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Merge remote-tracking branch 'origin/master' into issue-2634-increase-src-path-length

This commit is contained in:
Tadgh 2021-05-06 09:10:48 -04:00
parent 98cc301a27 1424d48912
commit cf864c2078
22 changed files with 307 additions and 159 deletions
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4
hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/5_4_0/2632-measure-evaluation-npe.yaml Normal file
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@ -0,0 +1,4 @@
---
type: fix
issue: 2632
title: "Certain calls to the $evaluate-measure operation could result in a NullPointerException. This is now corrected."

2
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/provider/dstu3/BaseJpaResourceProviderCompositionDstu3.java
View File

@ -81,7 +81,7 @@ public class BaseJpaResourceProviderCompositionDstu3 extends JpaResourceProvider
startRequest(theServletRequest);
try {
IBundleProvider bundleProvider = ((IFhirResourceDaoComposition<Composition>) getDao()).getDocumentForComposition(theServletRequest, theId, theCount, theOffset, theLastUpdated, theSortSpec, theRequestDetails);
List<IBaseResource> resourceList = bundleProvider.getResources(0, bundleProvider.size());
List<IBaseResource> resourceList = bundleProvider.getAllResources();
boolean foundCompositionResource = false;
Bundle bundle = new Bundle().setType(Bundle.BundleType.DOCUMENT);

2
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/provider/r4/BaseJpaResourceProviderCompositionR4.java
View File

@ -78,7 +78,7 @@ public class BaseJpaResourceProviderCompositionR4 extends JpaResourceProviderR4<
startRequest(theServletRequest);
try {
IBundleProvider bundleProvider = ((IFhirResourceDaoComposition<Composition>) getDao()).getDocumentForComposition(theServletRequest, theId, theCount, theOffset, theLastUpdated, theSortSpec, theRequestDetails);
List<IBaseResource> resourceList = bundleProvider.getResources(0, bundleProvider.size());
List<IBaseResource> resourceList = bundleProvider.getAllResources();
boolean foundCompositionResource = false;
Bundle bundle = new Bundle().setType(Bundle.BundleType.DOCUMENT);

4
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/provider/r5/BaseJpaResourceProviderCompositionR5.java
View File

@ -77,8 +77,8 @@ public class BaseJpaResourceProviderCompositionR5 extends JpaResourceProviderR5<
startRequest(theServletRequest);
try {
IBundleProvider bundleProvider = ((IFhirResourceDaoComposition<Composition>) getDao()).getDocumentForComposition(theServletRequest, theId, theCount, theOffset,theLastUpdated, theSortSpec, theRequestDetails);
List<IBaseResource> resourceList = bundleProvider.getResources(0, bundleProvider.size());
IBundleProvider bundleProvider = ((IFhirResourceDaoComposition<Composition>) getDao()).getDocumentForComposition(theServletRequest, theId, theCount, theOffset, theLastUpdated, theSortSpec, theRequestDetails);
List<IBaseResource> resourceList = bundleProvider.getAllResources();
boolean foundCompositionResource = false;
Bundle bundle = new Bundle().setType(Bundle.BundleType.DOCUMENT);

13
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/term/TermConceptMappingSvcImpl.java
View File

@ -202,7 +202,6 @@ public class TermConceptMappingSvcImpl implements ITermConceptMappingSvc {
termConceptMap = myConceptMapDao.save(termConceptMap);
int codesSaved = 0;
if (theConceptMap.hasGroup()) {
TermConceptMapGroup termConceptMapGroup;
for (ConceptMap.ConceptMapGroupComponent group : theConceptMap.getGroup()) {
@ -228,7 +227,7 @@ public class TermConceptMappingSvcImpl implements ITermConceptMappingSvc {
termConceptMapGroup.setSourceVersion(group.getSourceVersion());
termConceptMapGroup.setTarget(groupTarget);
termConceptMapGroup.setTargetVersion(group.getTargetVersion());
myConceptMapGroupDao.save(termConceptMapGroup);
termConceptMapGroup = myConceptMapGroupDao.save(termConceptMapGroup);
if (group.hasElement()) {
TermConceptMapGroupElement termConceptMapGroupElement;
@ -240,7 +239,7 @@ public class TermConceptMappingSvcImpl implements ITermConceptMappingSvc {
termConceptMapGroupElement.setConceptMapGroup(termConceptMapGroup);
termConceptMapGroupElement.setCode(element.getCode());
termConceptMapGroupElement.setDisplay(element.getDisplay());
myConceptMapGroupElementDao.save(termConceptMapGroupElement);
termConceptMapGroupElement = myConceptMapGroupElementDao.save(termConceptMapGroupElement);
if (element.hasTarget()) {
TermConceptMapGroupElementTarget termConceptMapGroupElementTarget;
@ -264,7 +263,7 @@ public class TermConceptMappingSvcImpl implements ITermConceptMappingSvc {
}
}
}
}
} else {
TermConceptMap existingTermConceptMap = optionalExistingTermConceptMapByUrl.get();
@ -558,9 +557,9 @@ public class TermConceptMappingSvcImpl implements ITermConceptMappingSvc {
private boolean alreadyContainsMapping(List<TranslateConceptResult> elements, TranslateConceptResult translationMatch) {
for (TranslateConceptResult nextExistingElement : elements) {
if (nextExistingElement.getSystem().equals(translationMatch.getSystem())) {
if (nextExistingElement.getSystemVersion().equals(translationMatch.getSystemVersion())) {
if (nextExistingElement.getCode().equals(translationMatch.getCode())) {
if (StringUtils.equals(nextExistingElement.getSystem(), translationMatch.getSystem())) {
if (StringUtils.equals(nextExistingElement.getSystemVersion(), translationMatch.getSystemVersion())) {
if (StringUtils.equals(nextExistingElement.getCode(), translationMatch.getCode())) {
return true;
}
}

