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Merge branch 'hapifhir:master' into fix_for_5.0.0-snapshot1

This commit is contained in:
Jens Kristian Villadsen 2022-04-29 20:13:42 +02:00 committed by GitHub
parent af3afa8a9d 06030094c8
commit 644b885ebe
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63 changed files with 2873 additions and 191 deletions
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97
hapi-fhir-base/src/main/java/ca/uhn/fhir/context/support/IValidationSupport.java
View File

@ -29,6 +29,7 @@ import org.apache.commons.lang3.Validate;
import org.apache.commons.lang3.builder.EqualsBuilder;
import org.apache.commons.lang3.builder.HashCodeBuilder;
import org.hl7.fhir.instance.model.api.IBase;
import org.hl7.fhir.instance.model.api.IBaseCoding;
import org.hl7.fhir.instance.model.api.IBaseParameters;
import org.hl7.fhir.instance.model.api.IBaseResource;
import org.hl7.fhir.instance.model.api.IPrimitiveType;
@ -806,21 +807,43 @@ public interface IValidationSupport {
class TranslateCodeRequest {
private final String mySourceSystemUrl;
private final String mySourceCode;
private List<IBaseCoding> myCodings;
private final String myTargetSystemUrl;
private final int myHashCode;
private final String myConceptMapUrl;
private final String myConceptMapVersion;
private final String mySourceValueSetUrl;
private final String myTargetValueSetUrl;
private final Long myResourcePid;
private final boolean myReverse;
public TranslateCodeRequest(String theSourceSystemUrl, String theSourceCode, String theTargetSystemUrl) {
mySourceSystemUrl = theSourceSystemUrl;
mySourceCode = theSourceCode;
public TranslateCodeRequest(List<IBaseCoding> theCodings, String theTargetSystemUrl) {
myCodings = theCodings;
myTargetSystemUrl = theTargetSystemUrl;
myConceptMapUrl = null;
myConceptMapVersion = null;
mySourceValueSetUrl = null;
myTargetValueSetUrl = null;
myResourcePid = null;
myReverse = false;
}
myHashCode = new HashCodeBuilder(17, 37)
.append(mySourceSystemUrl)
.append(mySourceCode)
.append(myTargetSystemUrl)
.toHashCode();
public TranslateCodeRequest(
List<IBaseCoding> theCodings,
String theTargetSystemUrl,
String theConceptMapUrl,
String theConceptMapVersion,
String theSourceValueSetUrl,
String theTargetValueSetUrl,
Long theResourcePid,
boolean theReverse) {
myCodings = theCodings;
myTargetSystemUrl = theTargetSystemUrl;
myConceptMapUrl = theConceptMapUrl;
myConceptMapVersion = theConceptMapVersion;
mySourceValueSetUrl = theSourceValueSetUrl;
myTargetValueSetUrl = theTargetValueSetUrl;
myResourcePid = theResourcePid;
myReverse = theReverse;
}
@Override
@ -836,28 +859,62 @@ public interface IValidationSupport {
TranslateCodeRequest that = (TranslateCodeRequest) theO;
return new EqualsBuilder()
.append(mySourceSystemUrl, that.mySourceSystemUrl)
.append(mySourceCode, that.mySourceCode)
.append(myCodings, that.myCodings)
.append(myTargetSystemUrl, that.myTargetSystemUrl)
.append(myConceptMapUrl, that.myConceptMapUrl)
.append(myConceptMapVersion, that.myConceptMapVersion)
.append(mySourceValueSetUrl, that.mySourceValueSetUrl)
.append(myTargetValueSetUrl, that.myTargetValueSetUrl)
.append(myResourcePid, that.myResourcePid)
.append(myReverse, that.myReverse)
.isEquals();
}
@Override
public int hashCode() {
return myHashCode;
return new HashCodeBuilder(17, 37)
.append(myCodings)
.append(myTargetSystemUrl)
.append(myConceptMapUrl)
.append(myConceptMapVersion)
.append(mySourceValueSetUrl)
.append(myTargetValueSetUrl)
.append(myResourcePid)
.append(myReverse)
.toHashCode();
}
public String getSourceSystemUrl() {
return mySourceSystemUrl;
}
public String getSourceCode() {
return mySourceCode;
public List<IBaseCoding> getCodings() {
return myCodings;
}
public String getTargetSystemUrl() {
return myTargetSystemUrl;
}
public String getConceptMapUrl() {
return myConceptMapUrl;
}
public String getConceptMapVersion() {
return myConceptMapVersion;
}
public String getSourceValueSetUrl() {
return mySourceValueSetUrl;
}
public String getTargetValueSetUrl() {
return myTargetValueSetUrl;
}
public Long getResourcePid() {
return myResourcePid;
}
public boolean isReverse() {
return myReverse;
}
}

2
hapi-fhir-base/src/main/java/ca/uhn/fhir/i18n/Msg.java
View File

@ -25,7 +25,7 @@ public final class Msg {
/**
* IMPORTANT: Please update the following comment after you add a new code
* Last code value: 2076
* Last code value: 2078
*/
private Msg() {}

8
hapi-fhir-base/src/main/java/ca/uhn/fhir/rest/api/Constants.java
View File

@ -22,12 +22,7 @@ package ca.uhn.fhir.rest.api;
import java.nio.charset.Charset;
import java.nio.charset.StandardCharsets;
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.*;
import static org.apache.commons.lang3.StringUtils.defaultIfBlank;
@ -217,6 +212,7 @@ public class Constants {
public static final String PARAMQUALIFIER_STRING_EXACT = ":exact";
public static final String PARAMQUALIFIER_TOKEN_TEXT = ":text";
public static final String PARAMQUALIFIER_MDM = ":mdm";
public static final String PARAMQUALIFIER_NICKNAME = ":nickname";
public static final String PARAMQUALIFIER_TOKEN_OF_TYPE = ":of-type";
public static final String PARAMQUALIFIER_TOKEN_NOT = ":not";
public static final int STATUS_HTTP_200_OK = 200;

22
hapi-fhir-base/src/main/java/ca/uhn/fhir/rest/param/StringParam.java
View File

@ -21,9 +21,11 @@ package ca.uhn.fhir.rest.param;
*/
import ca.uhn.fhir.context.FhirContext;
import ca.uhn.fhir.i18n.Msg;
import ca.uhn.fhir.model.api.IQueryParameterType;
import ca.uhn.fhir.model.primitive.StringDt;
import ca.uhn.fhir.rest.api.Constants;
import ca.uhn.fhir.rest.server.exceptions.InvalidRequestException;
import org.apache.commons.lang3.StringUtils;
import org.apache.commons.lang3.builder.EqualsBuilder;
import org.apache.commons.lang3.builder.HashCodeBuilder;
@ -38,7 +40,8 @@ public class StringParam extends BaseParam implements IQueryParameterType {
private boolean myExact;
private String myValue;
private Boolean myMdmExpand;
private Boolean myNicknameExpand;
/**
* Constructor
@ -77,12 +80,12 @@ public class StringParam extends BaseParam implements IQueryParameterType {
return ParameterUtil.escape(myValue);
}
public boolean isMdmExpand() {
return myMdmExpand != null && myMdmExpand;
public boolean isNicknameExpand() {
return myNicknameExpand != null && myNicknameExpand;
}
public StringParam setMdmExpand(boolean theMdmExpand) {
myMdmExpand = theMdmExpand;
public StringParam setNicknameExpand(boolean theNicknameExpand) {
myNicknameExpand = theNicknameExpand;
return this;
}
@ -98,6 +101,15 @@ public class StringParam extends BaseParam implements IQueryParameterType {
@Override
void doSetValueAsQueryToken(FhirContext theContext, String theParamName, String theQualifier, String theValue) {
if (Constants.PARAMQUALIFIER_NICKNAME.equals(theQualifier)) {
if ("name".equals(theParamName) || "given".equals(theParamName)) {
myNicknameExpand = true;
theQualifier = "";
} else {
throw new InvalidRequestException(Msg.code(2077) + "Modifier " + Constants.PARAMQUALIFIER_NICKNAME + " may only be used with 'name' and 'given' search parameters");
}
}
if (Constants.PARAMQUALIFIER_STRING_EXACT.equals(theQualifier)) {
setExact(true);
} else {

17
hapi-fhir-base/src/main/java/ca/uhn/fhir/util/SearchParameterUtil.java
View File

@ -58,8 +58,8 @@ public class SearchParameterUtil {
* 1. Attempt to find one called 'patient'
* 2. If that fails, find one called 'subject'
* 3. If that fails, find find by Patient Compartment.
* 3.1 If that returns >1 result, throw an error
* 3.2 If that returns 1 result, return it
* 3.1 If that returns >1 result, throw an error
* 3.2 If that returns 1 result, return it
*/
public static Optional<RuntimeSearchParam> getOnlyPatientSearchParamForResourceType(FhirContext theFhirContext, String theResourceType) {
RuntimeSearchParam myPatientSearchParam = null;
@ -115,7 +115,7 @@ public class SearchParameterUtil {
*/
public static boolean isResourceTypeInPatientCompartment(FhirContext theFhirContext, String theResourceType) {
RuntimeResourceDefinition runtimeResourceDefinition = theFhirContext.getResourceDefinition(theResourceType);
return getAllPatientCompartmentRuntimeSearchParams(runtimeResourceDefinition).size() > 0;
return getAllPatientCompartmentRuntimeSearchParams(runtimeResourceDefinition).size() > 0;
}
@ -147,4 +147,15 @@ public class SearchParameterUtil {
.map(t -> t.getValueAsString())
.orElse(null);
}
public static String stripModifier(String theSearchParam) {
String retval;
int colonIndex = theSearchParam.indexOf(":");
if (colonIndex == -1) {
retval = theSearchParam;
} else {
retval = theSearchParam.substring(0, colonIndex);
}
return retval;
}
}

3
hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/6_0_0/3442-remote-terminology-translate.yaml Normal file
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@ -0,0 +1,3 @@
type: add
issue: 3442
title: "Provided a Remote Terminology Service implementation for the $translate operation."

3
hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/6_0_0/3534-add-index-on-hfj-resource-table-indexing-multiple-columns.yaml Normal file
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@ -0,0 +1,3 @@
type: add
issue: 3534
title: "Added a new multi-column index on the HFJ_RESOURCE table indexing the columns RES_TYPE, RES_DELETED_AT, RES_UPDATED, PARTITION_ID and RES_ID and removed the existing single-column index on the RES_TYPE column. This new index will improve the performance of the $reindex operation and will be useful for some other queries a well."

5
hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/6_0_0/3534-remove-migration-timeout.yaml Normal file
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@ -0,0 +1,5 @@
type: change
issue: 3534
title: "Ensure that migration steps do not timeout.
Adding an index, and other migration steps can take exceed the default connection timeout.
This has been changed - migration steps now have no timeout and will run until completion."

5
hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/6_0_0/3563-nickname-matching.yaml Normal file
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@ -0,0 +1,5 @@
type: add
issue: 3563
title: "Added search parameter modifier :nickname that can be used with 'name' or 'given' search parameters.
E.g. ?Patient?given:nickname=Kenny will match a patient with the given name Kenneth. Also added MDM matching
algorithm named NICKNAME that matches based this."

4
hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/6_0_0/3569-extend-string-index.yaml Normal file
View File

@ -0,0 +1,4 @@
---
type: change
issue: 3569
title: "The normalized and exact string database indexes have been changed to provide faster string searches."

2
hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/docs/server_jpa/search.md
View File

@ -1,5 +1,7 @@
# JPA Server Search
## Limitations
The HAPI FHIR JPA Server fully implements most [FHIR search](https://www.hl7.org/fhir/search.html) operations for most versions of FHIR. However, there are some known limitations of the current implementation. Here is a partial list of search functionality that is not currently supported in HAPI FHIR:
### Chains within _has

8
hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/docs/server_jpa_mdm/mdm_rules.md
View File

@ -406,6 +406,14 @@ The following algorithms are currently supported:
Match names as strings in any order
</td>
<td>John Henry = John HENRY when exact=false, John Henry != Henry John</td>
</tr>
<tr>
<td>NICKNAME</td>
<td>matcher</td>
<td>
True if one name is a nickname of the other
</td>
<td>Ken = Kenneth, Kenny = Ken. Allen != Allan.</td>
</tr>
<tr>
<td>IDENTIFIER</td>

8
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/config/JpaConfig.java
View File

@ -128,6 +128,7 @@ import ca.uhn.fhir.jpa.search.warm.CacheWarmingSvcImpl;
import ca.uhn.fhir.jpa.search.warm.ICacheWarmingSvc;
import ca.uhn.fhir.jpa.searchparam.config.SearchParamConfig;
import ca.uhn.fhir.jpa.searchparam.extractor.IResourceLinkResolver;
import ca.uhn.fhir.jpa.searchparam.nickname.NicknameInterceptor;
import ca.uhn.fhir.jpa.searchparam.registry.ISearchParamProvider;
import ca.uhn.fhir.jpa.sp.ISearchParamPresenceSvc;
import ca.uhn.fhir.jpa.sp.SearchParamPresenceSvcImpl;
@ -164,6 +165,7 @@ import org.springframework.scheduling.concurrent.ConcurrentTaskScheduler;
import org.springframework.scheduling.concurrent.ScheduledExecutorFactoryBean;
import javax.annotation.Nullable;
import java.io.IOException;
import java.util.Date;
/*
@ -827,4 +829,10 @@ public class JpaConfig {
public MemberMatcherR4Helper memberMatcherR4Helper(FhirContext theFhirContext) {
return new MemberMatcherR4Helper(theFhirContext);
}
@Lazy
@Bean
public NicknameInterceptor nicknameInterceptor() throws IOException {
return new NicknameInterceptor();
}
}

44
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/FulltextSearchSvcImpl.java
View File

@ -36,6 +36,8 @@ import ca.uhn.fhir.jpa.model.search.ExtendedLuceneIndexData;
import ca.uhn.fhir.jpa.search.autocomplete.ValueSetAutocompleteOptions;
import ca.uhn.fhir.jpa.search.autocomplete.ValueSetAutocompleteSearch;
import ca.uhn.fhir.jpa.search.builder.ISearchQueryExecutor;
import ca.uhn.fhir.jpa.search.builder.SearchQueryExecutors;
import ca.uhn.fhir.jpa.search.builder.sql.SearchQueryExecutor;
import ca.uhn.fhir.jpa.searchparam.SearchParameterMap;
import ca.uhn.fhir.jpa.searchparam.extractor.ISearchParamExtractor;
import ca.uhn.fhir.jpa.searchparam.extractor.ResourceIndexedSearchParams;
@ -47,7 +49,9 @@ import ca.uhn.fhir.rest.server.util.ISearchParamRegistry;
import ca.uhn.fhir.rest.server.util.ResourceSearchParams;
import org.hibernate.search.backend.elasticsearch.ElasticsearchExtension;
import org.hibernate.search.engine.search.query.SearchScroll;
import org.hibernate.search.engine.search.query.dsl.SearchQueryOptionsStep;
import org.hibernate.search.mapper.orm.Search;
import org.hibernate.search.mapper.orm.search.loading.dsl.SearchLoadingOptionsStep;
import org.hibernate.search.mapper.orm.session.SearchSession;
import org.hibernate.search.mapper.orm.work.SearchIndexingPlan;
import org.hibernate.search.util.common.SearchException;
@ -132,14 +136,34 @@ public class FulltextSearchSvcImpl implements IFulltextSearchSvc {
private ISearchQueryExecutor doSearch(String theResourceType, SearchParameterMap theParams, ResourcePersistentId theReferencingPid) {
// keep this in sync with supportsSomeOf();
SearchSession session = getSearchSession();
if (theParams.getOffset() != null && theParams.getOffset() != 0) {
// perform an offset search instead of a scroll one, which doesn't allow for offset
List<Long> queryFetchResult = getSearchQueryOptionsStep(
theResourceType, theParams, theReferencingPid).fetchHits(theParams.getOffset(), theParams.getCount());
// indicate param was already processed, otherwise queries DB to process it
theParams.setOffset(null);
return SearchQueryExecutors.from(queryFetchResult);
}
SearchScroll<Long> esResult = getSearchScroll(theResourceType, theParams, theReferencingPid);
return new SearchScrollQueryExecutorAdaptor(esResult);
}
private SearchScroll<Long> getSearchScroll(String theResourceType, SearchParameterMap theParams, ResourcePersistentId theReferencingPid) {
int scrollSize = 50;
if (theParams.getCount()!=null) {
scrollSize = theParams.getCount();
}
SearchScroll<Long> esResult = session.search(ResourceTable.class)
return getSearchQueryOptionsStep(theResourceType, theParams, theReferencingPid).scroll(scrollSize);
}
private SearchQueryOptionsStep<?, Long, SearchLoadingOptionsStep, ?, ?> getSearchQueryOptionsStep(
String theResourceType, SearchParameterMap theParams, ResourcePersistentId theReferencingPid) {
return getSearchSession().search(ResourceTable.class)
// The document id is the PK which is pid. We use this instead of _myId to avoid fetching the doc body.
.select(
// adapt the String docRef.id() to the Long that it really is.
@ -188,11 +212,11 @@ public class FulltextSearchSvcImpl implements IFulltextSearchSvc {
//DROP EARLY HERE IF BOOL IS EMPTY?
})
).scroll(scrollSize);
return new SearchScrollQueryExecutorAdaptor(esResult);
);
}
@Nonnull
private SearchSession getSearchSession() {
return Search.session(myEntityManager);
@ -314,4 +338,14 @@ public class FulltextSearchSvcImpl implements IFulltextSearchSvc {
.map(p -> p.toResource(parser))
.collect(Collectors.toList());
}
@Override
public long count(String theResourceName, SearchParameterMap theParams) {
SearchQueryOptionsStep<?, Long, SearchLoadingOptionsStep, ?, ?> queryOptionsStep =
getSearchQueryOptionsStep(theResourceName, theParams, null);
return queryOptionsStep.fetchTotalHitCount();
}
}

