fhir.rest.server.exceptions.InvalidRequestException;
import ca.uhn.fhir.util.CoverageIgnore;
import com.github.benmanes.caffeine.cache.Cache;
import com.github.benmanes.caffeine.cache.Caffeine;
import org.apache.commons.lang3.Validate;
import org.apache.commons.lang3.time.DateUtils;
import org.fhir.ucum.UcumService;
import org.hl7.fhir.exceptions.FHIRException;
import org.hl7.fhir.exceptions.TerminologyServiceException;
@ -28,13 +31,14 @@ import org.hl7.fhir.utilities.TranslationServices;
import org.hl7.fhir.utilities.validation.ValidationMessage.IssueSeverity;
import java.util.*;
import java.util.concurrent.TimeUnit;
import static org.apache.commons.lang3.StringUtils.isBlank;
import static org.apache.commons.lang3.StringUtils.isNotBlank;
public final class HapiWorkerContext implements IWorkerContext, ValueSetExpander, ValueSetExpanderFactory {
private final FhirContext myCtx;
private Map<String, Resource> myFetchedResourceCache = new HashMap<String, Resource>();
private final Cache<String, Resource> myFetchedResourceCache;
private IValidationSupport myValidationSupport;
private ExpansionProfile myExpansionProfile;
@ -43,6 +47,13 @@ public final class HapiWorkerContext implements IWorkerContext, ValueSetExpander
Validate.notNull(theValidationSupport, "theValidationSupport must not be null");
myCtx = theCtx;
myValidationSupport = theValidationSupport;
long timeoutMillis = 10 * DateUtils.MILLIS_PER_SECOND;
if (System.getProperties().containsKey(ca.uhn.fhir.rest.api.Constants.TEST_SYSTEM_PROP_VALIDATION_RESOURCE_CACHES_MS)) {
timeoutMillis = Long.parseLong(System.getProperty(Constants.TEST_SYSTEM_PROP_VALIDATION_RESOURCE_CACHES_MS));
}
myFetchedResourceCache = Caffeine.newBuilder().expireAfterWrite(timeoutMillis, TimeUnit.MILLISECONDS).build();
}
@Override
@ -206,9 +217,9 @@ public final class HapiWorkerContext implements IWorkerContext, ValueSetExpander
ValueSetExpansionOutcome expandedValueSet = null;
/*
* The following valueset is a special case, since the BCP codesystem is very difficult to expand
*/
/*
* The following valueset is a special case, since the BCP codesystem is very difficult to expand
*/
if (theVs != null && "http://hl7.org/fhir/ValueSet/languages".equals(theVs.getId())) {
ValueSet expansion = new ValueSet();
for (ConceptSetComponent nextInclude : theVs.getCompose().getInclude()) {
@ -338,13 +349,9 @@ public final class HapiWorkerContext implements IWorkerContext, ValueSetExpander
return null;
} else {
@SuppressWarnings("unchecked")
T retVal = (T) myFetchedResourceCache.get(theUri);
if (retVal == null) {
retVal = myValidationSupport.fetchResource(myCtx, theClass, theUri);
if (retVal != null) {
myFetchedResourceCache.put(theUri, (Resource) retVal);
}
}
T retVal = (T) myFetchedResourceCache.get(theUri, t -> {
return myValidationSupport.fetchResource(myCtx, theClass, theUri);
});
return retVal;
}
}

14
hapi-fhir-structures-r4/src/test/java/ca/uhn/fhir/parser/JsonParserR4Test.java
View File

@ -36,6 +36,20 @@ public class JsonParserR4Test {
return b;
}
@Test
public void testDontStripVersions() {
FhirContext ctx = FhirContext.forR4();
ctx.getParserOptions().setDontStripVersionsFromReferencesAtPaths("QuestionnaireResponse.questionnaire");
QuestionnaireResponse qr = new QuestionnaireResponse();
qr.getQuestionnaireElement().setValueAsString("Questionnaire/123/_history/456");
String output = ctx.newJsonParser().setPrettyPrint(true).encodeResourceToString(qr);
ourLog.info(output);
assertThat(output, containsString("\"Questionnaire/123/_history/456\""));
}
/**
* See #814
*/

26
hapi-fhir-validation/src/main/java/org/hl7/fhir/dstu3/hapi/validation/FhirInstanceValidator.java
View File