118
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/r4/FhirResourceDaoR4ConceptMapTest.java
View File

@ -4,6 +4,9 @@ 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.api.model.TranslationRequest;
import ca.uhn.fhir.jpa.dao.data.ITermConceptMapGroupDao;
import ca.uhn.fhir.jpa.dao.data.ITermConceptMapGroupElementDao;
import ca.uhn.fhir.jpa.dao.data.ITermConceptMapGroupElementTargetDao;
import ca.uhn.fhir.jpa.entity.TermConceptMap;
import org.hl7.fhir.instance.model.api.IIdType;
import org.hl7.fhir.r4.model.CanonicalType;
@ -16,6 +19,7 @@ import org.junit.jupiter.api.BeforeEach;
import org.junit.jupiter.api.Test;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.data.domain.PageRequest;
import org.springframework.data.domain.Pageable;
import org.springframework.transaction.TransactionStatus;
@ -38,7 +42,12 @@ import static org.junit.jupiter.api.Assertions.assertTrue;
public class FhirResourceDaoR4ConceptMapTest extends BaseJpaR4Test {
private static final Logger ourLog = LoggerFactory.getLogger(FhirResourceDaoR4ConceptMapTest.class);
@Autowired
protected ITermConceptMapGroupDao myConceptMapGroupDao;
@Autowired
protected ITermConceptMapGroupElementDao myConceptMapGroupElementDao;
@Autowired
protected ITermConceptMapGroupElementTargetDao myConceptMapGroupElementTargetDao;
private IIdType myConceptMapId;
@BeforeEach
@ -597,6 +606,113 @@ public class FhirResourceDaoR4ConceptMapTest extends BaseJpaR4Test {
});
}
/**
* Make sure we can handle mapping where the system has no explicit version
* specified in the ConceptMap
*/
@Test
public void testTranslateWithReverse_NonVersionedSystem() {
ConceptMap conceptMap1 = new ConceptMap();
conceptMap1.setUrl(CM_URL);
conceptMap1.setSource(new UriType(VS_URL));
conceptMap1.setTarget(new UriType(VS_URL_2));
ConceptMap.ConceptMapGroupComponent group = conceptMap1.addGroup();
group.setSource(CS_URL);
group.setTarget(CS_URL_2);
ConceptMap.SourceElementComponent element = group.addElement();
element.setCode("12345");
element.setDisplay("Source Code 12345");
ConceptMap.TargetElementComponent target = element.addTarget();
target.setCode("34567");
target.setDisplay("Target Code 34567");
target.setEquivalence(ConceptMapEquivalence.EQUAL);
element = group.addElement();
element.setCode("23456");
element.setDisplay("Source Code 23456");
target = element.addTarget();
target.setCode("45678");
target.setDisplay("Target Code 45678");
target.setEquivalence(ConceptMapEquivalence.WIDER);
group = conceptMap1.addGroup();
group.setSource(CS_URL);
group.setTarget(CS_URL_3);
element = group.addElement();
element.setCode("12345");
element.setDisplay("Source Code 12345");
target = element.addTarget();
target.setCode("56789");
target.setDisplay("Target Code 56789");
target.setEquivalence(ConceptMapEquivalence.EQUAL);
target = element.addTarget();
target.setCode("67890");
target.setDisplay("Target Code 67890");
target.setEquivalence(ConceptMapEquivalence.WIDER);
group = conceptMap1.addGroup();
group.setSource(CS_URL_4);
group.setTarget(CS_URL_2);
element = group.addElement();
element.setCode("12345");
element.setDisplay("Source Code 12345");
target = element.addTarget();
target.setCode("34567");
target.setDisplay("Target Code 34567");
target.setEquivalence(ConceptMapEquivalence.NARROWER);
conceptMap1.setId(myConceptMapId);
myConceptMapDao.update(conceptMap1, mySrd).getId().toUnqualifiedVersionless();
runInTransaction(() -> {
/*
* Provided:
* source code
* reverse = true
*/
TranslationRequest translationRequest = new TranslationRequest();
translationRequest.getCodeableConcept().addCoding()
.setCode("34567");
translationRequest.setReverse(true);
TranslateConceptResults translationResult = myConceptMapDao.translate(translationRequest, null);
assertTrue(translationResult.getResult());
assertEquals("Matches found", translationResult.getMessage());
assertEquals(2, translationResult.getResults().size());
TranslateConceptResult translationMatch = translationResult.getResults().get(0);
assertEquals(ConceptMapEquivalence.EQUAL.toCode(), translationMatch.getEquivalence());
assertEquals("12345", translationMatch.getCode());
assertEquals("Source Code 12345", translationMatch.getDisplay());
assertEquals(CS_URL, translationMatch.getSystem());
assertEquals(null, translationMatch.getSystemVersion());
assertEquals(CM_URL, translationMatch.getConceptMapUrl());
translationMatch = translationResult.getResults().get(1);
assertEquals(ConceptMapEquivalence.NARROWER.toCode(), translationMatch.getEquivalence());
assertEquals("12345", translationMatch.getCode());
assertEquals("Source Code 12345", translationMatch.getDisplay());
assertEquals(CS_URL_4, translationMatch.getSystem());
assertEquals(null, translationMatch.getSystemVersion());
assertEquals(CM_URL, translationMatch.getConceptMapUrl());
});
}
@Test
public void testTranslateWithReverseHavingEquivalence() {
ConceptMap conceptMap = myConceptMapDao.read(myConceptMapId);