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

@ -45,6 +45,7 @@ public interface IFulltextSearchSvc {
*/
List<ResourcePersistentId> search(String theResourceName, SearchParameterMap theParams);
/**
* Query the index for a scrollable iterator of results.
* No max size to the result iterator.
@ -90,4 +91,8 @@ public interface IFulltextSearchSvc {
*/
List<IBaseResource> getResources(Collection<Long> thePids);
/**
* Returns accurate hit count
*/
long count(String theResourceName, SearchParameterMap theParams);
}

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

@ -41,7 +41,7 @@ public interface ISearchBuilder {
IResultIterator createQuery(SearchParameterMap theParams, SearchRuntimeDetails theSearchRuntime, RequestDetails theRequest, @Nonnull RequestPartitionId theRequestPartitionId);
Iterator<Long> createCountQuery(SearchParameterMap theParams, String theSearchUuid, RequestDetails theRequest, RequestPartitionId theRequestPartitionId);
Long createCountQuery(SearchParameterMap theParams, String theSearchUuid, RequestDetails theRequest, RequestPartitionId theRequestPartitionId);
void setMaxResultsToFetch(Integer theMaxResultsToFetch);

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

@ -227,14 +227,14 @@ public class LegacySearchBuilder implements ISearchBuilder {
}
@Override
public Iterator<Long> createCountQuery(SearchParameterMap theParams, String theSearchUuid, RequestDetails theRequest, @Nonnull RequestPartitionId theRequestPartitionId) {
public Long createCountQuery(SearchParameterMap theParams, String theSearchUuid, RequestDetails theRequest, @Nonnull RequestPartitionId theRequestPartitionId) {
assert theRequestPartitionId != null;
assert TransactionSynchronizationManager.isActualTransactionActive();
init(theParams, theSearchUuid, theRequestPartitionId);
List<TypedQuery<Long>> queries = createQuery(null, null, null, true, theRequest, null);
return new CountQueryIterator(queries.get(0));
return new CountQueryIterator(queries.get(0)).next();
}
/**

11
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/dstu3/FhirResourceDaoConceptMapDstu3.java
View File

@ -20,6 +20,7 @@ package ca.uhn.fhir.jpa.dao.dstu3;
* #L%
*/
import ca.uhn.fhir.context.support.IValidationSupport;
import ca.uhn.fhir.i18n.Msg;
import ca.uhn.fhir.context.support.TranslateConceptResults;
import ca.uhn.fhir.jpa.api.dao.IFhirResourceDaoConceptMap;
@ -38,19 +39,19 @@ import org.hl7.fhir.exceptions.FHIRException;
import org.hl7.fhir.instance.model.api.IBaseResource;
import org.springframework.beans.factory.annotation.Autowired;
import java.util.Collections;
import java.util.Date;
public class FhirResourceDaoConceptMapDstu3 extends BaseHapiFhirResourceDao<ConceptMap> implements IFhirResourceDaoConceptMap<ConceptMap> {
@Autowired
private ITermConceptMappingSvc myTermConceptMappingSvc;
@Autowired
private IValidationSupport myValidationSupport;
@Override
public TranslateConceptResults translate(TranslationRequest theTranslationRequest, RequestDetails theRequestDetails) {
if (theTranslationRequest.hasReverse() && theTranslationRequest.getReverseAsBoolean()) {
return myTermConceptMappingSvc.translateWithReverse(theTranslationRequest);
}
return myTermConceptMappingSvc.translate(theTranslationRequest);
IValidationSupport.TranslateCodeRequest translateCodeRequest = theTranslationRequest.asTranslateCodeRequest();
return myValidationSupport.translateConcept(translateCodeRequest);
}

16
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/r4/FhirResourceDaoConceptMapR4.java
View File

@ -20,6 +20,7 @@ package ca.uhn.fhir.jpa.dao.r4;
* #L%
*/
import ca.uhn.fhir.context.support.IValidationSupport;
import ca.uhn.fhir.context.support.TranslateConceptResults;
import ca.uhn.fhir.jpa.api.dao.IFhirResourceDaoConceptMap;
import ca.uhn.fhir.jpa.api.model.TranslationRequest;
@ -29,23 +30,28 @@ import ca.uhn.fhir.jpa.model.entity.ResourceTable;
import ca.uhn.fhir.jpa.term.api.ITermConceptMappingSvc;
import ca.uhn.fhir.rest.api.server.RequestDetails;
import ca.uhn.fhir.rest.api.server.storage.TransactionDetails;
import org.hl7.fhir.instance.model.api.IBase;
import org.hl7.fhir.instance.model.api.IBaseCoding;
import org.hl7.fhir.instance.model.api.IBaseResource;
import org.hl7.fhir.r4.model.CodeableConcept;
import org.hl7.fhir.r4.model.Coding;
import org.hl7.fhir.r4.model.ConceptMap;
import org.springframework.beans.factory.annotation.Autowired;
import java.util.Collections;
import java.util.Date;
import java.util.List;
public class FhirResourceDaoConceptMapR4 extends BaseHapiFhirResourceDao<ConceptMap> implements IFhirResourceDaoConceptMap<ConceptMap> {
@Autowired
private ITermConceptMappingSvc myTermConceptMappingSvc;
@Autowired
private IValidationSupport myValidationSupport;
@Override
public TranslateConceptResults translate(TranslationRequest theTranslationRequest, RequestDetails theRequestDetails) {
if (theTranslationRequest.hasReverse() && theTranslationRequest.getReverseAsBoolean()) {
return myTermConceptMappingSvc.translateWithReverse(theTranslationRequest);
}
return myTermConceptMappingSvc.translate(theTranslationRequest);
IValidationSupport.TranslateCodeRequest translateCodeRequest = theTranslationRequest.asTranslateCodeRequest();
return myValidationSupport.translateConcept(translateCodeRequest);
}
@Override

11
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/r5/FhirResourceDaoConceptMapR5.java
View File

@ -20,6 +20,7 @@ package ca.uhn.fhir.jpa.dao.r5;
* #L%
*/
import ca.uhn.fhir.context.support.IValidationSupport;
import ca.uhn.fhir.context.support.TranslateConceptResults;
import ca.uhn.fhir.jpa.api.dao.IFhirResourceDaoConceptMap;
import ca.uhn.fhir.jpa.api.model.TranslationRequest;
@ -35,19 +36,19 @@ import org.hl7.fhir.instance.model.api.IBaseResource;
import org.hl7.fhir.r5.model.ConceptMap;
import org.springframework.beans.factory.annotation.Autowired;
import java.util.Collections;
import java.util.Date;
public class FhirResourceDaoConceptMapR5 extends BaseHapiFhirResourceDao<ConceptMap> implements IFhirResourceDaoConceptMap<ConceptMap> {
@Autowired
private ITermConceptMappingSvc myTermConceptMappingSvc;
@Autowired
private IValidationSupport myValidationSupport;
@Override
public TranslateConceptResults translate(TranslationRequest theTranslationRequest, RequestDetails theRequestDetails) {
if (theTranslationRequest.hasReverse() && theTranslationRequest.getReverseAsBoolean()) {
return myTermConceptMappingSvc.translateWithReverse(theTranslationRequest);
}
return myTermConceptMappingSvc.translate(theTranslationRequest);
IValidationSupport.TranslateCodeRequest translateCodeRequest = theTranslationRequest.asTranslateCodeRequest();
return myValidationSupport.translateConcept(translateCodeRequest);
}
@Override

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

@ -102,6 +102,7 @@ public class ExtendedLuceneSearchBuilder {
case EMPTY_MODIFIER:
return true;
case Constants.PARAMQUALIFIER_MDM:
case Constants.PARAMQUALIFIER_NICKNAME:
default:
return false;
}

24
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/interceptor/MdmSearchExpandingInterceptor.java
View File

@ -30,13 +30,11 @@ import ca.uhn.fhir.mdm.log.Logs;
import ca.uhn.fhir.model.api.IQueryParameterType;
import ca.uhn.fhir.model.primitive.IdDt;
import ca.uhn.fhir.rest.param.ReferenceParam;
import ca.uhn.fhir.rest.param.StringParam;
import ca.uhn.fhir.rest.param.TokenParam;
import org.hl7.fhir.instance.model.api.IIdType;
import org.slf4j.Logger;
import org.springframework.beans.factory.annotation.Autowired;
import java.lang.reflect.Constructor;
import java.util.ArrayList;
import java.util.List;
import java.util.Map;
@ -92,7 +90,7 @@ public class MdmSearchExpandingInterceptor {
// If we failed, attempt to expand as a golden resource
if (expandedResourceIds.isEmpty()) {
expandedResourceIds = myMdmLinkExpandSvc.expandMdmByGoldenResourceId(new IdDt(refParam.getValue()));
expandedResourceIds = myMdmLinkExpandSvc.expandMdmByGoldenResourceId(new IdDt(refParam.getValue()));
}
//Rebuild the search param list.
@ -104,8 +102,7 @@ public class MdmSearchExpandingInterceptor {
.forEach(toAdd::add);
}
}
}
else if (theParamName.equalsIgnoreCase("_id")) {
} else if (theParamName.equalsIgnoreCase("_id")) {
expandIdParameter(iQueryParameterType, toAdd, toRemove);
}
}
@ -117,6 +114,7 @@ public class MdmSearchExpandingInterceptor {
/**
* Expands out the provided _id parameter into all the various
* ids of linked resources.
*
* @param theIdParameter
* @param theAddList
* @param theRemoveList
@ -130,29 +128,21 @@ public class MdmSearchExpandingInterceptor {
IIdType id;
Creator<? extends IQueryParameterType> creator;
boolean mdmExpand = false;
if (theIdParameter instanceof StringParam) {
StringParam param = (StringParam) theIdParameter;
mdmExpand = param.isMdmExpand();
id = new IdDt(param.getValue());
creator = StringParam::new;
}
else if (theIdParameter instanceof TokenParam) {
if (theIdParameter instanceof TokenParam) {
TokenParam param = (TokenParam) theIdParameter;
mdmExpand = param.isMdmExpand();
id = new IdDt(param.getValue());
creator = TokenParam::new;
}
else {
} else {
creator = null;
id = null;
}
if (id == null || creator == null) {
if (id == null) {
// in case the _id paramter type is different from the above
ourLog.warn("_id parameter of incorrect type. Expected StringParam or TokenParam, but got {}. No expansion will be done!",
theIdParameter.getClass().getSimpleName());
}
else if (mdmExpand) {
} else if (mdmExpand) {
ourLog.debug("_id parameter must be expanded out from: {}", id.getValue());
Set<String> expandedResourceIds = myMdmLinkExpandSvc.expandMdmBySourceResourceId(id);

40
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/migrate/tasks/HapiFhirJpaMigrationTasks.java
View File

@ -295,6 +295,46 @@ public class HapiFhirJpaMigrationTasks extends BaseMigrationTasks<VersionEnum> {
version
.onTable("HFJ_BLK_EXPORT_JOB").modifyColumn("20220423.1", "EXP_TIME").nullable().withType(ColumnTypeEnum.DATE_TIMESTAMP);
// New Index on HFJ_RESOURCE for $reindex Operation - hapi-fhir #3534
{
version.onTable("HFJ_RESOURCE")
.addIndex("20220425.1", "IDX_RES_TYPE_DEL_UPDATED")
.unique(false)
.online(true)
.withColumns("RES_TYPE", "RES_DELETED_AT", "RES_UPDATED", "PARTITION_ID", "RES_ID");
// Drop existing Index on HFJ_RESOURCE.RES_TYPE since the new Index will meet the overall Index Demand
version
.onTable("HFJ_RESOURCE")
.dropIndexOnline("20220425.2", "IDX_RES_TYPE");
}
/**
* Update string indexing
* @see ca.uhn.fhir.jpa.search.builder.predicate.StringPredicateBuilder
* @see ResourceIndexedSearchParamString
*/
{
Builder.BuilderWithTableName tokenTable = version.onTable("HFJ_SPIDX_STRING");
// add res_id, and partition_id so queries are covered without row-reads.
tokenTable
.addIndex("20220428.1", "IDX_SP_STRING_HASH_NRM_V2")
.unique(false)
.online(true)
.withColumns("HASH_NORM_PREFIX", "SP_VALUE_NORMALIZED", "RES_ID", "PARTITION_ID");
tokenTable.dropIndexOnline("20220428.2", "IDX_SP_STRING_HASH_NRM");
tokenTable
.addIndex("20220428.3", "IDX_SP_STRING_HASH_EXCT_V2")
.unique(false)
.online(true)
.withColumns("HASH_EXACT", "RES_ID", "PARTITION_ID");
tokenTable.dropIndexOnline("20220428.4", "IDX_SP_STRING_HASH_EXCT");
// we will drop the updated column. Start with the index.
tokenTable.dropIndexOnline("20220428.5", "IDX_SP_STRING_UPDATED");
}
}
/**

8
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/search/SearchCoordinatorSvcImpl.java
View File

@ -508,6 +508,7 @@ public class SearchCoordinatorSvcImpl implements ISearchCoordinatorSvc {
return candidate.orElse(null);
}
private IBundleProvider executeQuery(String theResourceType, SearchParameterMap theParams, RequestDetails theRequestDetails, String theSearchUuid, ISearchBuilder theSb, Integer theLoadSynchronousUpTo, RequestPartitionId theRequestPartitionId) {
SearchRuntimeDetails searchRuntimeDetails = new SearchRuntimeDetails(theRequestDetails, theSearchUuid);
searchRuntimeDetails.setLoadSynchronous(true);
@ -533,12 +534,11 @@ public class SearchCoordinatorSvcImpl implements ISearchCoordinatorSvc {
List<List<IQueryParameterType>> contentAndTerms = theParams.get(Constants.PARAM_CONTENT);
List<List<IQueryParameterType>> textAndTerms = theParams.get(Constants.PARAM_TEXT);
Iterator<Long> countIterator = theSb.createCountQuery(theParams, theSearchUuid, theRequestDetails, theRequestPartitionId);
count = theSb.createCountQuery(theParams, theSearchUuid, theRequestDetails, theRequestPartitionId);
if (contentAndTerms != null) theParams.put(Constants.PARAM_CONTENT, contentAndTerms);
if (textAndTerms != null) theParams.put(Constants.PARAM_TEXT, textAndTerms);
count = countIterator.next();
ourLog.trace("Got count {}", count);
}
@ -1233,8 +1233,8 @@ public class SearchCoordinatorSvcImpl implements ISearchCoordinatorSvc {
* we will have to clone those parameters here so that
* the "correct" params are used in createQuery below
*/
Iterator<Long> countIterator = sb.createCountQuery(myParams.clone(), mySearch.getUuid(), myRequest, myRequestPartitionId);
Long count = countIterator.hasNext() ? countIterator.next() : 0L;
Long count = sb.createCountQuery(myParams.clone(), mySearch.getUuid(), myRequest, myRequestPartitionId);
ourLog.trace("Got count {}", count);
TransactionTemplate txTemplate = new TransactionTemplate(myManagedTxManager);