@ -2,6 +2,7 @@ package org.hl7.fhir.dstu3.hapi.validation;
import ca.uhn.fhir.context.ConfigurationException;
import ca.uhn.fhir.context.FhirContext;
import ca.uhn.fhir.rest.api.Constants;
import ca.uhn.fhir.rest.api.EncodingEnum;
import ca.uhn.fhir.rest.server.exceptions.InternalErrorException;
import ca.uhn.fhir.validation.IValidationContext;
@ -15,6 +16,7 @@ import com.google.gson.JsonObject;
import org.apache.commons.lang3.Validate;
import org.apache.commons.lang3.builder.EqualsBuilder;
import org.apache.commons.lang3.builder.HashCodeBuilder;
import org.apache.commons.lang3.time.DateUtils;
import org.fhir.ucum.UcumService;
import org.hl7.fhir.convertors.VersionConvertor_30_40;
import org.hl7.fhir.dstu3.hapi.ctx.HapiWorkerContext;
@ -272,14 +274,24 @@ public class FhirInstanceValidator extends BaseValidatorBridge implements IValid
private final HapiWorkerContext myWrap;
private final VersionConvertor_30_40 myConverter;
private volatile List<org.hl7.fhir.r4.model.StructureDefinition> myAllStructures;
private LoadingCache<ResourceKey, org.hl7.fhir.r4.model.Resource> myFetchResourceCache
= Caffeine.newBuilder()
.expireAfterWrite(10, TimeUnit.SECONDS)
private LoadingCache<ResourceKey, org.hl7.fhir.r4.model.Resource> myFetchResourceCache;
public WorkerContextWrapper(HapiWorkerContext theWorkerContext) {
myWrap = theWorkerContext;
myConverter = new VersionConvertor_30_40();
long timeoutMillis = 10 * DateUtils.MILLIS_PER_SECOND;
if (System.getProperties().containsKey(ca.uhn.fhir.rest.api.Constants.TEST_SYSTEM_PROP_VALIDATION_RESOURCE_CACHES_MS)) {
timeoutMillis = Long.parseLong(System.getProperty(Constants.TEST_SYSTEM_PROP_VALIDATION_RESOURCE_CACHES_MS));
}
myFetchResourceCache = Caffeine.newBuilder()
.expireAfterWrite(timeoutMillis, TimeUnit.MILLISECONDS)
.maximumSize(10000)
.build(new CacheLoader<ResourceKey, org.hl7.fhir.r4.model.Resource>() {
@Override
public org.hl7.fhir.r4.model.Resource load(FhirInstanceValidator.ResourceKey key) throws Exception {
org.hl7.fhir.dstu3.model.Resource fetched;
public org.hl7.fhir.r4.model.Resource load(ResourceKey key) throws Exception {
Resource fetched;
switch (key.getResourceName()) {
case "StructureDefinition":
fetched = myWrap.fetchResource(StructureDefinition.class, key.getUri());
@ -308,10 +320,6 @@ public class FhirInstanceValidator extends BaseValidatorBridge implements IValid
}
}
});
public WorkerContextWrapper(HapiWorkerContext theWorkerContext) {
myWrap = theWorkerContext;
myConverter = new VersionConvertor_30_40();
}
@Override

7
pom.xml
View File

@ -465,12 +465,13 @@
<name>Ana Maria Radu</name>
<organization>Cerner Corporation</organization>
</developer>
<developer>
<id>jbalbien</id>
</developer>
<developer>
<id>alinleonard</id>
<name>Alin Leonard</name>
<organization>Cerner Corporation</organization>
</developer>
<developer>
<id>jbalbien</id>
</developer>
</developers>

13
src/changes/changes.xml
View File

@ -289,6 +289,19 @@
was never depended on by anyone. Please post on the HAPI FHIR mailing list if this
change affects you.
</action>
<action type="fix">
A crash was fixed when using the ConceptMap/$translate operation to translate a mapping
where the equivalence was not specified.
</action>
<action type="add">
The maximum length for codes in the JPA server terminology service have been increased
to 500 in order to better accomodate code systems with very long codes.
</action>
<action type="fix">
A bug in the DSTU3 validator was fixed where validation resources such as StructureDefinitions
and Questionnaires were cached in a cache that never expired, leading to validations against
stale versions of resources.
</action>
</release>
<release version="3.4.0" date="2018-05-28">
<action type="add">