7
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/interceptor/PartitioningInterceptorR4Test.java
View File

@ -12,6 +12,7 @@ import ca.uhn.fhir.jpa.interceptor.ex.PartitionInterceptorReadPartitionsBasedOnS
import ca.uhn.fhir.jpa.model.config.PartitionSettings;
import ca.uhn.fhir.jpa.model.entity.ResourceTable;
import ca.uhn.fhir.jpa.partition.IPartitionLookupSvc;
import ca.uhn.fhir.jpa.partition.SystemRequestDetails;
import ca.uhn.fhir.jpa.searchparam.SearchParameterMap;
import ca.uhn.fhir.rest.api.server.IBundleProvider;
import ca.uhn.fhir.rest.server.exceptions.InternalErrorException;
@ -92,7 +93,7 @@ public class PartitioningInterceptorR4Test extends BaseJpaR4SystemTest {
StructureDefinition sd = new StructureDefinition();
sd.setUrl("http://foo");
myStructureDefinitionDao.create(sd);
myStructureDefinitionDao.create(sd, new ServletRequestDetails());
runInTransaction(()->{
List<ResourceTable> resources = myResourceTableDao.findAll();
@ -108,7 +109,7 @@ public class PartitioningInterceptorR4Test extends BaseJpaR4SystemTest {
StructureDefinition sd = new StructureDefinition();
sd.setUrl("http://foo");
myStructureDefinitionDao.create(sd);
myStructureDefinitionDao.create(sd, new ServletRequestDetails());
runInTransaction(()->{
List<ResourceTable> resources = myResourceTableDao.findAll();
@ -124,7 +125,7 @@ public class PartitioningInterceptorR4Test extends BaseJpaR4SystemTest {
StructureDefinition sd = new StructureDefinition();
sd.setUrl("http://foo");
try {
myStructureDefinitionDao.create(sd);
myStructureDefinitionDao.create(sd, new ServletRequestDetails());
fail();
} catch (UnprocessableEntityException e) {
assertEquals("Resource type StructureDefinition can not be partitioned", e.getMessage());

5
hapi-fhir-jpaserver-cql/src/main/java/ca/uhn/fhir/cql/common/retrieve/JpaFhirRetrieveProvider.java
View File

@ -95,10 +95,7 @@ public class JpaFhirRetrieveProvider extends SearchParamFhirRetrieveProvider {
if (bundleProvider.size() == null) {
return resolveResourceList(bundleProvider.getResources(0, 10000));
}
if (bundleProvider.size() == 0) {
return new ArrayList<>();
}
List<IBaseResource> resourceList = bundleProvider.getResources(0, bundleProvider.size());
List<IBaseResource> resourceList = bundleProvider.getAllResources();
return resolveResourceList(resourceList);
}

6
hapi-fhir-jpaserver-cql/src/main/java/ca/uhn/fhir/cql/config/CqlDstu3Config.java
View File