40
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/search/builder/SearchBuilder.java
View File

@ -75,6 +75,7 @@ import ca.uhn.fhir.model.valueset.BundleEntrySearchModeEnum;
import ca.uhn.fhir.rest.api.Constants;
import ca.uhn.fhir.rest.api.RestSearchParameterTypeEnum;
import ca.uhn.fhir.rest.api.SearchContainedModeEnum;
import ca.uhn.fhir.rest.api.SearchTotalModeEnum;
import ca.uhn.fhir.rest.api.SortOrderEnum;
import ca.uhn.fhir.rest.api.SortSpec;
import ca.uhn.fhir.rest.api.server.IPreResourceAccessDetails;
@ -97,6 +98,7 @@ import com.google.common.collect.Streams;
import com.healthmarketscience.sqlbuilder.Condition;
import org.apache.commons.lang3.Validate;
import org.apache.commons.lang3.math.NumberUtils;
import org.apache.jena.sparql.engine.QueryIterator;
import org.hl7.fhir.instance.model.api.IAnyResource;
import org.hl7.fhir.instance.model.api.IBaseResource;
import org.slf4j.Logger;
@ -119,6 +121,7 @@ import javax.persistence.criteria.From;
import javax.persistence.criteria.Predicate;
import javax.persistence.criteria.Root;
import java.util.ArrayList;
import java.util.Arrays;
import java.util.Collection;
import java.util.Collections;
import java.util.HashMap;
@ -271,18 +274,24 @@ public class SearchBuilder implements ISearchBuilder {
@SuppressWarnings("ConstantConditions")
@Override
public Iterator<Long> createCountQuery(SearchParameterMap theParams, String theSearchUuid, RequestDetails theRequest, @Nonnull RequestPartitionId theRequestPartitionId) {
public Long createCountQuery(SearchParameterMap theParams, String theSearchUuid,
RequestDetails theRequest, @Nonnull RequestPartitionId theRequestPartitionId) {
assert theRequestPartitionId != null;
assert TransactionSynchronizationManager.isActualTransactionActive();
init(theParams, theSearchUuid, theRequestPartitionId);
List<ISearchQueryExecutor> queries = createQuery(myParams, null, null, null, true, theRequest, null);
if (queries.isEmpty()) {
return Collections.emptyIterator();
if (checkUseHibernateSearch()) {
long count = myFulltextSearchSvc.count(myResourceName, theParams.clone());
return count;
}
try (ISearchQueryExecutor queryExecutor = queries.get(0)) {
return Lists.newArrayList(queryExecutor.next()).iterator();
List<ISearchQueryExecutor> queries = createQuery(theParams.clone(), null, null, null, true, theRequest, null);
if (queries.isEmpty()) {
return 0L;
} else {
return queries.get(0).next();
}
}
@ -309,6 +318,7 @@ public class SearchBuilder implements ISearchBuilder {
return new QueryIterator(theSearchRuntimeDetails, theRequest);
}
private void init(SearchParameterMap theParams, String theSearchUuid, RequestPartitionId theRequestPartitionId) {
myCriteriaBuilder = myEntityManager.getCriteriaBuilder();
myParams = theParams;
@ -316,7 +326,7 @@ public class SearchBuilder implements ISearchBuilder {
myRequestPartitionId = theRequestPartitionId;
}
private List<ISearchQueryExecutor> createQuery(SearchParameterMap theParams, SortSpec sort, Integer theOffset, Integer theMaximumResults, boolean theCount, RequestDetails theRequest,
private List<ISearchQueryExecutor> createQuery(SearchParameterMap theParams, SortSpec sort, Integer theOffset, Integer theMaximumResults, boolean theCountOnlyFlag, RequestDetails theRequest,
SearchRuntimeDetails theSearchRuntimeDetails) {
ArrayList<ISearchQueryExecutor> queries = new ArrayList<>();
@ -359,8 +369,6 @@ public class SearchBuilder implements ISearchBuilder {
!fulltextExecutor.hasNext() ||
// Our hibernate search query doesn't respect partitions yet
(!myPartitionSettings.isPartitioningEnabled() &&
// we don't support _count=0 yet.
!theCount &&
// were there AND terms left? Then we still need the db.
theParams.isEmpty() &&
// not every param is a param. :-(
@ -382,11 +390,11 @@ public class SearchBuilder implements ISearchBuilder {
// We break the pids into chunks that fit in the 1k limit for jdbc bind params.
// wipmb change chunk to take iterator
new QueryChunker<Long>()
.chunk(Streams.stream(fulltextExecutor).collect(Collectors.toList()), t -> doCreateChunkedQueries(theParams, t, theOffset, sort, theCount, theRequest, queries));
.chunk(Streams.stream(fulltextExecutor).collect(Collectors.toList()), t -> doCreateChunkedQueries(theParams, t, theOffset, sort, theCountOnlyFlag, theRequest, queries));
}
} else {
// do everything in the database.
Optional<SearchQueryExecutor> query = createChunkedQuery(theParams, sort, theOffset, theMaximumResults, theCount, theRequest, null);
Optional<SearchQueryExecutor> query = createChunkedQuery(theParams, sort, theOffset, theMaximumResults, theCountOnlyFlag, theRequest, null);
query.ifPresent(queries::add);
}
@ -408,7 +416,7 @@ public class SearchBuilder implements ISearchBuilder {
}
// TODO MB someday we'll want a query planner to figure out if we _should_ or _must_ use the ft index, not just if we can.
return fulltextEnabled &&
return fulltextEnabled && myParams != null &&
myParams.getSearchContainedMode() == SearchContainedModeEnum.FALSE &&
myFulltextSearchSvc.supportsSomeOf(myParams);
}
@ -506,9 +514,9 @@ public class SearchBuilder implements ISearchBuilder {
}
}
private Optional<SearchQueryExecutor> createChunkedQuery(SearchParameterMap theParams, SortSpec sort, Integer theOffset, Integer theMaximumResults, boolean theCount, RequestDetails theRequest, List<Long> thePidList) {
private Optional<SearchQueryExecutor> createChunkedQuery(SearchParameterMap theParams, SortSpec sort, Integer theOffset, Integer theMaximumResults, boolean theCountOnlyFlag, RequestDetails theRequest, List<Long> thePidList) {
String sqlBuilderResourceName = myParams.getEverythingMode() == null ? myResourceName : null;
SearchQueryBuilder sqlBuilder = new SearchQueryBuilder(myContext, myDaoConfig.getModelConfig(), myPartitionSettings, myRequestPartitionId, sqlBuilderResourceName, mySqlBuilderFactory, myDialectProvider, theCount);
SearchQueryBuilder sqlBuilder = new SearchQueryBuilder(myContext, myDaoConfig.getModelConfig(), myPartitionSettings, myRequestPartitionId, sqlBuilderResourceName, mySqlBuilderFactory, myDialectProvider, theCountOnlyFlag);
QueryStack queryStack3 = new QueryStack(theParams, myDaoConfig, myDaoConfig.getModelConfig(), myContext, sqlBuilder, mySearchParamRegistry, myPartitionSettings);
if (theParams.keySet().size() > 1 || theParams.getSort() != null || theParams.keySet().contains(Constants.PARAM_HAS) || isPotentiallyContainedReferenceParameterExistsAtRoot(theParams)) {
@ -533,7 +541,7 @@ public class SearchBuilder implements ISearchBuilder {
// is basically a reverse-include search. For type/Everything (as opposed to instance/Everything)
// the one problem with this approach is that it doesn't catch Patients that have absolutely
// nothing linked to them. So we do one additional query to make sure we catch those too.
SearchQueryBuilder fetchPidsSqlBuilder = new SearchQueryBuilder(myContext, myDaoConfig.getModelConfig(), myPartitionSettings, myRequestPartitionId, myResourceName, mySqlBuilderFactory, myDialectProvider, theCount);
SearchQueryBuilder fetchPidsSqlBuilder = new SearchQueryBuilder(myContext, myDaoConfig.getModelConfig(), myPartitionSettings, myRequestPartitionId, myResourceName, mySqlBuilderFactory, myDialectProvider, theCountOnlyFlag);
GeneratedSql allTargetsSql = fetchPidsSqlBuilder.generate(theOffset, myMaxResultsToFetch);
String sql = allTargetsSql.getSql();
Object[] args = allTargetsSql.getBindVariables().toArray(new Object[0]);
@ -613,7 +621,7 @@ public class SearchBuilder implements ISearchBuilder {
* finds the appropriate resources) in an outer search which is then sorted
*/
if (sort != null) {
assert !theCount;
assert !theCountOnlyFlag;
createSort(queryStack3, sort);
}

16
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/term/TermConceptMappingSvcImpl.java
View File

@ -47,6 +47,8 @@ import org.apache.commons.lang3.StringUtils;
import org.hibernate.ScrollMode;
import org.hibernate.ScrollableResults;
import org.hl7.fhir.exceptions.FHIRException;
import org.hl7.fhir.instance.model.api.IBase;
import org.hl7.fhir.instance.model.api.IBaseCoding;
import org.hl7.fhir.r4.model.BooleanType;
import org.hl7.fhir.r4.model.CodeType;
import org.hl7.fhir.r4.model.CodeableConcept;
@ -118,16 +120,10 @@ public class TermConceptMappingSvcImpl implements ITermConceptMappingSvc {
@Override
@Transactional
public TranslateConceptResults translateConcept(TranslateCodeRequest theRequest) {
CodeableConcept sourceCodeableConcept = new CodeableConcept();
sourceCodeableConcept
.addCoding()
.setSystem(theRequest.getSourceSystemUrl())
.setCode(theRequest.getSourceCode());
TranslationRequest request = new TranslationRequest();
request.setCodeableConcept(sourceCodeableConcept);
request.setTargetSystem(new UriType(theRequest.getTargetSystemUrl()));
TranslationRequest request = TranslationRequest.fromTranslateCodeRequest(theRequest);
if (request.hasReverse() && request.getReverseAsBoolean()) {
return translateWithReverse(request);
}
return translate(request);
}

4
hapi-fhir-jpaserver-mdm/src/main/java/ca/uhn/fhir/jpa/mdm/svc/MdmSearchParamSvc.java
View File

@ -31,6 +31,7 @@ import ca.uhn.fhir.jpa.searchparam.MatchUrlService;
import ca.uhn.fhir.jpa.searchparam.SearchParameterMap;
import ca.uhn.fhir.jpa.searchparam.extractor.SearchParamExtractorService;
import ca.uhn.fhir.rest.server.util.ISearchParamRegistry;
import ca.uhn.fhir.util.SearchParameterUtil;
import org.apache.commons.lang3.StringUtils;
import org.hl7.fhir.instance.model.api.IBaseResource;
import org.springframework.beans.factory.annotation.Autowired;
@ -61,7 +62,8 @@ public class MdmSearchParamSvc {
public List<String> getValueFromResourceForSearchParam(IBaseResource theResource, String theSearchParam) {
String resourceType = myFhirContext.getResourceType(theResource);
RuntimeSearchParam activeSearchParam = mySearchParamRegistry.getActiveSearchParam(resourceType, theSearchParam);
String searchParam = SearchParameterUtil.stripModifier(theSearchParam);
RuntimeSearchParam activeSearchParam = mySearchParamRegistry.getActiveSearchParam(resourceType, searchParam);
return mySearchParamExtractorService.extractParamValuesAsStrings(activeSearchParam, theResource);
}

179
hapi-fhir-jpaserver-mdm/src/test/java/ca/uhn/fhir/jpa/mdm/provider/MdmProviderMatchR4Test.java
View File

@ -15,6 +15,7 @@ import org.junit.jupiter.api.Test;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import java.io.IOException;
import java.util.List;
import java.util.stream.Collectors;
@ -161,68 +162,134 @@ public class MdmProviderMatchR4Test extends BaseProviderR4Test {
public void testMatchWithCoarseDateGranularity() throws Exception {
setMdmRuleJson("mdm/coarse-birthdate-mdm-rules.json");
String granularPatient = "{\n" +
" \"resourceType\": \"Patient\",\n" +
" \"active\": true,\n" +
" \"name\": [\n" +
" {\n" +
" \"family\": \"PETERSON\",\n" +
" \"given\": [\n" +
" \"GARY\",\n" +
" \"D\"\n" +
" ]\n" +
" }\n" +
" ],\n" +
" \"telecom\": [\n" +
" {\n" +
" \"system\": \"phone\",\n" +
" \"value\": \"100100100\",\n" +
" \"use\": \"home\"\n" +
" }\n" +
" ],\n" +
" \"gender\": \"male\",\n" +
" \"birthDate\": \"1991-10-10\",\n" +
" \"address\": [\n" +
" {\n" +
" \"state\": \"NY\",\n" +
" \"postalCode\": \"12313\"\n" +
" }\n" +
" ]\n" +
"}";
String granularPatient = """
{
"resourceType": "Patient",
"active": true,
"name": [
{
"family": "PETERSON",
"given": [
"GARY",
"D"
]
}
],
"telecom": [
{
"system": "phone",
"value": "100100100",
"use": "home"
}
],
"gender": "male",
"birthDate": "1991-10-10",
"address": [
{
"state": "NY",
"postalCode": "12313"
}
]
}""";
IBaseResource iBaseResource = myFhirContext.newJsonParser().parseResource(granularPatient);
createPatient((Patient) iBaseResource);
String coarsePatient = "{\n" +
" \"resourceType\": \"Patient\",\n" +
" \"active\": true,\n" +
" \"name\": [\n" +
" {\n" +
" \"family\": \"PETERSON\",\n" +
" \"given\": [\n" +
" \"GARY\",\n" +
" \"D\"\n" +
" ]\n" +
" }\n" +
" ],\n" +
" \"telecom\": [\n" +
" {\n" +
" \"system\": \"phone\",\n" +
" \"value\": \"100100100\",\n" +
" \"use\": \"home\"\n" +
" }\n" +
" ],\n" +
" \"gender\": \"male\",\n" +
" \"birthDate\": \"1991-10\",\n" +
" \"address\": [\n" +
" {\n" +
" \"state\": \"NY\",\n" +
" \"postalCode\": \"12313\"\n" +
" }\n" +
" ]\n" +
"}";
String coarsePatient = """
{
"resourceType": "Patient",
"active": true,
"name": [
{
"family": "PETERSON",
"given": [
"GARY",
"D"
]
}
],
"telecom": [
{
"system": "phone",
"value": "100100100",
"use": "home"
}
],
"gender": "male",
"birthDate": "1991-10",
"address": [
{
"state": "NY",
"postalCode": "12313"
}
]
}""";
IBaseResource coarseResource = myFhirContext.newJsonParser().parseResource(coarsePatient);
Bundle result = (Bundle) myMdmProvider.match((Patient) coarseResource, new SystemRequestDetails());
assertEquals(1, result.getEntry().size());
}
@Test
public void testNicknameMatch() throws IOException {
setMdmRuleJson("mdm/nickname-mdm-rules.json");
String formalPatientJson = """
{
"resourceType": "Patient",
"active": true,
"name": [
{
"family": "PETERSON",
"given": [
"Gregory"
]
}
],
"gender": "male"
}""";
Patient formalPatient = (Patient) myFhirContext.newJsonParser().parseResource(formalPatientJson);
createPatient(formalPatient);
String noMatchPatientJson = """
{
"resourceType": "Patient",
"active": true,
"name": [
{
"family": "PETERSON",
"given": [
"Bob"
]
}
],
"gender": "male"
}""";
Patient noMatchPatient = (Patient) myFhirContext.newJsonParser().parseResource(noMatchPatientJson);
createPatient(noMatchPatient);
{
Bundle result = (Bundle) myMdmProvider.match(noMatchPatient, new SystemRequestDetails());
assertEquals(0, result.getEntry().size());
}
String nickPatientJson = """
{
"resourceType": "Patient",
"active": true,
"name": [
{
"family": "PETERSON",
"given": [
"Greg"
]
}
],
"gender": "male"
}""";
{
Patient nickPatient = (Patient) myFhirContext.newJsonParser().parseResource(nickPatientJson);
Bundle result = (Bundle) myMdmProvider.match(nickPatient, new SystemRequestDetails());
assertEquals(1, result.getEntry().size());
}
}
}