@ -33,10 +33,8 @@ import ca.uhn.fhir.cql.dstu3.provider.MeasureOperationsProvider;
import ca.uhn.fhir.jpa.api.dao.DaoRegistry;
import ca.uhn.fhir.jpa.api.dao.IFhirResourceDao;
import ca.uhn.fhir.jpa.cache.IResourceChangeListenerRegistry;
import ca.uhn.fhir.jpa.term.api.ITermReadSvcDstu3;
import ca.uhn.fhir.jpa.searchparam.SearchParameterMap;
import ca.uhn.fhir.jpa.term.api.ITermReadSvcDstu3;
import org.cqframework.cql.cql2elm.CqlTranslatorOptions;
import org.cqframework.cql.cql2elm.model.Model;
import org.cqframework.cql.elm.execution.Library;
@ -99,7 +97,7 @@ public class CqlDstu3Config extends BaseCqlConfig {
@Bean
public ElmCacheResourceChangeListener elmCacheResourceChangeListener(IResourceChangeListenerRegistry resourceChangeListenerRegistry, IFhirResourceDao<org.hl7.fhir.dstu3.model.Library> libraryDao, Map<org.cqframework.cql.elm.execution.VersionedIdentifier, Library> globalLibraryCache) {
ElmCacheResourceChangeListener listener = new ElmCacheResourceChangeListener(libraryDao, globalLibraryCache);
resourceChangeListenerRegistry.registerResourceResourceChangeListener("Library", new SearchParameterMap(), listener, 1000);
resourceChangeListenerRegistry.registerResourceResourceChangeListener("Library", SearchParameterMap.newSynchronous(), listener, 1000);
return listener;
}
}

6
hapi-fhir-jpaserver-cql/src/main/java/ca/uhn/fhir/cql/config/CqlR4Config.java
View File

@ -34,10 +34,8 @@ import ca.uhn.fhir.cql.r4.provider.MeasureOperationsProvider;
import ca.uhn.fhir.jpa.api.dao.DaoRegistry;
import ca.uhn.fhir.jpa.api.dao.IFhirResourceDao;
import ca.uhn.fhir.jpa.cache.IResourceChangeListenerRegistry;
import ca.uhn.fhir.jpa.term.api.ITermReadSvcR4;
import ca.uhn.fhir.jpa.searchparam.SearchParameterMap;
import ca.uhn.fhir.jpa.term.api.ITermReadSvcR4;
import org.cqframework.cql.cql2elm.CqlTranslatorOptions;
import org.cqframework.cql.cql2elm.model.Model;
import org.cqframework.cql.elm.execution.Library;
@ -110,7 +108,7 @@ public class CqlR4Config extends BaseCqlConfig {
@Bean
public ElmCacheResourceChangeListener elmCacheResourceChangeListener(IResourceChangeListenerRegistry resourceChangeListenerRegistry, IFhirResourceDao<org.hl7.fhir.r4.model.Library> libraryDao, Map<org.cqframework.cql.elm.execution.VersionedIdentifier, Library> globalLibraryCache) {
ElmCacheResourceChangeListener listener = new ElmCacheResourceChangeListener(libraryDao, globalLibraryCache);
resourceChangeListenerRegistry.registerResourceResourceChangeListener("Library", new SearchParameterMap(), listener, 1000);
resourceChangeListenerRegistry.registerResourceResourceChangeListener("Library", SearchParameterMap.newSynchronous(), listener, 1000);
return listener;
}
}

17
hapi-fhir-jpaserver-cql/src/main/java/ca/uhn/fhir/cql/dstu3/evaluation/MeasureEvaluation.java
View File

@ -33,7 +33,6 @@ import org.hl7.fhir.dstu3.model.CodeableConcept;
import org.hl7.fhir.dstu3.model.Coding;
import org.hl7.fhir.dstu3.model.Extension;
import org.hl7.fhir.dstu3.model.IdType;
import org.hl7.fhir.dstu3.model.IntegerType;
import org.hl7.fhir.dstu3.model.ListResource;
import org.hl7.fhir.dstu3.model.Measure;
import org.hl7.fhir.dstu3.model.MeasureReport;
@ -67,8 +66,8 @@ public class MeasureEvaluation {
private static final Logger logger = LoggerFactory.getLogger(MeasureEvaluation.class);
private Interval measurementPeriod;
private DaoRegistry registry;
private final Interval measurementPeriod;
private final DaoRegistry registry;
public MeasureEvaluation(DaoRegistry registry, Interval measurementPeriod) {
this.registry = registry;
@ -107,21 +106,21 @@ public class MeasureEvaluation {
}
private List<Patient> getPractitionerPatients(String practitionerRef) {
SearchParameterMap map = new SearchParameterMap();
SearchParameterMap map = SearchParameterMap.newSynchronous();
map.add("general-practitioner", new ReferenceParam(
practitionerRef.startsWith("Practitioner/") ? practitionerRef : "Practitioner/" + practitionerRef));
List<Patient> patients = new ArrayList<>();
IBundleProvider patientProvider = registry.getResourceDao("Patient").search(map);
List<IBaseResource> patientList = patientProvider.getResources(0, patientProvider.size());
List<IBaseResource> patientList = patientProvider.getAllResources();
patientList.forEach(x -> patients.add((Patient) x));
return patients;
}
private List<Patient> getAllPatients() {
List<Patient> patients = new ArrayList<>();
IBundleProvider patientProvider = registry.getResourceDao("Patient").search(new SearchParameterMap());
List<IBaseResource> patientList = patientProvider.getResources(0, patientProvider.size());
IBundleProvider patientProvider = registry.getResourceDao("Patient").search(SearchParameterMap.newSynchronous());
List<IBaseResource> patientList = patientProvider.getAllResources();
patientList.forEach(x -> patients.add((Patient) x));
return patients;
}
@ -567,7 +566,7 @@ public class MeasureEvaluation {
}
if (!list.isEmpty()) {
list.setId("List/" + UUID.randomUUID().toString());
list.setId("List/" + UUID.randomUUID());
list.setTitle(key);
resources.put(list.getId(), list);
list.getEntry().forEach(listResource -> evaluatedResourcesList.add(listResource.getItem().getReference()));
@ -716,9 +715,7 @@ public class MeasureEvaluation {
Resource r = (Resource) o;
String id = (r.getIdElement().getResourceType() != null ? (r.getIdElement().getResourceType() + "/")
: "") + r.getIdElement().getIdPart();
if (!codeHashSet.contains(id)) {
codeHashSet.add(id);
}
if (!resources.containsKey(id)) {
resources.put(id, r);

4
hapi-fhir-jpaserver-cql/src/main/java/ca/uhn/fhir/cql/dstu3/provider/JpaTerminologyProvider.java
View File

@ -96,8 +96,8 @@ public class JpaTerminologyProvider implements TerminologyProvider {
}
IBundleProvider bundleProvider = myValueSetDao
.search(new SearchParameterMap().add(ValueSet.SP_URL, new UriParam(valueSet.getId())));
List<IBaseResource> valueSets = bundleProvider.getResources(0, bundleProvider.size());
.search(SearchParameterMap.newSynchronous().add(ValueSet.SP_URL, new UriParam(valueSet.getId())));
List<IBaseResource> valueSets = bundleProvider.getAllResources();
if (valueSets.isEmpty()) {
throw new IllegalArgumentException(String.format("Could not resolve value set %s.", valueSet.getId()));
} else if (valueSets.size() == 1) {

12
hapi-fhir-jpaserver-cql/src/main/java/ca/uhn/fhir/cql/dstu3/provider/LibraryResolutionProviderImpl.java
View File

@ -67,7 +67,7 @@ public class LibraryResolutionProviderImpl implements LibraryResolutionProvider<
version = parts[1];
}
SearchParameterMap map = new SearchParameterMap();
SearchParameterMap map = SearchParameterMap.newSynchronous();
map.add("url", new UriParam(resourceUrl));
if (version != null) {
map.add("version", new TokenParam(version));
@ -75,10 +75,10 @@ public class LibraryResolutionProviderImpl implements LibraryResolutionProvider<
ca.uhn.fhir.rest.api.server.IBundleProvider bundleProvider = myLibraryDao.search(map);
if (bundleProvider.size() == 0) {
if (bundleProvider.size() == null || bundleProvider.size() == 0) {
return null;
}
List<IBaseResource> resourceList = bundleProvider.getResources(0, bundleProvider.size());
List<IBaseResource> resourceList = bundleProvider.getAllResources();
return LibraryResolutionProvider.selectFromList(resolveLibraries(resourceList), version, x -> x.getVersion());
}
@ -97,14 +97,14 @@ public class LibraryResolutionProviderImpl implements LibraryResolutionProvider<
private Iterable<org.hl7.fhir.dstu3.model.Library> getLibrariesByName(String name) {
// Search for libraries by name
SearchParameterMap map = new SearchParameterMap();
SearchParameterMap map = SearchParameterMap.newSynchronous();
map.add("name", new StringParam(name, true));
ca.uhn.fhir.rest.api.server.IBundleProvider bundleProvider = myLibraryDao.search(map);
if (bundleProvider.size() == 0) {
if (bundleProvider.size() == null || bundleProvider.size() == 0) {
return new ArrayList<>();
}
List<IBaseResource> resourceList = bundleProvider.getResources(0, bundleProvider.size());
List<IBaseResource> resourceList = bundleProvider.getAllResources();
return resolveLibraries(resourceList);
}

19
hapi-fhir-jpaserver-cql/src/main/java/ca/uhn/fhir/cql/r4/evaluation/MeasureEvaluation.java
View File