2
hapi-fhir-jpaserver-mdm/src/test/java/ca/uhn/fhir/jpa/mdm/svc/MdmCandidateSearchCriteriaBuilderSvcTest.java
View File

@ -1,8 +1,8 @@
package ca.uhn.fhir.jpa.mdm.svc;
import ca.uhn.fhir.mdm.rules.json.MdmResourceSearchParamJson;
import ca.uhn.fhir.jpa.mdm.BaseMdmR4Test;
import ca.uhn.fhir.jpa.mdm.svc.candidate.MdmCandidateSearchCriteriaBuilderSvc;
import ca.uhn.fhir.mdm.rules.json.MdmResourceSearchParamJson;
import org.hl7.fhir.r4.model.HumanName;
import org.hl7.fhir.r4.model.Patient;
import org.junit.jupiter.api.Test;

57
hapi-fhir-jpaserver-mdm/src/test/java/ca/uhn/fhir/jpa/mdm/svc/MdmCandidateSearchSvcIT.java
View File

@ -4,15 +4,21 @@ import ca.uhn.fhir.interceptor.model.RequestPartitionId;
import ca.uhn.fhir.jpa.mdm.BaseMdmR4Test;
import ca.uhn.fhir.jpa.mdm.svc.candidate.MdmCandidateSearchSvc;
import ca.uhn.fhir.jpa.mdm.svc.candidate.TooManyCandidatesException;
import ca.uhn.fhir.jpa.searchparam.MatchUrlService;
import ca.uhn.fhir.jpa.searchparam.SearchParameterMap;
import ca.uhn.fhir.jpa.searchparam.nickname.NicknameInterceptor;
import ca.uhn.fhir.mdm.rules.config.MdmSettings;
import ca.uhn.fhir.rest.api.server.IBundleProvider;
import org.hl7.fhir.instance.model.api.IAnyResource;
import org.hl7.fhir.r4.model.Patient;
import org.hl7.fhir.r4.model.Practitioner;
import org.hl7.fhir.r4.model.Reference;
import org.junit.jupiter.api.AfterEach;
import org.junit.jupiter.api.BeforeEach;
import org.junit.jupiter.api.Test;
import org.springframework.beans.factory.annotation.Autowired;
import java.io.IOException;
import java.util.Collection;
import java.util.Collections;
import java.util.Date;
@ -28,10 +34,21 @@ public class MdmCandidateSearchSvcIT extends BaseMdmR4Test {
MdmCandidateSearchSvc myMdmCandidateSearchSvc;
@Autowired
MdmSettings myMdmSettings;
@Autowired
MatchUrlService myMatchUrlService;
private NicknameInterceptor myNicknameInterceptor;
@BeforeEach
public void before() throws IOException {
myNicknameInterceptor = new NicknameInterceptor();
myInterceptorRegistry.registerInterceptor(myNicknameInterceptor);
}
@AfterEach
public void resetMdmSettings() {
myMdmSettings.setCandidateSearchLimit(MdmSettings.DEFAULT_CANDIDATE_SEARCH_LIMIT);
myInterceptorRegistry.unregisterInterceptor(myNicknameInterceptor);
}
@Test
@ -43,6 +60,42 @@ public class MdmCandidateSearchSvcIT extends BaseMdmR4Test {
assertEquals(1, result.size());
}
@Test
public void testNickname() {
Practitioner formal = new Practitioner();
formal.getNameFirstRep().addGiven("William");
formal.getNameFirstRep().setFamily("Shatner");
formal.setActive(true);
myPractitionerDao.create(formal);
{
// First confirm we can search for this practitioner using a nickname search
SearchParameterMap map = myMatchUrlService.getResourceSearch("Practitioner?given:nickname=Bill&family=Shatner").getSearchParameterMap();
map.setLoadSynchronous(true);
IBundleProvider result = myPractitionerDao.search(map);
assertEquals(1, result.size());
Practitioner first = (Practitioner) result.getResources(0, 1).get(0);
assertEquals("William", first.getNameFirstRep().getGivenAsSingleString());
}
{
// Now achieve the same match via mdm
Practitioner nick = new Practitioner();
nick.getNameFirstRep().addGiven("Bill");
nick.getNameFirstRep().setFamily("Shatner");
Collection<IAnyResource> result = myMdmCandidateSearchSvc.findCandidates("Practitioner", nick, RequestPartitionId.allPartitions());
assertEquals(1, result.size());
}
{
// Should not match Bob
Practitioner noMatch = new Practitioner();
noMatch.getNameFirstRep().addGiven("Bob");
noMatch.getNameFirstRep().setFamily("Shatner");
Collection<IAnyResource> result = myMdmCandidateSearchSvc.findCandidates("Practitioner", noMatch, RequestPartitionId.allPartitions());
assertEquals(0, result.size());
}
}
@Test
public void findCandidatesMultipleMatchesDoNotCauseDuplicates() {
@ -83,9 +136,9 @@ public class MdmCandidateSearchSvcIT extends BaseMdmR4Test {
Patient newJane = buildJanePatient();
createActivePatient();
assertEquals(1, runInTransaction(()->myMdmCandidateSearchSvc.findCandidates("Patient", newJane, RequestPartitionId.allPartitions()).size()));
assertEquals(1, runInTransaction(() -> myMdmCandidateSearchSvc.findCandidates("Patient", newJane, RequestPartitionId.allPartitions()).size()));
createActivePatient();
assertEquals(2, runInTransaction(()->myMdmCandidateSearchSvc.findCandidates("Patient", newJane, RequestPartitionId.allPartitions()).size()));
assertEquals(2, runInTransaction(() -> myMdmCandidateSearchSvc.findCandidates("Patient", newJane, RequestPartitionId.allPartitions()).size()));
try {
createActivePatient();

7
hapi-fhir-jpaserver-mdm/src/test/resources/mdm/mdm-rules.json
View File

@ -25,6 +25,13 @@
"searchParams": [
"general-practitioner"
]
},
{
"resourceType": "Practitioner",
"searchParams": [
"given:nickname",
"family"
]
}
],
"candidateFilterSearchParams": [

44
hapi-fhir-jpaserver-mdm/src/test/resources/mdm/nickname-mdm-rules.json Normal file
View File

@ -0,0 +1,44 @@
{
"version":"1",
"mdmTypes": ["Patient", "Practitioner"],
"candidateSearchParams":[
{
"resourceType": "*",
"searchParams": [
"given:nickname",
"family"
]
}
],
"candidateFilterSearchParams":[],
"matchFields":[
{
"name":"gender",
"resourceType":"Patient",
"resourcePath":"gender",
"matcher":{
"algorithm":"STRING"
}
},
{
"name":"nickname",
"resourceType":"*",
"resourcePath":"name.given",
"matcher":{
"algorithm":"NICKNAME"
}
},
{
"name":"lastname",
"resourceType":"*",
"resourcePath":"name.family",
"matcher":{
"algorithm":"STRING",
"exact": true
}
}
],
"matchResultMap":{
"nickname,lastname": "MATCH"
}
}

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

@ -59,10 +59,9 @@ import static org.apache.commons.lang3.StringUtils.defaultString;
// This is used for sorting, and for :contains queries currently
@Index(name = "IDX_SP_STRING_HASH_IDENT", columnList = "HASH_IDENTITY"),
@Index(name = "IDX_SP_STRING_HASH_NRM", columnList = "HASH_NORM_PREFIX,SP_VALUE_NORMALIZED"),
@Index(name = "IDX_SP_STRING_HASH_EXCT", columnList = "HASH_EXACT"),
@Index(name = "IDX_SP_STRING_HASH_NRM_V2", columnList = "HASH_NORM_PREFIX,SP_VALUE_NORMALIZED,RES_ID,PARTITION_ID"),
@Index(name = "IDX_SP_STRING_HASH_EXCT_V2", columnList = "HASH_EXACT,RES_ID,PARTITION_ID"),
@Index(name = "IDX_SP_STRING_UPDATED", columnList = "SP_UPDATED"),
@Index(name = "IDX_SP_STRING_RESID", columnList = "RES_ID")
})
public class ResourceIndexedSearchParamString extends BaseResourceIndexedSearchParam {

4
hapi-fhir-jpaserver-model/src/main/java/ca/uhn/fhir/jpa/model/entity/ResourceTable.java
View File

@ -73,9 +73,9 @@ import java.util.stream.Collectors;
@Indexed(routingBinder= @RoutingBinderRef(type = ResourceTableRoutingBinder.class))
@Entity
@Table(name = "HFJ_RESOURCE", uniqueConstraints = {}, indexes = {
// Do not reuse previously used index name: IDX_INDEXSTATUS
// Do not reuse previously used index name: IDX_INDEXSTATUS, IDX_RES_TYPE
@Index(name = "IDX_RES_DATE", columnList = "RES_UPDATED"),
@Index(name = "IDX_RES_TYPE", columnList = "RES_TYPE"),
@Index(name = "IDX_RES_TYPE_DEL_UPDATED", columnList = "RES_TYPE,RES_DELETED_AT,RES_UPDATED,PARTITION_ID,RES_ID"),
})
@NamedEntityGraph(name = "Resource.noJoins")
public class ResourceTable extends BaseHasResource implements Serializable, IBasePersistedResource, IResourceLookup {

10
hapi-fhir-jpaserver-searchparam/src/main/java/ca/uhn/fhir/jpa/searchparam/MatchUrlService.java
View File

@ -33,6 +33,7 @@ import ca.uhn.fhir.model.api.Include;
import ca.uhn.fhir.rest.api.Constants;
import ca.uhn.fhir.rest.api.QualifiedParamList;
import ca.uhn.fhir.rest.api.RestSearchParameterTypeEnum;
import ca.uhn.fhir.rest.api.SearchTotalModeEnum;
import ca.uhn.fhir.rest.param.DateRangeParam;
import ca.uhn.fhir.rest.param.ParameterUtil;
import ca.uhn.fhir.rest.server.exceptions.InvalidRequestException;
@ -113,6 +114,15 @@ public class MatchUrlService {
throw new InvalidRequestException(Msg.code(485) + "Invalid " + Constants.PARAM_COUNT + " value: " + intString);
}
}
} else if (Constants.PARAM_SEARCH_TOTAL_MODE.equals(nextParamName)) {
if (paramList != null && ! paramList.isEmpty() && ! paramList.get(0).isEmpty()) {
String totalModeEnumStr = paramList.get(0).get(0);
try {
paramMap.setSearchTotalMode(SearchTotalModeEnum.valueOf(totalModeEnumStr));
} catch (IllegalArgumentException e) {
throw new InvalidRequestException(Msg.code(2078) + "Invalid " + Constants.PARAM_SEARCH_TOTAL_MODE + " value: " + totalModeEnumStr);
}
}
} else if (Constants.PARAM_OFFSET.equals(nextParamName)) {
if (paramList != null && paramList.size() > 0 && paramList.get(0).size() > 0) {
String intString = paramList.get(0).get(0);

67
hapi-fhir-jpaserver-searchparam/src/main/java/ca/uhn/fhir/jpa/searchparam/nickname/NicknameInterceptor.java Normal file
View File

@ -0,0 +1,67 @@
package ca.uhn.fhir.jpa.searchparam.nickname;
import ca.uhn.fhir.interceptor.api.Hook;
import ca.uhn.fhir.interceptor.api.Pointcut;
import ca.uhn.fhir.jpa.searchparam.SearchParameterMap;
import ca.uhn.fhir.model.api.IQueryParameterType;
import ca.uhn.fhir.rest.param.StringParam;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import java.io.IOException;
import java.util.ArrayList;
import java.util.List;
import java.util.Locale;
import java.util.Map;
public class NicknameInterceptor {
private static final Logger ourLog = LoggerFactory.getLogger(NicknameInterceptor.class);
private final NicknameSvc myNicknameSvc;
public NicknameInterceptor() throws IOException {
myNicknameSvc = new NicknameSvc();
}
@Hook(Pointcut.STORAGE_PRESEARCH_REGISTERED)
public void expandNicknames(SearchParameterMap theSearchParameterMap) {
for (Map.Entry<String, List<List<IQueryParameterType>>> set : theSearchParameterMap.entrySet()) {
String paramName = set.getKey();
List<List<IQueryParameterType>> andList = set.getValue();
for (List<IQueryParameterType> orList : andList) {
// here we will know if it's an _id param or not
// from theSearchParameterMap.keySet()
expandAnyNicknameParameters(paramName, orList);
}
}
}
/**
* If a Parameter is a string parameter, and it has been set to expand Nicknames, perform the expansion.
*/
private void expandAnyNicknameParameters(String theParamName, List<IQueryParameterType> orList) {
List<IQueryParameterType> toAdd = new ArrayList<>();
List<IQueryParameterType> toRemove = new ArrayList<>();
for (IQueryParameterType iQueryParameterType : orList) {
if (iQueryParameterType instanceof StringParam) {
StringParam stringParam = (StringParam) iQueryParameterType;
if (stringParam.isNicknameExpand()) {
ourLog.debug("Found a nickname parameter to expand: {} {}", theParamName, stringParam);
toRemove.add(stringParam);
//First, attempt to expand as a formal name
String name = stringParam.getValue().toLowerCase(Locale.ROOT);
List<String> expansions = myNicknameSvc.getEquivalentNames(name);
if (expansions == null) {
continue;
}
ourLog.debug("Parameter has been expanded to: {} {}", theParamName, String.join(", ", expansions));
expansions.stream()
.map(StringParam::new)
.forEach(toAdd::add);
}
}
}
orList.removeAll(toRemove);
orList.addAll(toAdd);
}
}

47
hapi-fhir-jpaserver-searchparam/src/main/java/ca/uhn/fhir/jpa/searchparam/nickname/NicknameMap.java Normal file
View File

@ -0,0 +1,47 @@
package ca.uhn.fhir.jpa.searchparam.nickname;
import java.io.BufferedReader;
import java.io.IOException;
import java.io.Reader;
import java.util.ArrayList;
import java.util.Arrays;
import java.util.HashMap;
import java.util.List;
import java.util.Map;
class NicknameMap {
private final Map<String, List<String>> myFormalToNick = new HashMap<>();
private final Map<String, List<String>> myNicknameToFormal = new HashMap<>();
void load(Reader theReader) throws IOException {
try (BufferedReader reader = new BufferedReader(theReader)) {
String line;
while ((line = reader.readLine()) != null) {
String[] parts = line.split(",");
String key = parts[0];
List<String> values = new ArrayList<>(Arrays.asList(parts).subList(1, parts.length));
add(key, values);
}
}
}
private void add(String theKey, List<String> theValues) {
myFormalToNick.put(theKey, theValues);
for (String value : theValues) {
myNicknameToFormal.putIfAbsent(value, new ArrayList<>());
myNicknameToFormal.get(value).add(theKey);
}
}
int size() {
return myFormalToNick.size();
}
List<String> getNicknamesFromFormalNameOrNull(String theName) {
return myFormalToNick.get(theName);
}
List<String> getFormalNamesFromNicknameOrNull(String theNickname) {
return myNicknameToFormal.get(theNickname);
}
}

53
hapi-fhir-jpaserver-searchparam/src/main/java/ca/uhn/fhir/jpa/searchparam/nickname/NicknameSvc.java Normal file
View File

@ -0,0 +1,53 @@
package ca.uhn.fhir.jpa.searchparam.nickname;
import org.springframework.core.io.ClassPathResource;
import org.springframework.core.io.Resource;
import java.io.IOException;
import java.io.InputStream;
import java.io.InputStreamReader;
import java.io.Reader;
import java.util.ArrayList;
import java.util.List;
public class NicknameSvc {
private final NicknameMap myNicknameMap = new NicknameMap();
public NicknameSvc() throws IOException {
Resource nicknameCsvResource = new ClassPathResource("/nickname/names.csv");
try (InputStream inputStream = nicknameCsvResource.getInputStream()) {
try (Reader reader = new InputStreamReader(inputStream)) {
myNicknameMap.load(reader);
}
}
}
public int size() {
return myNicknameMap.size();
}
public List<String> getEquivalentNames(String theName) {
List<String> retval = new ArrayList<>();
retval.add(theName);
List<String> expansions;
expansions = getNicknamesFromFormalNameOrNull(theName);
if (expansions != null) {
retval.addAll(expansions);
} else {
expansions = getFormalNamesFromNicknameOrNull(theName);
if (expansions != null) {
retval.addAll(expansions);
}
}
return retval;
}
List<String> getNicknamesFromFormalNameOrNull(String theName) {
return myNicknameMap.getNicknamesFromFormalNameOrNull(theName);
}
List<String> getFormalNamesFromNicknameOrNull(String theNickname) {
return myNicknameMap.getFormalNamesFromNicknameOrNull(theNickname);
}
}

201
hapi-fhir-jpaserver-searchparam/src/main/resources/nickname/License.txt Normal file
View File

@ -0,0 +1,201 @@
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12
hapi-fhir-jpaserver-searchparam/src/main/resources/nickname/README.md Normal file
View File

@ -0,0 +1,12 @@
# nickname-and-diminutive-names-lookup
A simple CSV file containing US given names (first name) and their associated nicknames or diminutive names.
This lookup file was initially created by mining this
<a href="http://www.caagri.org/nicknames.html">genealogy page</a>. Because the lookup originates from a dataset used for genealogy purposes there are old names that aren't commonly used these days, but there are recent ones as well. Examples are "gregory", "greg", or "geoffrey", "geoff". There was also a significant effort to make it machine readable, i.e. separate it with commas, remove human conventions, like "rickie(y)" would need to be made into two different names "rickie", and "ricky".
There are Java, Perl, Python, and R parsers provided for convenience.
This is a relatively large list with roughly 1600 names. Any help from people to clean this list up and add to it is greatly appreciated.
This project was created by <a href="http://www.odu.edu/">Old Dominion University</a> - <a href="http://ws-dl.blogspot.com/">Web Science and Digital Libraries Research Group</a>. More information about the creation of this lookup can be found <a href="https://ws-dl.blogspot.com/2010/08/lookup-for-nicknames-and-diminutive.html">here</a>.

2
hapi-fhir-jpaserver-searchparam/src/main/resources/nickname/README.txt Normal file
View File

@ -0,0 +1,2 @@
The files in this folder were cloned from https://github.com/carltonnorthern/nickname-and-diminutive-names-lookup

1084
hapi-fhir-jpaserver-searchparam/src/main/resources/nickname/names.csv Normal file
View File

File diff suppressed because it is too large Load Diff

59
hapi-fhir-jpaserver-searchparam/src/test/java/ca/uhn/fhir/jpa/searchparam/nickname/NicknameInterceptorTest.java Normal file
View File

@ -0,0 +1,59 @@
package ca.uhn.fhir.jpa.searchparam.nickname;
import ca.uhn.fhir.jpa.searchparam.SearchParameterMap;
import ca.uhn.fhir.rest.param.StringParam;
import org.junit.jupiter.api.Test;
import java.io.IOException;
import static org.junit.jupiter.api.Assertions.assertEquals;
class NicknameInterceptorTest {
@Test
public void testExpandForward() throws IOException {
// setup
String formalName = "kenneth";
SearchParameterMap sp = new SearchParameterMap();
sp.add("name", new StringParam(formalName).setNicknameExpand(true));
NicknameInterceptor svc = new NicknameInterceptor();
// execute
svc.expandNicknames(sp);
// verify
String newSearch = sp.toNormalizedQueryString(null);
assertEquals("?name=ken,kendrick,kenneth,kenny", newSearch);
}
@Test
public void testExpandBackward() throws IOException {
// setup
String nickname = "ken";
SearchParameterMap sp = new SearchParameterMap();
sp.add("name", new StringParam(nickname).setNicknameExpand(true));
NicknameInterceptor svc = new NicknameInterceptor();
// execute
svc.expandNicknames(sp);
// verify
String newSearch = sp.toNormalizedQueryString(null);
assertEquals("?name=ken,kendall,kendrick,kendrik,kenneth,kenny,kent,mckenna", newSearch);
}
@Test
public void testNothingToExpand() throws IOException {
// setup
String unusualName = "X Æ A-12";
SearchParameterMap sp = new SearchParameterMap();
sp.add("name", new StringParam(unusualName).setNicknameExpand(true));
NicknameInterceptor svc = new NicknameInterceptor();
// execute
svc.expandNicknames(sp);
// verify
String newSearch = sp.toNormalizedQueryString(null);
assertEquals("?name=x%20%C3%A6%20a-12", newSearch);
}
}

30
hapi-fhir-jpaserver-searchparam/src/test/java/ca/uhn/fhir/jpa/searchparam/nickname/NicknameMapTest.java Normal file
View File

@ -0,0 +1,30 @@
package ca.uhn.fhir.jpa.searchparam.nickname;
import org.junit.jupiter.api.Test;
import java.io.IOException;
import java.io.StringReader;
import static org.hamcrest.MatcherAssert.assertThat;
import static org.hamcrest.Matchers.containsInAnyOrder;
import static org.junit.jupiter.api.Assertions.assertEquals;
class NicknameMapTest {
@Test
public void testLoad() throws IOException {
String testData = """
kendall,ken,kenny
kendra,kenj,kenji,kay,kenny
kendrick,ken,kenny
kendrik,ken,kenny
kenneth,ken,kenny,kendrick
kenny,ken,kenneth
kent,ken,kenny,kendrick
""";
NicknameMap map = new NicknameMap();
map.load(new StringReader(testData));
assertEquals(7, map.size());
assertThat(map.getNicknamesFromFormalNameOrNull("kenneth"), containsInAnyOrder("ken", "kenny", "kendrick"));
assertThat(map.getFormalNamesFromNicknameOrNull("ken"), containsInAnyOrder("kendall", "kendrick", "kendrik", "kenneth", "kenny", "kent"));
}
}

15
hapi-fhir-jpaserver-searchparam/src/test/java/ca/uhn/fhir/jpa/searchparam/nickname/NicknameSvcTest.java Normal file
View File

@ -0,0 +1,15 @@
package ca.uhn.fhir.jpa.searchparam.nickname;
import org.junit.jupiter.api.Test;
import java.io.IOException;
import static org.junit.jupiter.api.Assertions.assertEquals;
class NicknameSvcTest {
@Test
public void testReadfile() throws IOException {
NicknameSvc nicknameSvc = new NicknameSvc();
assertEquals(1082, nicknameSvc.size());
}
}

7
hapi-fhir-jpaserver-test-utilities/src/test/java/ca/uhn/fhir/jpa/dao/TestDaoSearch.java
View File

@ -19,6 +19,7 @@ import org.springframework.web.util.UriComponentsBuilder;
import javax.annotation.Nonnull;
import java.util.List;
import java.util.stream.Collectors;
/**
* Simplistic implementation of FHIR queries.
@ -51,11 +52,13 @@ public class TestDaoSearch {
return result.getAllResources();
}
public List<String> searchForIds(String theQueryUrl) {
public List<String> searchForIds(String theQueryUrl) {
// fake out the server url parsing
IBundleProvider result = searchForBundleProvider(theQueryUrl);
List<String> resourceIds = result.getAllResourceIds();
// getAllResources is not safe as size is not always set
List<String> resourceIds = result.getResources(0, Integer.MAX_VALUE)
.stream().map(resource -> resource.getIdElement().getIdPart()).collect(Collectors.toList());
return resourceIds;
}

6
hapi-fhir-jpaserver-test-utilities/src/test/java/ca/uhn/fhir/jpa/dao/r4/FhirResourceDaoR4ConceptMapTest.java
View File

@ -12,6 +12,7 @@ import ca.uhn.fhir.jpa.test.BaseJpaR4Test;
import org.hl7.fhir.instance.model.api.IIdType;
import org.hl7.fhir.r4.model.CanonicalType;
import org.hl7.fhir.r4.model.CodeableConcept;
import org.hl7.fhir.r4.model.Coding;
import org.hl7.fhir.r4.model.ConceptMap;
import org.hl7.fhir.r4.model.Enumerations.ConceptMapEquivalence;
import org.hl7.fhir.r4.model.Enumerations.PublicationStatus;
@ -30,6 +31,7 @@ import org.springframework.transaction.support.TransactionTemplate;
import javax.annotation.Nonnull;
import java.io.IOException;
import java.util.Collections;
import java.util.HashSet;
import java.util.List;
import java.util.Optional;
@ -1139,7 +1141,9 @@ public class FhirResourceDaoR4ConceptMapTest extends BaseJpaR4Test {
});
List<TranslateConceptResult> translationResults = myValidationSupport.translateConcept(new IValidationSupport.TranslateCodeRequest("http://source", "source1", "http://target")).getResults();
CodeableConcept sourceCodeableConcept = new CodeableConcept();
sourceCodeableConcept.addCoding(new Coding("http://source", "source1", null));
List<TranslateConceptResult> translationResults = myValidationSupport.translateConcept(new IValidationSupport.TranslateCodeRequest(Collections.unmodifiableList(sourceCodeableConcept.getCoding()), "http://target")).getResults();
assertThat(translationResults.toString(), translationResults, hasItem(
new TranslateConceptResult()
.setSystem("http://target")

93
hapi-fhir-jpaserver-test-utilities/src/test/java/ca/uhn/fhir/jpa/dao/r4/FhirResourceDaoR4SearchWithElasticSearchIT.java
View File

@ -30,6 +30,7 @@ import ca.uhn.fhir.jpa.test.config.TestR4Config;
import ca.uhn.fhir.parser.DataFormatException;
import ca.uhn.fhir.parser.IParser;
import ca.uhn.fhir.rest.api.Constants;
import ca.uhn.fhir.rest.api.SearchTotalModeEnum;
import ca.uhn.fhir.rest.api.server.IBundleProvider;
import ca.uhn.fhir.rest.api.server.storage.ResourcePersistentId;
import ca.uhn.fhir.rest.param.ReferenceParam;
@ -45,6 +46,7 @@ import ca.uhn.fhir.test.utilities.LogbackLevelOverrideExtension;
import ca.uhn.fhir.test.utilities.docker.RequiresDocker;
import ca.uhn.fhir.validation.FhirValidator;
import ca.uhn.fhir.validation.ValidationResult;
import com.google.common.collect.Lists;
import org.hamcrest.Matchers;
import org.hl7.fhir.instance.model.api.IBaseCoding;
import org.hl7.fhir.instance.model.api.IBaseResource;
@ -71,6 +73,8 @@ import org.junit.jupiter.api.Nested;
import org.junit.jupiter.api.Test;
import org.junit.jupiter.api.extension.ExtendWith;
import org.junit.jupiter.api.extension.RegisterExtension;
import org.junit.jupiter.params.ParameterizedTest;
import org.junit.jupiter.params.provider.EnumSource;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.beans.factory.annotation.Qualifier;
import org.springframework.test.annotation.DirtiesContext;
@ -84,8 +88,11 @@ import org.springframework.transaction.PlatformTransactionManager;
import javax.persistence.EntityManager;
import java.io.IOException;
import java.time.Month;
import java.util.ArrayList;
import java.util.Arrays;
import java.util.List;
import java.util.function.Consumer;
import java.util.stream.Collectors;
import static ca.uhn.fhir.jpa.model.util.UcumServiceUtil.UCUM_CODESYSTEM_URL;
@ -99,6 +106,7 @@ import static org.hamcrest.Matchers.hasSize;
import static org.hamcrest.Matchers.not;
import static org.hamcrest.Matchers.stringContainsInOrder;
import static org.junit.jupiter.api.Assertions.assertEquals;
import static org.junit.jupiter.api.Assertions.assertFalse;
import static org.junit.jupiter.api.Assertions.assertThrows;
import static org.junit.jupiter.api.Assertions.assertTrue;
@ -1472,9 +1480,9 @@ public class FhirResourceDaoR4SearchWithElasticSearchIT extends BaseJpaTest {
}
private IIdType withObservationWithQuantity(double theValue, String theSystem, String theCode) {
myResourceId = myTestDataBuilder.createObservation(
myResourceId = myTestDataBuilder.createObservation(asArray(
myTestDataBuilder.withQuantityAtPath("valueQuantity", theValue, theSystem, theCode)
);
));
return myResourceId;
}
@ -1490,6 +1498,87 @@ public class FhirResourceDaoR4SearchWithElasticSearchIT extends BaseJpaTest {
}
@Nested
public class TotalParameter {
@ParameterizedTest
@EnumSource(SearchTotalModeEnum.class)
public void totalParamSkipsSql(SearchTotalModeEnum theTotalModeEnum) {
myTestDataBuilder.createObservation(asArray(myTestDataBuilder.withObservationCode("http://example.com/", "theCode")));
myCaptureQueriesListener.clear();
myTestDaoSearch.searchForIds("Observation?code=theCode&_total=" + theTotalModeEnum);
myCaptureQueriesListener.logSelectQueriesForCurrentThread();
assertEquals(1, myCaptureQueriesListener.getSelectQueriesForCurrentThread().size(), "bundle was built with no sql");
}
@Test
public void totalIsCorrect() {
myTestDataBuilder.createObservation(asArray(myTestDataBuilder.withObservationCode("http://example.com/", "code-1")));
myTestDataBuilder.createObservation(asArray(myTestDataBuilder.withObservationCode("http://example.com/", "code-2")));
myTestDataBuilder.createObservation(asArray(myTestDataBuilder.withObservationCode("http://example.com/", "code-3")));
IBundleProvider resultBundle = myTestDaoSearch.searchForBundleProvider("Observation?_total=" + SearchTotalModeEnum.ACCURATE);
assertEquals(3, resultBundle.size());
}
}
@Nested
public class OffsetParameter {
@BeforeEach
public void enableResourceStorage() {
myDaoConfig.setStoreResourceInLuceneIndex(true);
}
@Test
public void offsetNoCount() {
myTestDataBuilder.createObservation(asArray(myTestDataBuilder.withObservationCode("http://example.com/", "code-1")));
IIdType idCode2 = myTestDataBuilder.createObservation(asArray(myTestDataBuilder.withObservationCode("http://example.com/", "code-2")));
IIdType idCode3 = myTestDataBuilder.createObservation(asArray(myTestDataBuilder.withObservationCode("http://example.com/", "code-3")));
myCaptureQueriesListener.clear();
List<String> resultIds = myTestDaoSearch.searchForIds("Observation?code=code-1,code-2,code-3&_offset=1");
myCaptureQueriesListener.logSelectQueriesForCurrentThread();
assertThat(resultIds, containsInAnyOrder(idCode2.getIdPart(), idCode3.getIdPart()));
// make also sure no extra SQL queries were executed
assertEquals(0, myCaptureQueriesListener.getSelectQueriesForCurrentThread().size(), "bundle was built with no sql");
}
@Test
public void offsetAndCount() {
myTestDataBuilder.createObservation(asArray(myTestDataBuilder.withObservationCode("http://example.com/", "code-1")));
IIdType idCode2 = myTestDataBuilder.createObservation(asArray(myTestDataBuilder.withObservationCode("http://example.com/", "code-2")));
myTestDataBuilder.createObservation(asArray(myTestDataBuilder.withObservationCode("http://example.com/", "code-3")));
myCaptureQueriesListener.clear();
List<String> resultIds = myTestDaoSearch.searchForIds("Observation?code=code-1,code-2,code-3&_offset=1&_count=1");
myCaptureQueriesListener.logSelectQueriesForCurrentThread();
assertThat(resultIds, containsInAnyOrder(idCode2.getIdPart()));
// also validate no extra SQL queries were executed
assertEquals(0, myCaptureQueriesListener.getSelectQueriesForCurrentThread().size(), "bundle was built with no sql");
}
}
private Consumer<IBaseResource>[] asArray(Consumer<IBaseResource> theIBaseResourceConsumer) {
@SuppressWarnings("unchecked")
Consumer<IBaseResource>[] array = (Consumer<IBaseResource>[]) new Consumer[]{theIBaseResourceConsumer};
return array;
}
/**
* Disallow context dirtying for nested classes
*/