@ -35,7 +35,6 @@ import org.hl7.fhir.r4.model.CodeableConcept;
import org.hl7.fhir.r4.model.Coding;
import org.hl7.fhir.r4.model.Extension;
import org.hl7.fhir.r4.model.IdType;
import org.hl7.fhir.r4.model.IntegerType;
import org.hl7.fhir.r4.model.ListResource;
import org.hl7.fhir.r4.model.Measure;
import org.hl7.fhir.r4.model.MeasureReport;
@ -68,9 +67,9 @@ public class MeasureEvaluation {
private static final Logger logger = LoggerFactory.getLogger(MeasureEvaluation.class);
private DataProvider provider;
private Interval measurementPeriod;
private DaoRegistry registry;
private final DataProvider provider;
private final Interval measurementPeriod;
private final DaoRegistry registry;
public MeasureEvaluation(DataProvider provider, DaoRegistry registry, Interval measurementPeriod) {
this.provider = provider;
@ -106,21 +105,21 @@ public class MeasureEvaluation {
}
private List<Patient> getPractitionerPatients(String practitionerRef) {
SearchParameterMap map = new SearchParameterMap();
SearchParameterMap map = SearchParameterMap.newSynchronous();
map.add("general-practitioner", new ReferenceParam(
practitionerRef.startsWith("Practitioner/") ? practitionerRef : "Practitioner/" + practitionerRef));
List<Patient> patients = new ArrayList<>();
IBundleProvider patientProvider = registry.getResourceDao("Patient").search(map);
List<IBaseResource> patientList = patientProvider.getResources(0, patientProvider.size());
List<IBaseResource> patientList = patientProvider.getAllResources();
patientList.forEach(x -> patients.add((Patient) x));
return patients;
}
private List<Patient> getAllPatients() {
List<Patient> patients = new ArrayList<>();
IBundleProvider patientProvider = registry.getResourceDao("Patient").search(new SearchParameterMap());
List<IBaseResource> patientList = patientProvider.getResources(0, patientProvider.size());
IBundleProvider patientProvider = registry.getResourceDao("Patient").search(SearchParameterMap.newSynchronous());
List<IBaseResource> patientList = patientProvider.getAllResources();
patientList.forEach(x -> patients.add((Patient) x));
return patients;
}
@ -552,7 +551,7 @@ public class MeasureEvaluation {
}
if (!list.isEmpty()) {
list.setId("List/" + UUID.randomUUID().toString());
list.setId("List/" + UUID.randomUUID());
list.setTitle(key);
resources.put(list.getId(), list);
list.getEntry().forEach(listResource -> evaluatedResourcesList.add(listResource.getItem().getReference()));
@ -701,9 +700,7 @@ public class MeasureEvaluation {
Resource r = (Resource) o;
String id = (r.getIdElement().getResourceType() != null ? (r.getIdElement().getResourceType() + "/") : "")
+ r.getIdElement().getIdPart();
if (!codeHashSet.contains(id)) {
codeHashSet.add(id);
}
if (!resources.containsKey(id)) {
resources.put(id, r);

4
hapi-fhir-jpaserver-cql/src/main/java/ca/uhn/fhir/cql/r4/provider/JpaTerminologyProvider.java
View File

@ -94,8 +94,8 @@ public class JpaTerminologyProvider implements TerminologyProvider {
}
IBundleProvider bundleProvider = myValueSetDao
.search(new SearchParameterMap().add(ValueSet.SP_URL, new UriParam(valueSet.getId())));
List<IBaseResource> valueSets = bundleProvider.getResources(0, bundleProvider.size());
.search(SearchParameterMap.newSynchronous().add(ValueSet.SP_URL, new UriParam(valueSet.getId())));
List<IBaseResource> valueSets = bundleProvider.getAllResources();
if (valueSets.isEmpty()) {
throw new IllegalArgumentException(String.format("Could not resolve value set %s.", valueSet.getId()));
} else if (valueSets.size() == 1) {

12
hapi-fhir-jpaserver-cql/src/main/java/ca/uhn/fhir/cql/r4/provider/LibraryResolutionProviderImpl.java
View File

@ -86,7 +86,7 @@ public class LibraryResolutionProviderImpl implements LibraryResolutionProvider<
version = parts[1];
}
SearchParameterMap map = new SearchParameterMap();
SearchParameterMap map = SearchParameterMap.newSynchronous();
map.add("url", new UriParam(resourceUrl));
if (version != null) {
map.add("version", new TokenParam(version));
@ -94,23 +94,23 @@ public class LibraryResolutionProviderImpl implements LibraryResolutionProvider<
ca.uhn.fhir.rest.api.server.IBundleProvider bundleProvider = myLibraryDao.search(map);
if (bundleProvider.size() == 0) {
if (bundleProvider.size() == null || bundleProvider.size() == 0) {
return null;
}
List<IBaseResource> resourceList = bundleProvider.getResources(0, bundleProvider.size());
List<IBaseResource> resourceList = bundleProvider.getAllResources();
return LibraryResolutionProvider.selectFromList(resolveLibraries(resourceList), version, x -> x.getVersion());
}
private Iterable<org.hl7.fhir.r4.model.Library> getLibrariesByName(String name) {
// Search for libraries by name
SearchParameterMap map = new SearchParameterMap();
SearchParameterMap map = SearchParameterMap.newSynchronous();
map.add("name", new StringParam(name, true));
ca.uhn.fhir.rest.api.server.IBundleProvider bundleProvider = myLibraryDao.search(map);
if (bundleProvider.size() == 0) {
if (bundleProvider.size() == null || bundleProvider.size() == 0) {
return new ArrayList<>();
}
List<IBaseResource> resourceList = bundleProvider.getResources(0, bundleProvider.size());
List<IBaseResource> resourceList = bundleProvider.getAllResources();
return resolveLibraries(resourceList);
}