57
hapi-fhir-jpaserver-test-utilities/src/test/java/ca/uhn/fhir/jpa/provider/r4/NicknameSearchR4Test.java Normal file
View File

@ -0,0 +1,57 @@
package ca.uhn.fhir.jpa.provider.r4;
import ca.uhn.fhir.jpa.searchparam.nickname.NicknameInterceptor;
import ca.uhn.fhir.util.BundleUtil;
import org.hl7.fhir.r4.model.Bundle;
import org.hl7.fhir.r4.model.Patient;
import org.junit.jupiter.api.AfterEach;
import org.junit.jupiter.api.BeforeEach;
import org.junit.jupiter.api.Test;
import org.springframework.beans.factory.annotation.Autowired;
import java.util.List;
import static org.hamcrest.MatcherAssert.assertThat;
import static org.hamcrest.Matchers.hasSize;
import static org.junit.jupiter.api.Assertions.assertEquals;
public class NicknameSearchR4Test extends BaseResourceProviderR4Test {
@Autowired
NicknameInterceptor myNicknameInterceptor;
@Override
@AfterEach
public void after() throws Exception {
super.after();
myInterceptorRegistry.unregisterInterceptor(myNicknameInterceptor);
}
@BeforeEach
@Override
public void before() throws Exception {
super.before();
myInterceptorRegistry.registerInterceptor(myNicknameInterceptor);
}
@Test
public void testExpandNickname() {
Patient patient1 = new Patient();
patient1.getNameFirstRep().addGiven("ken");
myClient.create().resource(patient1).execute();
Patient patient2 = new Patient();
patient2.getNameFirstRep().addGiven("bob");
myClient.create().resource(patient2).execute();
Bundle result = myClient
.loadPage()
.byUrl(ourServerBase + "/Patient?name:nickname=kenneth")
.andReturnBundle(Bundle.class)
.execute();
List<Patient> resources = BundleUtil.toListOfResourcesOfType(myFhirContext,result, Patient.class);
assertThat(resources, hasSize(1));
assertEquals("ken", resources.get(0).getNameFirstRep().getGivenAsSingleString());
}
}

47
hapi-fhir-jpaserver-test-utilities/src/test/java/ca/uhn/fhir/jpa/provider/r4/ResourceProviderR4ElasticTest.java
View File

@ -36,6 +36,7 @@ import java.time.Instant;
import java.util.Date;
import java.util.List;
import java.util.Objects;
import java.util.stream.IntStream;
import static org.hamcrest.MatcherAssert.assertThat;
import static org.hamcrest.Matchers.hasItem;
@ -43,6 +44,7 @@ import static org.hamcrest.Matchers.is;
import static org.hamcrest.Matchers.not;
import static org.hamcrest.Matchers.nullValue;
import static org.junit.jupiter.api.Assertions.assertEquals;
import static org.junit.jupiter.api.Assertions.assertNull;
import static org.junit.jupiter.api.Assertions.assertTrue;
@ExtendWith(SpringExtension.class)
@ -148,7 +150,7 @@ public class ResourceProviderR4ElasticTest extends BaseResourceProviderR4Test {
.useHttpGet()
.execute();
assertEquals( 1, respParam.getParameter().size(), "Expected only 1 observation for blood count code");
assertEquals(1, respParam.getParameter().size(), "Expected only 1 observation for blood count code");
Bundle bundle = (Bundle) respParam.getParameter().get(0).getResource();
Observation observation = (Observation) bundle.getEntryFirstRep().getResource();
@ -157,4 +159,47 @@ public class ResourceProviderR4ElasticTest extends BaseResourceProviderR4Test {
}
@Test
public void testCountReturnsExpectedSizeOfResources() throws IOException {
IntStream.range(0, 10).forEach(index -> {
Coding blood_count = new Coding("http://loinc.org", "789-8", "Erythrocytes in Blood by Automated count for code: " + (index + 1));
createObservationWithCode(blood_count);
});
HttpGet countQuery = new HttpGet(ourServerBase + "/Observation?code=789-8&_count=5");
myCaptureQueriesListener.clear();
try (CloseableHttpResponse response = ourHttpClient.execute(countQuery)) {
myCaptureQueriesListener.logSelectQueriesForCurrentThread();
// then
assertEquals(Constants.STATUS_HTTP_200_OK, response.getStatusLine().getStatusCode());
String text = IOUtils.toString(response.getEntity().getContent(), StandardCharsets.UTF_8);
Bundle bundle = myFhirContext.newXmlParser().parseResource(Bundle.class, text);
assertEquals(10, bundle.getTotal(), "Expected total 10 observations matching query");
assertEquals(5, bundle.getEntry().size(), "Expected 5 observation entries to match page size");
assertTrue(bundle.getLink("next").hasRelation());
assertEquals(0, myCaptureQueriesListener.getSelectQueriesForCurrentThread().size(), "we build the bundle with no sql");
}
}
@Test
public void testCountZeroReturnsNoResourceEntries() throws IOException {
IntStream.range(0, 10).forEach(index -> {
Coding blood_count = new Coding("http://loinc.org", "789-8", "Erythrocytes in Blood by Automated count for code: " + (index + 1));
createObservationWithCode(blood_count);
});
HttpGet countQuery = new HttpGet(ourServerBase + "/Observation?code=789-8&_count=0");
myCaptureQueriesListener.clear();
try (CloseableHttpResponse response = ourHttpClient.execute(countQuery)) {
myCaptureQueriesListener.logSelectQueriesForCurrentThread();
assertEquals(Constants.STATUS_HTTP_200_OK, response.getStatusLine().getStatusCode());
String text = IOUtils.toString(response.getEntity().getContent(), StandardCharsets.UTF_8);
Bundle bundle = myFhirContext.newXmlParser().parseResource(Bundle.class, text);
assertEquals(10, bundle.getTotal(), "Expected total 10 observations matching query");
assertEquals(0, bundle.getEntry().size(), "Expected no entries in bundle");
assertNull(bundle.getLink("next"), "Expected no 'next' link");
assertNull(bundle.getLink("prev"), "Expected no 'prev' link");
assertEquals(0, myCaptureQueriesListener.getSelectQueriesForCurrentThread().size(), "we build the bundle with no sql");
}
}
}

2
hapi-fhir-jpaserver-test-utilities/src/test/java/ca/uhn/fhir/jpa/search/SearchCoordinatorSvcImplTest.java
View File

@ -561,7 +561,7 @@ public class SearchCoordinatorSvcImplTest {
params.setSearchTotalMode(SearchTotalModeEnum.ACCURATE);
List<ResourcePersistentId> pids = createPidSequence(30);
when(mySearchBuilder.createCountQuery(same(params), any(String.class), nullable(RequestDetails.class), nullable(RequestPartitionId.class))).thenReturn(Lists.newArrayList(Long.valueOf(20L)).iterator());
when(mySearchBuilder.createCountQuery(same(params), any(String.class),nullable(RequestDetails.class), nullable(RequestPartitionId.class))).thenReturn(20L);
when(mySearchBuilder.createQuery(same(params), any(), nullable(RequestDetails.class), nullable(RequestPartitionId.class))).thenReturn(new ResultIterator(pids.subList(10, 20).iterator()));
doAnswer(loadPids()).when(mySearchBuilder).loadResourcesByPid(any(Collection.class), any(Collection.class), any(List.class), anyBoolean(), any());

106
hapi-fhir-jpaserver-test-utilities/src/test/java/ca/uhn/fhir/jpa/term/TermConceptMappingSvcImplTest.java
View File

@ -1,5 +1,6 @@
package ca.uhn.fhir.jpa.term;
import ca.uhn.fhir.context.support.IValidationSupport;
import ca.uhn.fhir.context.support.TranslateConceptResult;
import ca.uhn.fhir.context.support.TranslateConceptResults;
import ca.uhn.fhir.i18n.Msg;
@ -8,14 +9,19 @@ import ca.uhn.fhir.jpa.entity.TermConceptMap;
import ca.uhn.fhir.jpa.entity.TermConceptMapGroup;
import ca.uhn.fhir.jpa.entity.TermConceptMapGroupElement;
import ca.uhn.fhir.jpa.entity.TermConceptMapGroupElementTarget;
import ca.uhn.fhir.jpa.term.api.ITermConceptMappingSvc;
import ca.uhn.fhir.rest.server.exceptions.UnprocessableEntityException;
import org.hl7.fhir.instance.model.api.IIdType;
import org.hl7.fhir.r4.model.CanonicalType;
import org.hl7.fhir.r4.model.CodeableConcept;
import org.hl7.fhir.r4.model.Coding;
import org.hl7.fhir.r4.model.ConceptMap;
import org.hl7.fhir.r4.model.Enumerations;
import org.hl7.fhir.r4.model.StringType;
import org.hl7.fhir.r4.model.UriType;
import org.hl7.fhir.r4.model.codesystems.HttpVerb;
import org.junit.jupiter.api.Test;
import org.mockito.ArgumentCaptor;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import org.springframework.data.domain.PageRequest;
@ -25,6 +31,7 @@ import org.springframework.transaction.support.TransactionCallbackWithoutResult;
import org.springframework.transaction.support.TransactionTemplate;
import javax.annotation.Nonnull;
import java.util.Collections;
import java.util.List;
import static org.junit.jupiter.api.Assertions.assertEquals;
@ -32,6 +39,11 @@ import static org.junit.jupiter.api.Assertions.assertFalse;
import static org.junit.jupiter.api.Assertions.assertNotNull;
import static org.junit.jupiter.api.Assertions.assertTrue;
import static org.junit.jupiter.api.Assertions.fail;
import static org.mockito.Mockito.doReturn;
import static org.mockito.Mockito.mock;
import static org.mockito.Mockito.spy;
import static org.mockito.Mockito.verify;
import static org.mockito.Mockito.when;
public class TermConceptMappingSvcImplTest extends BaseTermR4Test {
private static final Logger ourLog = LoggerFactory.getLogger(TermConceptMappingSvcImplTest.class);
@ -1547,6 +1559,100 @@ public class TermConceptMappingSvcImplTest extends BaseTermR4Test {
});
}
@Test
public void testTranslateCodeRequestToTranslationRequestMapping() {
CodeableConcept codeableConcept = new CodeableConcept();
Coding coding = new Coding("theSourceSystemUrl", "theSourceCode", null);
codeableConcept.addCoding(coding);
IValidationSupport.TranslateCodeRequest theRequest = new IValidationSupport.TranslateCodeRequest(
Collections.unmodifiableList(codeableConcept.getCoding()),
"theTargetSystemUrl",
"theConceptMapUrl",
"theConceptMapVersion",
"theSourceValueSetUrl",
"theTargetValueSetUrl",
0L,
false
);
CodeableConcept sourceCodeableConcept = new CodeableConcept();
sourceCodeableConcept
.addCoding()
.setSystem(coding.getSystem())
.setCode(coding.getCode());
TranslationRequest expected = new TranslationRequest();
expected.setCodeableConcept(sourceCodeableConcept);
expected.setConceptMapVersion(new StringType(theRequest.getConceptMapVersion()));
expected.setUrl(new UriType(theRequest.getConceptMapUrl()));
expected.setSource(new UriType(theRequest.getSourceValueSetUrl()));
expected.setTarget(new UriType(theRequest.getTargetValueSetUrl()));
expected.setTargetSystem(new UriType(theRequest.getTargetSystemUrl()));
expected.setResourceId(theRequest.getResourcePid());
expected.setReverse(theRequest.isReverse());
ITermConceptMappingSvc mock = mock(TermConceptMappingSvcImpl.class);
ArgumentCaptor<TranslationRequest> argument = ArgumentCaptor.forClass(TranslationRequest.class);
when(mock.translate(expected)).thenReturn(new TranslateConceptResults());
when(mock.translateConcept(theRequest)).thenCallRealMethod();
mock.translateConcept(theRequest);
verify(mock).translate(argument.capture());
assertSameTranslationRequest(expected, argument.getValue());
}
@Test
public void testTranslateCodeRequestWithReverseToTranslationRequestMapping() {
CodeableConcept codeableConcept = new CodeableConcept();
Coding coding = new Coding("theSourceSystemUrl", "theSourceCode", null);
codeableConcept.addCoding(coding);
IValidationSupport.TranslateCodeRequest theRequest = new IValidationSupport.TranslateCodeRequest(
Collections.unmodifiableList(codeableConcept.getCoding()),
"theTargetSystemUrl",
"theConceptMapUrl",
"theConceptMapVersion",
"theSourceValueSetUrl",
"theTargetValueSetUrl",
0L,
true
);
CodeableConcept sourceCodeableConcept = new CodeableConcept();
sourceCodeableConcept
.addCoding()
.setSystem(coding.getSystem())
.setCode(coding.getCode());
TranslationRequest expected = new TranslationRequest();
expected.setCodeableConcept(sourceCodeableConcept);
expected.setConceptMapVersion(new StringType(theRequest.getConceptMapVersion()));
expected.setUrl(new UriType(theRequest.getConceptMapUrl()));
expected.setSource(new UriType(theRequest.getSourceValueSetUrl()));
expected.setTarget(new UriType(theRequest.getTargetValueSetUrl()));
expected.setTargetSystem(new UriType(theRequest.getTargetSystemUrl()));
expected.setResourceId(theRequest.getResourcePid());
expected.setReverse(theRequest.isReverse());
ITermConceptMappingSvc mock = mock(TermConceptMappingSvcImpl.class);
ArgumentCaptor<TranslationRequest> argument = ArgumentCaptor.forClass(TranslationRequest.class);
when(mock.translate(expected)).thenReturn(new TranslateConceptResults());
when(mock.translateConcept(theRequest)).thenCallRealMethod();
mock.translateConcept(theRequest);
verify(mock).translateWithReverse(argument.capture());
assertSameTranslationRequest(expected, argument.getValue());
}
private static void assertSameTranslationRequest(TranslationRequest expected, TranslationRequest actual) {
assertTrue(expected.getCodeableConcept().equalsDeep(actual.getCodeableConcept()));
assertEquals(expected.getConceptMapVersion().asStringValue(), actual.getConceptMapVersion().asStringValue());
assertEquals(expected.getUrl().asStringValue(), actual.getUrl().asStringValue());
assertEquals(expected.getSource().asStringValue(), actual.getSource().asStringValue());
assertEquals(expected.getTarget().asStringValue(), actual.getTarget().asStringValue());
assertEquals(expected.getTargetSystem().asStringValue(), actual.getTargetSystem().asStringValue());
assertEquals(expected.getResourceId(), actual.getResourceId());
assertEquals(expected.getReverseAsBoolean(), actual.getReverseAsBoolean());
}
private void createAndPersistConceptMap() {
ConceptMap conceptMap = createConceptMap();

8
hapi-fhir-server-mdm/src/main/java/ca/uhn/fhir/mdm/rules/config/MdmRuleValidator.java
View File