10
hapi-fhir-jpaserver-mdm/src/main/java/ca/uhn/fhir/jpa/mdm/svc/candidate/MdmCandidateSearchSvc.java
View File

@ -20,15 +20,15 @@ package ca.uhn.fhir.jpa.mdm.svc.candidate;
* #L%
*/
import ca.uhn.fhir.mdm.api.IMdmSettings;
import ca.uhn.fhir.mdm.log.Logs;
import ca.uhn.fhir.mdm.rules.json.MdmFilterSearchParamJson;
import ca.uhn.fhir.mdm.rules.json.MdmResourceSearchParamJson;
import ca.uhn.fhir.jpa.api.dao.DaoRegistry;
import ca.uhn.fhir.jpa.api.dao.IFhirResourceDao;
import ca.uhn.fhir.jpa.dao.index.IdHelperService;
import ca.uhn.fhir.jpa.mdm.svc.MdmSearchParamSvc;
import ca.uhn.fhir.jpa.searchparam.SearchParameterMap;
import ca.uhn.fhir.mdm.api.IMdmSettings;
import ca.uhn.fhir.mdm.log.Logs;
import ca.uhn.fhir.mdm.rules.json.MdmFilterSearchParamJson;
import ca.uhn.fhir.mdm.rules.json.MdmResourceSearchParamJson;
import ca.uhn.fhir.rest.api.server.IBundleProvider;
import org.hl7.fhir.instance.model.api.IAnyResource;
import org.hl7.fhir.instance.model.api.IBaseResource;
@ -136,7 +136,7 @@ public class MdmCandidateSearchSvc {
//3.
IFhirResourceDao<?> resourceDao = myDaoRegistry.getResourceDao(theResourceType);
IBundleProvider search = resourceDao.search(searchParameterMap);
List<IBaseResource> resources = search.getResources(0, search.size());
List<IBaseResource> resources = search.getAllResources();
int initialSize = theMatchedPidsToResources.size();

4
hapi-fhir-jpaserver-mdm/src/test/java/ca/uhn/fhir/jpa/mdm/svc/MdmBatchSvcImplTest.java → hapi-fhir-jpaserver-mdm/src/test/java/ca/uhn/fhir/jpa/mdm/svc/MdmBatchSvcImplIT.java
View File

@ -1,9 +1,9 @@
package ca.uhn.fhir.jpa.mdm.svc;
import ca.uhn.fhir.mdm.api.IMdmSubmitSvc;
import ca.uhn.fhir.interceptor.api.IInterceptorService;
import ca.uhn.fhir.interceptor.api.Pointcut;
import ca.uhn.fhir.jpa.mdm.BaseMdmR4Test;
import ca.uhn.fhir.mdm.api.IMdmSubmitSvc;
import ca.uhn.test.concurrency.PointcutLatch;
import org.apache.commons.lang3.time.DateUtils;
import org.junit.jupiter.api.AfterEach;
@ -14,7 +14,7 @@ import org.springframework.beans.factory.annotation.Autowired;
import java.io.IOException;
import java.util.Date;
class MdmBatchSvcImplTest extends BaseMdmR4Test {
class MdmBatchSvcImplIT extends BaseMdmR4Test {
@Autowired
IMdmSubmitSvc myMdmSubmitSvc;

4
hapi-fhir-jpaserver-subscription/src/main/java/ca/uhn/fhir/jpa/subscription/match/deliver/resthook/SubscriptionDeliveringRestHookSubscriber.java
View File

@ -66,7 +66,7 @@ import static org.apache.commons.lang3.StringUtils.isNotBlank;
@Scope("prototype")
public class SubscriptionDeliveringRestHookSubscriber extends BaseSubscriptionDeliverySubscriber {
private static Logger ourLog = LoggerFactory.getLogger(SubscriptionDeliveringRestHookSubscriber.class);
private static final Logger ourLog = LoggerFactory.getLogger(SubscriptionDeliveringRestHookSubscriber.class);
@Autowired
private DaoRegistry myDaoRegistry;
@ -155,7 +155,7 @@ public class SubscriptionDeliveringRestHookSubscriber extends BaseSubscriptionDe
IBundleProvider searchResults = dao.search(payloadSearchMap);
BundleBuilder builder = new BundleBuilder(myFhirContext);
for (IBaseResource next : searchResults.getResources(0, searchResults.size())) {
for (IBaseResource next : searchResults.getAllResources()) {
builder.addTransactionUpdateEntry(next);
}