@ -20,14 +20,14 @@ package ca.uhn.fhir.mdm.rules.config;
* #L%
*/
import ca.uhn.fhir.i18n.Msg;
import ca.uhn.fhir.context.ConfigurationException;
import ca.uhn.fhir.context.FhirContext;
import ca.uhn.fhir.context.FhirVersionEnum;
import ca.uhn.fhir.context.RuntimeResourceDefinition;
import ca.uhn.fhir.fhirpath.IFhirPath;
import ca.uhn.fhir.mdm.api.MdmConstants;
import ca.uhn.fhir.i18n.Msg;
import ca.uhn.fhir.mdm.api.IMdmRuleValidator;
import ca.uhn.fhir.mdm.api.MdmConstants;
import ca.uhn.fhir.mdm.rules.json.MdmFieldMatchJson;
import ca.uhn.fhir.mdm.rules.json.MdmFilterSearchParamJson;
import ca.uhn.fhir.mdm.rules.json.MdmResourceSearchParamJson;
@ -36,6 +36,7 @@ import ca.uhn.fhir.mdm.rules.json.MdmSimilarityJson;
import ca.uhn.fhir.parser.DataFormatException;
import ca.uhn.fhir.rest.server.util.ISearchParamRegistry;
import ca.uhn.fhir.util.FhirTerser;
import ca.uhn.fhir.util.SearchParameterUtil;
import org.hl7.fhir.instance.model.api.IBaseResource;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
@ -150,7 +151,8 @@ public class MdmRuleValidator implements IMdmRuleValidator {
}
private void validateResourceSearchParam(String theFieldName, String theResourceType, String theSearchParam) {
if (mySearchParamRetriever.getActiveSearchParam(theResourceType, theSearchParam) == null) {
String searchParam = SearchParameterUtil.stripModifier(theSearchParam);
if (mySearchParamRetriever.getActiveSearchParam(theResourceType, searchParam) == null) {
throw new ConfigurationException(Msg.code(1511) + "Error in " + theFieldName + ": " + theResourceType + " does not have a search parameter called '" + theSearchParam + "'");
}
}

1
hapi-fhir-server-mdm/src/main/java/ca/uhn/fhir/mdm/rules/matcher/MdmMatcherEnum.java
View File

@ -40,6 +40,7 @@ public enum MdmMatcherEnum {
NYSIIS(new HapiStringMatcher(new PhoneticEncoderMatcher(PhoneticEncoderEnum.NYSIIS))),
REFINED_SOUNDEX(new HapiStringMatcher(new PhoneticEncoderMatcher(PhoneticEncoderEnum.REFINED_SOUNDEX))),
SOUNDEX(new HapiStringMatcher(new PhoneticEncoderMatcher(PhoneticEncoderEnum.SOUNDEX))),
NICKNAME(new HapiStringMatcher(new NicknameMatcher())),
STRING(new HapiStringMatcher()),
SUBSTRING(new HapiStringMatcher(new SubstringStringMatcher())),

30
hapi-fhir-server-mdm/src/main/java/ca/uhn/fhir/mdm/rules/matcher/NicknameMatcher.java Normal file
View File

@ -0,0 +1,30 @@
package ca.uhn.fhir.mdm.rules.matcher;
import ca.uhn.fhir.context.ConfigurationException;
import ca.uhn.fhir.i18n.Msg;
import ca.uhn.fhir.jpa.searchparam.nickname.NicknameSvc;
import java.io.IOException;
import java.util.List;
import java.util.Locale;
public class NicknameMatcher implements IMdmStringMatcher {
private final NicknameSvc myNicknameSvc;
public NicknameMatcher() {
try {
myNicknameSvc = new NicknameSvc();
} catch (IOException e) {
throw new ConfigurationException(Msg.code(2078) + "Unable to load nicknames", e);
}
}
@Override
public boolean matches(String theLeftString, String theRightString) {
String leftString = theLeftString.toLowerCase(Locale.ROOT);
String rightString = theRightString.toLowerCase(Locale.ROOT);
List<String> leftNames = myNicknameSvc.getEquivalentNames(leftString);
return leftNames.contains(rightString);
}
}

25
hapi-fhir-server-mdm/src/test/java/ca/uhn/fhir/mdm/rules/matcher/NicknameMatcherTest.java Normal file
View File

@ -0,0 +1,25 @@
package ca.uhn.fhir.mdm.rules.matcher;
import org.junit.jupiter.api.Test;
import static org.junit.jupiter.api.Assertions.assertFalse;
import static org.junit.jupiter.api.Assertions.assertTrue;
class NicknameMatcherTest {
IMdmStringMatcher matcher = new NicknameMatcher();
@Test
public void testMatches() {
assertTrue(matcher.matches("Ken", "ken"));
assertTrue(matcher.matches("ken", "Ken"));
assertTrue(matcher.matches("Ken", "Ken"));
assertTrue(matcher.matches("Kenneth", "Ken"));
assertTrue(matcher.matches("Kenneth", "Kenny"));
assertTrue(matcher.matches("Ken", "Kenneth"));
assertTrue(matcher.matches("Kenny", "Kenneth"));
assertFalse(matcher.matches("Ken", "Bob"));
// These aren't nickname matches. If you want matches like these use a phonetic matcher
assertFalse(matcher.matches("Allen", "Allan"));
}
}

23
hapi-fhir-server/src/main/java/ca/uhn/fhir/rest/server/interceptor/ResponseTerminologyTranslationInterceptor.java
View File

@ -36,9 +36,11 @@ import com.google.common.collect.ArrayListMultimap;
import com.google.common.collect.Multimap;
import org.apache.commons.lang3.Validate;
import org.hl7.fhir.instance.model.api.IBase;
import org.hl7.fhir.instance.model.api.IBaseCoding;
import org.hl7.fhir.instance.model.api.IBaseResource;
import org.hl7.fhir.instance.model.api.IPrimitiveType;
import java.util.ArrayList;
import java.util.HashMap;
import java.util.List;
import java.util.Map;
@ -153,12 +155,17 @@ public class ResponseTerminologyTranslationInterceptor extends BaseResponseTermi
if (!foundSystemsToCodes.containsKey(wantTargetSystem)) {
for (String code : foundSystemsToCodes.get(nextSourceSystem)) {
TranslateConceptResults translateConceptResults = myValidationSupport.translateConcept(new IValidationSupport.TranslateCodeRequest(nextSourceSystem, code, wantTargetSystem));
List<IBaseCoding> codings = new ArrayList<IBaseCoding>();
codings.add(createCodingFromPrimitives(nextSourceSystem, code, null));
TranslateConceptResults translateConceptResults = myValidationSupport.translateConcept(new IValidationSupport.TranslateCodeRequest(codings, wantTargetSystem));
if (translateConceptResults != null) {
List<TranslateConceptResult> mappings = translateConceptResults.getResults();
for (TranslateConceptResult nextMapping : mappings) {
IBase newCoding = createCodingFromMappingTarget(nextMapping);
IBase newCoding = createCodingFromPrimitives(
nextMapping.getSystem(),
nextMapping.getCode(),
nextMapping.getDisplay());
// Add coding to existing CodeableConcept
myCodeableConceptCodingChild.getMutator().addValue(theElement, newCoding);
@ -174,14 +181,14 @@ public class ResponseTerminologyTranslationInterceptor extends BaseResponseTermi
}
private IBase createCodingFromMappingTarget(TranslateConceptResult nextMapping) {
IBase newCoding = myCodingDefinitition.newInstance();
IPrimitiveType<?> newSystem = myUriDefinition.newInstance(nextMapping.getSystem());
private IBaseCoding createCodingFromPrimitives(String system, String code, String display) {
IBaseCoding newCoding = (IBaseCoding) myCodingDefinitition.newInstance();
IPrimitiveType<?> newSystem = myUriDefinition.newInstance(system);
myCodingSystemChild.getMutator().addValue(newCoding, newSystem);
IPrimitiveType<?> newCode = myCodeDefinition.newInstance(nextMapping.getCode());
IPrimitiveType<?> newCode = myCodeDefinition.newInstance(code);
myCodingCodeChild.getMutator().addValue(newCoding, newCode);
if (isNotBlank(nextMapping.getDisplay())) {
IPrimitiveType<?> newDisplay = myStringDefinition.newInstance(nextMapping.getDisplay());
if (isNotBlank(display)) {
IPrimitiveType<?> newDisplay = myStringDefinition.newInstance(display);
myCodingDisplayChild.getMutator().addValue(newCoding, newDisplay);
}
return newCoding;

19
hapi-fhir-server/src/main/java/ca/uhn/fhir/rest/server/interceptor/auth/RuleTarget.java
View File

@ -48,11 +48,24 @@ public class RuleTarget {
for (Map.Entry<String, String[]> entry : theParameters.entrySet()) {
String key = entry.getKey();
String[] value = entry.getValue();
if (key.endsWith(Constants.PARAMQUALIFIER_MDM)) {
key = key.split(Constants.PARAMQUALIFIER_MDM)[0];
}
key = stripMdmQualifier(key);
key = stripNicknameQualifier(key);
retval.put(key, value);
}
return retval;
}
private String stripMdmQualifier(String theKey) {
if (theKey.endsWith(Constants.PARAMQUALIFIER_MDM)) {
theKey = theKey.split(Constants.PARAMQUALIFIER_MDM)[0];
}
return theKey;
}
private String stripNicknameQualifier(String theKey) {
if (theKey.endsWith(Constants.PARAMQUALIFIER_NICKNAME)) {
theKey = theKey.split(Constants.PARAMQUALIFIER_NICKNAME)[0];
}
return theKey;
}
}

2
hapi-fhir-sql-migrate/src/main/java/ca/uhn/fhir/jpa/migrate/taskdef/BaseTask.java
View File

@ -162,6 +162,8 @@ public abstract class BaseTask {
private int doExecuteSql(@Language("SQL") String theSql, Object[] theArguments) {
JdbcTemplate jdbcTemplate = getConnectionProperties().newJdbcTemplate();
// 0 means no timeout -- we use this for index rebuilds that may take time.
jdbcTemplate.setQueryTimeout(0);
try {
int changesCount = jdbcTemplate.update(theSql, theArguments);
if (!"true".equals(System.getProperty("unit_test_mode"))) {

39
hapi-fhir-storage/src/main/java/ca/uhn/fhir/jpa/api/model/TranslationRequest.java
View File

@ -20,7 +20,9 @@ package ca.uhn.fhir.jpa.api.model;
* #L%
*/
import ca.uhn.fhir.context.support.IValidationSupport;
import org.apache.commons.lang3.Validate;
import org.hl7.fhir.instance.model.api.IBaseCoding;
import org.hl7.fhir.r4.model.BooleanType;
import org.hl7.fhir.r4.model.CodeableConcept;
import org.hl7.fhir.r4.model.Coding;
@ -28,6 +30,7 @@ import org.hl7.fhir.r4.model.StringType;
import org.hl7.fhir.r4.model.UriType;
import java.util.ArrayList;
import java.util.Collections;
import java.util.List;
public class TranslationRequest {
@ -208,4 +211,40 @@ public class TranslationRequest {
public boolean hasTargetSystem() {
return myTargetSystem != null && myTargetSystem.hasValue();
}
public IValidationSupport.TranslateCodeRequest asTranslateCodeRequest() {
return new IValidationSupport.TranslateCodeRequest(
Collections.unmodifiableList(this.getCodeableConcept().getCoding()),
this.getTargetSystem() != null ? this.getTargetSystem().asStringValue() : null,
this.getUrl() != null ? this.getUrl().asStringValue() : null,
this.getConceptMapVersion() != null ? this.getConceptMapVersion().asStringValue() : null,
this.getSource() != null ? this.getSource().asStringValue() : null,
this.getTarget() != null ? this.getTarget().asStringValue() : null,
this.getResourceId(),
this.getReverseAsBoolean()
);
}
public static TranslationRequest fromTranslateCodeRequest(IValidationSupport.TranslateCodeRequest theRequest) {
CodeableConcept sourceCodeableConcept = new CodeableConcept();
for (IBaseCoding aCoding : theRequest.getCodings()) {
sourceCodeableConcept
.addCoding()
.setSystem(aCoding.getSystem())
.setCode(aCoding.getCode())
.setVersion(((Coding) aCoding).getVersion());
}
TranslationRequest translationRequest = new TranslationRequest();
translationRequest.setCodeableConcept(sourceCodeableConcept);
translationRequest.setConceptMapVersion(new StringType(theRequest.getConceptMapVersion()));
translationRequest.setUrl(new UriType(theRequest.getConceptMapUrl()));
translationRequest.setSource(new UriType(theRequest.getSourceValueSetUrl()));
translationRequest.setTarget(new UriType(theRequest.getTargetValueSetUrl()));
translationRequest.setTargetSystem(new UriType(theRequest.getTargetSystemUrl()));
translationRequest.setResourceId(theRequest.getResourcePid());
translationRequest.setReverse(theRequest.isReverse());
return translationRequest;
}
}

30
hapi-fhir-structures-r4/src/test/java/ca/uhn/fhir/rest/param/TokenParamTest.java
View File

@ -2,12 +2,14 @@ package ca.uhn.fhir.rest.param;
import ca.uhn.fhir.context.FhirContext;
import ca.uhn.fhir.rest.api.Constants;
import ca.uhn.fhir.rest.server.exceptions.InvalidRequestException;
import org.junit.jupiter.api.Test;
import static org.junit.jupiter.api.Assertions.assertEquals;
import static org.junit.jupiter.api.Assertions.assertFalse;
import static org.junit.jupiter.api.Assertions.assertNotEquals;
import static org.junit.jupiter.api.Assertions.assertTrue;
import static org.junit.jupiter.api.Assertions.fail;
public class TokenParamTest {
private static final FhirContext ourCtx = FhirContext.forR4Cached();
@ -48,4 +50,32 @@ public class TokenParamTest {
assertEquals("type-value|identifier-value", param.getValue());
}
@Test
public void testNameNickname() {
StringParam param = new StringParam();
assertFalse(param.isNicknameExpand());
param.setValueAsQueryToken(ourCtx, "name", Constants.PARAMQUALIFIER_NICKNAME, "kenny");
assertTrue(param.isNicknameExpand());
}
@Test
public void testGivenNickname() {
StringParam param = new StringParam();
assertFalse(param.isNicknameExpand());
param.setValueAsQueryToken(ourCtx, "given", Constants.PARAMQUALIFIER_NICKNAME, "kenny");
assertTrue(param.isNicknameExpand());
}
@Test
public void testInvalidNickname() {
StringParam param = new StringParam();
assertFalse(param.isNicknameExpand());
try {
param.setValueAsQueryToken(ourCtx, "family", Constants.PARAMQUALIFIER_NICKNAME, "kenny");
fail();
} catch (InvalidRequestException e) {
assertEquals("HAPI-2077: Modifier :nickname may only be used with 'name' and 'given' search parameters", e.getMessage());
}
}
}

131
hapi-fhir-validation/src/main/java/org/hl7/fhir/common/hapi/validation/support/RemoteTerminologyServiceValidationSupport.java
View File