22
hapi-fhir-server/src/main/java/ca/uhn/fhir/rest/api/server/IBundleProvider.java
View File

@ -1,11 +1,13 @@
package ca.uhn.fhir.rest.api.server;
import ca.uhn.fhir.context.ConfigurationException;
import org.apache.commons.lang3.Validate;
import org.hl7.fhir.instance.model.api.IBaseResource;
import org.hl7.fhir.instance.model.api.IPrimitiveType;
import javax.annotation.Nonnull;
import javax.annotation.Nullable;
import java.util.ArrayList;
import java.util.Date;
import java.util.List;
@ -113,6 +115,26 @@ public interface IBundleProvider {
@Nonnull
List<IBaseResource> getResources(int theFromIndex, int theToIndex);
/**
* Get all resources
*
* @return getResources(0, this.size ()). Return an empty list if size() is zero.
* @throws ConfigurationException if size() is null
*/
@Nonnull
default List<IBaseResource> getAllResources() {
List<IBaseResource> retval = new ArrayList<>();
Integer size = size();
if (size == null) {
throw new ConfigurationException("Attempt to request all resources from an asynchronous search result. The SearchParameterMap for this search probably should have been synchronous.");
}
if (size > 0) {
retval.addAll(getResources(0, size));
}
return retval;
}
/**
* Returns the UUID associated with this search. Note that this
* does not need to return a non-null value unless it a

17
hapi-fhir-server/src/main/java/ca/uhn/fhir/rest/server/method/TransactionMethodBinding.java
View File

@ -19,12 +19,6 @@ package ca.uhn.fhir.rest.server.method;
* limitations under the License.
* #L%
*/
import static org.apache.commons.lang3.StringUtils.isNotBlank;
import java.lang.reflect.Method;
import java.util.List;
import org.hl7.fhir.instance.model.api.IBaseResource;
import ca.uhn.fhir.context.ConfigurationException;
import ca.uhn.fhir.context.FhirContext;
@ -34,13 +28,20 @@ import ca.uhn.fhir.rest.annotation.Transaction;
import ca.uhn.fhir.rest.annotation.TransactionParam;
import ca.uhn.fhir.rest.api.RequestTypeEnum;
import ca.uhn.fhir.rest.api.RestOperationTypeEnum;
import ca.uhn.fhir.rest.api.server.*;
import ca.uhn.fhir.rest.api.server.IBundleProvider;
import ca.uhn.fhir.rest.api.server.IRestfulServer;
import ca.uhn.fhir.rest.api.server.RequestDetails;
import ca.uhn.fhir.rest.server.exceptions.InternalErrorException;
import ca.uhn.fhir.rest.server.exceptions.InvalidRequestException;
import ca.uhn.fhir.rest.server.interceptor.IServerInterceptor.ActionRequestDetails;
import ca.uhn.fhir.rest.server.method.TransactionParameter.ParamStyle;
import org.hl7.fhir.instance.model.api.IBaseResource;
import javax.annotation.Nonnull;
import java.lang.reflect.Method;
import java.util.List;
import static org.apache.commons.lang3.StringUtils.isNotBlank;
public class TransactionMethodBinding extends BaseResourceReturningMethodBinding {
@ -127,7 +128,7 @@ public class TransactionMethodBinding extends BaseResourceReturningMethodBinding
* " entries, but server method response contained " + retVal.size() + " entries (must be the same)"); } }
*/
List<IBaseResource> retResources = retVal.getResources(0, retVal.size());
List<IBaseResource> retResources = retVal.getAllResources();
for (int i = 0; i < retResources.size(); i++) {
IBaseResource newRes = retResources.get(i);
if (newRes.getIdElement() == null || newRes.getIdElement().isEmpty()) {

18
hapi-fhir-server/src/test/java/ca/uhn/fhir/rest/api/server/IBundleProviderTest.java
View File

@ -1,12 +1,15 @@
package ca.uhn.fhir.rest.api.server;
import ca.uhn.fhir.context.ConfigurationException;
import ca.uhn.fhir.rest.server.SimpleBundleProvider;
import com.google.common.collect.Lists;
import org.hl7.fhir.instance.model.api.IBaseResource;
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.assertTrue;
import static org.junit.jupiter.api.Assertions.fail;
import static org.mockito.Mockito.mock;
public class IBundleProviderTest {
@ -39,4 +42,19 @@ public class IBundleProviderTest {
assertFalse(provider.isEmpty());
}
@Test
void getResources() {
SimpleBundleProvider provider = new SimpleBundleProvider() {
@Override
public Integer size() {
return null;
}
};
try {
provider.getAllResources();
fail();
} catch (ConfigurationException e) {
assertEquals("Attempt to request all resources from an asynchronous search result. The SearchParameterMap for this search probably should have been synchronous.", e.getMessage());
}
}
}