@ -1,5 +1,11 @@
package org.hl7.fhir.common.hapi.validation.support;
import ca.uhn.fhir.context.BaseRuntimeChildDefinition;
import ca.uhn.fhir.context.BaseRuntimeElementCompositeDefinition;
import ca.uhn.fhir.context.BaseRuntimeElementDefinition;
import ca.uhn.fhir.context.RuntimePrimitiveDatatypeDefinition;
import ca.uhn.fhir.context.support.TranslateConceptResult;
import ca.uhn.fhir.context.support.TranslateConceptResults;
import ca.uhn.fhir.i18n.Msg;
import ca.uhn.fhir.context.FhirContext;
import ca.uhn.fhir.context.FhirVersionEnum;
@ -11,20 +17,29 @@ import ca.uhn.fhir.rest.client.api.IGenericClient;
import ca.uhn.fhir.util.BundleUtil;
import ca.uhn.fhir.util.JsonUtil;
import ca.uhn.fhir.util.ParametersUtil;
import ca.uhn.fhir.util.StringUtil;
import org.apache.commons.lang3.StringUtils;
import org.apache.commons.lang3.Validate;
import org.hl7.fhir.instance.model.api.IBase;
import org.hl7.fhir.instance.model.api.IBaseBundle;
import org.hl7.fhir.instance.model.api.IBaseCoding;
import org.hl7.fhir.instance.model.api.IBaseParameters;
import org.hl7.fhir.instance.model.api.IBaseResource;
import org.hl7.fhir.instance.model.api.IPrimitiveType;
import org.hl7.fhir.r4.model.CodeSystem;
import org.hl7.fhir.r4.model.Coding;
import org.hl7.fhir.r4.model.Parameters;
import org.hl7.fhir.r4.model.ValueSet;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import javax.annotation.Nonnull;
import java.io.IOException;
import java.sql.Array;
import java.util.ArrayList;
import java.util.List;
import java.util.Objects;
import java.util.Optional;
import static org.apache.commons.lang3.StringUtils.isBlank;
import static org.apache.commons.lang3.StringUtils.isNotBlank;
@ -331,6 +346,23 @@ public class RemoteTerminologyServiceValidationSupport extends BaseValidationSup
return fetchValueSet(theValueSetUrl) != null;
}
@Override
public TranslateConceptResults translateConcept(TranslateCodeRequest theRequest) {
IGenericClient client = provideClient();
FhirContext fhirContext = client.getFhirContext();
IBaseParameters params = buildTranslateInputParameters(fhirContext, theRequest);
IBaseParameters outcome = client
.operation()
.onType("ConceptMap")
.named("$translate")
.withParameters(params)
.execute();
return translateOutcomeToResults(fhirContext, outcome);
}
private IGenericClient provideClient() {
IGenericClient retVal = myCtx.newRestfulGenericClient(myBaseUrl);
for (Object next : myClientInterceptors) {
@ -442,4 +474,103 @@ public class RemoteTerminologyServiceValidationSupport extends BaseValidationSup
myClientInterceptors.add(theClientInterceptor);
}
private IBaseParameters buildTranslateInputParameters(FhirContext fhirContext, TranslateCodeRequest theRequest) {
IBaseParameters params = ParametersUtil.newInstance(fhirContext);
if (!StringUtils.isEmpty(theRequest.getConceptMapUrl())) {
ParametersUtil.addParameterToParametersUri(fhirContext, params, "url", theRequest.getConceptMapUrl());
}
if (!StringUtils.isEmpty(theRequest.getConceptMapVersion())) {
ParametersUtil.addParameterToParametersString(fhirContext, params, "conceptMapVersion", theRequest.getConceptMapVersion());
}
if (theRequest.getCodings() != null) {
addCodingsToTranslateParameters(fhirContext, theRequest.getCodings(), params);
}
if (!StringUtils.isEmpty(theRequest.getSourceValueSetUrl())) {
ParametersUtil.addParameterToParametersUri(fhirContext, params, "source", theRequest.getSourceValueSetUrl());
}
if (!StringUtils.isEmpty(theRequest.getTargetValueSetUrl())) {
ParametersUtil.addParameterToParametersUri(fhirContext, params, "target", theRequest.getTargetValueSetUrl());
}
if (!StringUtils.isEmpty(theRequest.getTargetSystemUrl())) {
ParametersUtil.addParameterToParametersUri(fhirContext, params, "targetsystem", theRequest.getTargetSystemUrl());
}
if (theRequest.isReverse()) {
ParametersUtil.addParameterToParametersBoolean(fhirContext, params, "reverse", theRequest.isReverse());
}
return params;
}
private void addCodingsToTranslateParameters(FhirContext fhirContext, List<IBaseCoding> theCodings, IBaseParameters theParams) {
BaseRuntimeElementCompositeDefinition<?> codeableConceptDef = (BaseRuntimeElementCompositeDefinition<?>) Objects.requireNonNull(fhirContext.getElementDefinition("CodeableConcept"));
BaseRuntimeChildDefinition codings = codeableConceptDef.getChildByName("coding");
BaseRuntimeElementCompositeDefinition<?> codingDef = (BaseRuntimeElementCompositeDefinition<?>) Objects.requireNonNull(fhirContext.getElementDefinition("Coding"));
BaseRuntimeChildDefinition codingSystemChild = codingDef.getChildByName("system");
BaseRuntimeChildDefinition codingCodeChild = codingDef.getChildByName("code");
BaseRuntimeElementDefinition<IPrimitiveType<?>> systemDef = (RuntimePrimitiveDatatypeDefinition) fhirContext.getElementDefinition("uri");
BaseRuntimeElementDefinition<IPrimitiveType<?>> codeDef = (RuntimePrimitiveDatatypeDefinition) fhirContext.getElementDefinition("code");
IBase codeableConcept = codeableConceptDef.newInstance();
for (IBaseCoding aCoding : theCodings) {
IBaseCoding newCoding = (IBaseCoding) codingDef.newInstance();
IPrimitiveType<?> newSystem = systemDef.newInstance(aCoding.getSystem());
codingSystemChild.getMutator().addValue(newCoding, newSystem);
IPrimitiveType<?> newCode = codeDef.newInstance(aCoding.getCode());
codingCodeChild.getMutator().addValue(newCoding, newCode);
codings.getMutator().addValue(codeableConcept, newCoding);
}
ParametersUtil.addParameterToParameters(fhirContext, theParams, "codeableConcept", codeableConcept);
}
private TranslateConceptResults translateOutcomeToResults(FhirContext fhirContext, IBaseParameters outcome) {
Optional<String> result = ParametersUtil.getNamedParameterValueAsString(fhirContext, outcome, "result");
Optional<String> message = ParametersUtil.getNamedParameterValueAsString(fhirContext, outcome, "message");
List<IBase> matches = ParametersUtil.getNamedParameters(fhirContext, outcome, "match");
TranslateConceptResults retVal = new TranslateConceptResults();
if (result.isPresent()) {
retVal.setResult(Boolean.parseBoolean(result.get()));
}
if (message.isPresent()) {
retVal.setMessage(message.get());
}
if (!matches.isEmpty()) {
retVal.setResults(matchesToTranslateConceptResults(fhirContext, matches));
}
return retVal;
}
private List<TranslateConceptResult> matchesToTranslateConceptResults(FhirContext fhirContext, List<IBase> theMatches) {
List<TranslateConceptResult> resultList = new ArrayList();
for (IBase m : theMatches) {
TranslateConceptResult match = new TranslateConceptResult();
String equivalence = ParametersUtil.getParameterPartValueAsString(fhirContext, m, "equivalence");
Optional<IBase> concept = ParametersUtil.getParameterPartValue(fhirContext, m, "concept");
String source = ParametersUtil.getParameterPartValueAsString(fhirContext, m, "source");
if (StringUtils.isNotBlank(equivalence)) {
match.setEquivalence(equivalence);
}
if (concept.isPresent()) {
IBaseCoding matchedCoding = (IBaseCoding) concept.get();
match.setSystem(matchedCoding.getSystem());
match.setCode(matchedCoding.getCode());
match.setDisplay(matchedCoding.getDisplay());
if (StringUtils.isNotBlank(source)) {
match.setConceptMapUrl(source);
}
resultList.add(match);
}
}
return resultList;
}
}

150
hapi-fhir-validation/src/test/java/org/hl7/fhir/common/hapi/validation/support/RemoteTerminologyServiceValidationSupportTest.java
View File

@ -3,6 +3,8 @@ package org.hl7.fhir.common.hapi.validation.support;
import ca.uhn.fhir.context.FhirContext;
import ca.uhn.fhir.context.support.ConceptValidationOptions;
import ca.uhn.fhir.context.support.IValidationSupport;
import ca.uhn.fhir.context.support.TranslateConceptResult;
import ca.uhn.fhir.context.support.TranslateConceptResults;
import ca.uhn.fhir.jpa.model.util.JpaConstants;
import ca.uhn.fhir.parser.IJsonLikeParser;
import ca.uhn.fhir.rest.annotation.IdParam;
@ -20,11 +22,14 @@ import ca.uhn.fhir.rest.server.IResourceProvider;
import ca.uhn.fhir.test.utilities.server.RestfulServerExtension;
import ca.uhn.fhir.util.ParametersUtil;
import com.google.common.collect.Lists;
import org.hl7.fhir.instance.model.api.IBaseCoding;
import org.hl7.fhir.instance.model.api.IBaseResource;
import org.hl7.fhir.r4.model.BooleanType;
import org.hl7.fhir.r4.model.CodeSystem;
import org.hl7.fhir.r4.model.CodeType;
import org.hl7.fhir.r4.model.CodeableConcept;
import org.hl7.fhir.r4.model.Coding;
import org.hl7.fhir.r4.model.ConceptMap;
import org.hl7.fhir.r4.model.IdType;
import org.hl7.fhir.r4.model.Parameters;
import org.hl7.fhir.r4.model.StringType;
@ -58,7 +63,18 @@ public class RemoteTerminologyServiceValidationSupportTest {
private static final String CODE_SYSTEM_VERSION_AS_TEXT = "v2.1.12";
private static final String CODE = "CODE";
private static final String VALUE_SET_URL = "http://value.set/url";
private static final String TARGET_SYSTEM = "http://target.system/url";
private static final String CONCEPT_MAP_URL = "http://concept.map/url";
private static final String CONCEPT_MAP_VERSION = "2.1";
private static final String SOURCE_VALUE_SET_URL = "http://source.vs.system/url";
private static final String TARGET_VALUE_SET_URL = "http://target.vs.system/url";
private static final String TARGET_CODE = "CODE";
private static final String TARGET_CODE_DISPLAY = "code";
private static final boolean REVERSE = true;
private static final String EQUIVALENCE_CODE = "equivalent";
private static final String ERROR_MESSAGE = "This is an error message";
private static final String SUCCESS_MESSAGE = "This is a success message";
private static FhirContext ourCtx = FhirContext.forR4Cached();
@ -68,6 +84,7 @@ public class RemoteTerminologyServiceValidationSupportTest {
private MyValueSetProvider myValueSetProvider;
private RemoteTerminologyServiceValidationSupport mySvc;
private MyCodeSystemProvider myCodeSystemProvider;
private MyConceptMapProvider myConceptMapProvider;
@BeforeEach
public void before() {
@ -77,6 +94,9 @@ public class RemoteTerminologyServiceValidationSupportTest {
myCodeSystemProvider = new MyCodeSystemProvider();
myRestfulServerExtension.getRestfulServer().registerProvider(myCodeSystemProvider);
myConceptMapProvider = new MyConceptMapProvider();
myRestfulServerExtension.getRestfulServer().registerProvider(myConceptMapProvider);
String baseUrl = "http://localhost:" + myRestfulServerExtension.getPort();
mySvc = new RemoteTerminologyServiceValidationSupport(ourCtx);
@ -277,6 +297,91 @@ public class RemoteTerminologyServiceValidationSupportTest {
assertEquals(null, outcome);
}
@Test
public void testTranslateCode_AllInParams_AllOutParams() {
myConceptMapProvider.myNextReturnParams = new Parameters();
myConceptMapProvider.myNextReturnParams.addParameter("result", true);
myConceptMapProvider.myNextReturnParams.addParameter("message", ERROR_MESSAGE);
TranslateConceptResults expectedResults = new TranslateConceptResults();
expectedResults.setResult(true);
// Add 2 matches
addMatchToTranslateRequest(myConceptMapProvider.myNextReturnParams);
addMatchToTranslateRequest(myConceptMapProvider.myNextReturnParams);
List<TranslateConceptResult> translateResults = new ArrayList<>();
TranslateConceptResult singleResult = new TranslateConceptResult();
singleResult
.setEquivalence(EQUIVALENCE_CODE)
.setSystem(TARGET_SYSTEM)
.setCode(TARGET_CODE)
.setConceptMapUrl(CONCEPT_MAP_URL)
.setDisplay(TARGET_CODE_DISPLAY);
translateResults.add(singleResult);
translateResults.add(singleResult);
expectedResults.setResults(translateResults);
CodeableConcept codeableConcept = new CodeableConcept();
codeableConcept.addCoding(new Coding(CODE_SYSTEM, CODE, null));
IValidationSupport.TranslateCodeRequest request = new IValidationSupport.TranslateCodeRequest(
Collections.unmodifiableList(codeableConcept.getCoding()),
TARGET_SYSTEM,
CONCEPT_MAP_URL,
CONCEPT_MAP_VERSION,
SOURCE_VALUE_SET_URL,
TARGET_VALUE_SET_URL,
null,
REVERSE);
TranslateConceptResults results = mySvc.translateConcept(request);
assertEquals(results.getResult(), true);
assertEquals(results.getResults().size(), 2);
for(TranslateConceptResult result : results.getResults()) {
assertEquals(singleResult, result);
}
assertTrue(codeableConcept.equalsDeep(myConceptMapProvider.myLastCodeableConcept));
assertEquals(TARGET_SYSTEM, myConceptMapProvider.myLastTargetCodeSystem.getValue());
assertEquals(CONCEPT_MAP_URL, myConceptMapProvider.myLastConceptMapUrl.getValue());
assertEquals(CONCEPT_MAP_VERSION, myConceptMapProvider.myLastConceptMapVersion.getValue());
assertEquals(SOURCE_VALUE_SET_URL, myConceptMapProvider.myLastSourceValueSet.getValue());
assertEquals(TARGET_VALUE_SET_URL, myConceptMapProvider.myLastTargetValueSet.getValue());
assertEquals(REVERSE, myConceptMapProvider.myLastReverse.getValue());
}
@Test
public void testTranslateCode_NoInParams_NoOutParams() {
myConceptMapProvider.myNextReturnParams = new Parameters();
List<IBaseCoding> codings = new ArrayList<>();
codings.add(new Coding(null, null, null));
IValidationSupport.TranslateCodeRequest request = new IValidationSupport.TranslateCodeRequest(codings, null);
TranslateConceptResults results = mySvc.translateConcept(request);
assertEquals(results.getResult(), false);
assertEquals(results.getResults().size(), 0);
assertNull(myConceptMapProvider.myLastCodeableConcept);
assertNull(myConceptMapProvider.myLastTargetCodeSystem);
assertNull(myConceptMapProvider.myLastConceptMapUrl);
assertNull(myConceptMapProvider.myLastConceptMapVersion);
assertNull(myConceptMapProvider.myLastSourceValueSet);
assertNull(myConceptMapProvider.myLastTargetValueSet);
assertNull(myConceptMapProvider.myLastReverse);
}
private void addMatchToTranslateRequest(Parameters params) {
Parameters.ParametersParameterComponent matchParam = params.addParameter().setName("match");
matchParam.addPart().setName("equivalence").setValue(new CodeType(EQUIVALENCE_CODE));
Coding value = new Coding(TARGET_SYSTEM, TARGET_CODE, TARGET_CODE_DISPLAY);
matchParam.addPart().setName("concept").setValue(value);
matchParam.addPart().setName("source").setValue(new UriType(CONCEPT_MAP_URL));
}
/**
* Remote terminology services can be used to validate codes when code system is present,
* even when inferSystem is true
@ -636,5 +741,50 @@ public class RemoteTerminologyServiceValidationSupportTest {
}
private static class MyConceptMapProvider implements IResourceProvider {
private UriType myLastConceptMapUrl;
private StringType myLastConceptMapVersion;
private CodeableConcept myLastCodeableConcept;
private UriType myLastSourceValueSet;
private UriType myLastTargetValueSet;
private UriType myLastTargetCodeSystem;
private BooleanType myLastReverse;
private int myInvocationCount;
private Parameters myNextReturnParams;
@Operation(name = JpaConstants.OPERATION_TRANSLATE, idempotent = true, returnParameters = {
@OperationParam(name = "result", type = BooleanType.class, min = 1, max = 1),
@OperationParam(name = "message", type = StringType.class, min = 0, max = 1),
})
public Parameters translate(
HttpServletRequest theServletRequest,
@IdParam(optional = true) IdType theId,
@OperationParam(name = "url", min = 0, max = 1) UriType theConceptMapUrl,
@OperationParam(name = "conceptMapVersion", min = 0, max = 1) StringType theConceptMapVersion,
@OperationParam(name = "codeableConcept", min = 0, max = 1) CodeableConcept theSourceCodeableConcept,
@OperationParam(name = "source", min = 0, max = 1) UriType theSourceValueSet,
@OperationParam(name = "target", min = 0, max = 1) UriType theTargetValueSet,
@OperationParam(name = "targetsystem", min = 0, max = 1) UriType theTargetCodeSystem,
@OperationParam(name = "reverse", min = 0, max = 1) BooleanType theReverse,
RequestDetails theRequestDetails
) {
myInvocationCount++;
myLastConceptMapUrl = theConceptMapUrl;
myLastConceptMapVersion = theConceptMapVersion;
myLastCodeableConcept = theSourceCodeableConcept;
myLastSourceValueSet = theSourceValueSet;
myLastTargetValueSet = theTargetValueSet;
myLastTargetCodeSystem = theTargetCodeSystem;
myLastReverse = theReverse;
return myNextReturnParams;
}
@Override
public Class<? extends IBaseResource> getResourceType() {
return ConceptMap.class;
}
}
}