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hapi-fhir
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Merge remote-tracking branch 'remotes/origin/master' into ks-flyway

This commit is contained in:
Ken Stevens 2019-10-31 09:38:30 -04:00
parent 29752465c8 97d5edc0b0
commit 9c9193b401
33 changed files with 870 additions and 228 deletions
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33
hapi-fhir-base/src/main/java/ca/uhn/fhir/util/MetaUtil.java
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@ -26,18 +26,47 @@ import ca.uhn.fhir.context.FhirContext;
import ca.uhn.fhir.context.FhirVersionEnum;
import ca.uhn.fhir.rest.api.Constants;
import org.hl7.fhir.instance.model.api.*;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import java.util.List;
public class MetaUtil {
private static final Logger ourLog = LoggerFactory.getLogger(MetaUtil.class);
private MetaUtil() {
// non-instantiable
}
public static String getSource(FhirContext theContext, IBaseMetaType theMeta) {
BaseRuntimeElementCompositeDefinition<?> elementDef = (BaseRuntimeElementCompositeDefinition<?>) theContext.getElementDefinition(theMeta.getClass());
if (theContext.getVersion().getVersion().isEqualOrNewerThan(FhirVersionEnum.R4)) {
return getSourceR4Plus(theContext, theMeta);
} else if (theContext.getVersion().getVersion().equals(FhirVersionEnum.DSTU3)) {
return getSourceDstu3((IBaseHasExtensions) theMeta);
} else {
throw new UnsupportedOperationException(MetaUtil.class.getSimpleName() + ".getSource() not supported on FHIR Version " + theContext.getVersion().getVersion());
}
}
private static String getSourceDstu3(IBaseHasExtensions theMeta) {
IBaseHasExtensions metaWithExtensions = theMeta;
List<? extends IBaseExtension<?, ?>> extensions = metaWithExtensions.getExtension();
for (IBaseExtension extension : extensions) {
if (Constants.EXT_META_SOURCE.equals(extension.getUrl())) {
IPrimitiveType<String> value = (IPrimitiveType<String>) extension.getValue();
return value.getValueAsString();
}
}
return null;
}
private static String getSourceR4Plus(FhirContext theFhirContext, IBaseMetaType theMeta) {
BaseRuntimeElementCompositeDefinition<?> elementDef = (BaseRuntimeElementCompositeDefinition<?>) theFhirContext.getElementDefinition(theMeta.getClass());
BaseRuntimeChildDefinition sourceChild = elementDef.getChildByName("source");
if (sourceChild == null) {
return null;
}
List<IBase> sourceValues = sourceChild.getAccessor().getValues(theMeta);
String retVal = null;
if (sourceValues.size() > 0) {
@ -66,6 +95,8 @@ public class MetaUtil {
IPrimitiveType<String> value = (IPrimitiveType<String>) theContext.getElementDefinition("uri").newInstance();
value.setValue(theValue);
sourceExtension.setValue(value);
} else {
ourLog.error(MetaUtil.class.getSimpleName() + ".setSource() not supported on FHIR Version " + theContext.getVersion().getVersion());
}
}

1
hapi-fhir-base/src/main/resources/ca/uhn/fhir/i18n/hapi-messages.properties
View File

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

32
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/provider/r4/JpaConformanceProviderR4.java
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@ -19,24 +19,25 @@ package ca.uhn.fhir.jpa.provider.r4;
* limitations under the License.
* #L%
*/
import java.util.*;
import javax.servlet.http.HttpServletRequest;
import ca.uhn.fhir.jpa.searchparam.registry.ISearchParamRegistry;
import ca.uhn.fhir.rest.api.Constants;
import ca.uhn.fhir.rest.api.server.RequestDetails;
import org.hl7.fhir.r4.model.*;
import org.hl7.fhir.r4.model.CapabilityStatement.*;
import org.hl7.fhir.r4.model.Enumerations.SearchParamType;
import ca.uhn.fhir.context.RuntimeResourceDefinition;
import ca.uhn.fhir.context.RuntimeSearchParam;
import ca.uhn.fhir.jpa.dao.DaoConfig;
import ca.uhn.fhir.jpa.dao.IFhirSystemDao;
import ca.uhn.fhir.jpa.searchparam.registry.ISearchParamRegistry;
import ca.uhn.fhir.rest.api.Constants;
import ca.uhn.fhir.rest.api.server.RequestDetails;
import ca.uhn.fhir.rest.server.RestfulServer;
import ca.uhn.fhir.util.CoverageIgnore;
import ca.uhn.fhir.util.ExtensionConstants;
import org.hl7.fhir.r4.model.*;
import org.hl7.fhir.r4.model.CapabilityStatement.*;
import org.hl7.fhir.r4.model.Enumerations.SearchParamType;
import javax.servlet.http.HttpServletRequest;
import java.util.Collection;
import java.util.Collections;
import java.util.Map;
import static org.apache.commons.lang3.ObjectUtils.defaultIfNull;
import static org.apache.commons.lang3.StringUtils.isNotBlank;
@ -141,6 +142,9 @@ public class JpaConformanceProviderR4 extends org.hl7.fhir.r4.hapi.rest.server.S
case URI:
confSp.setType(SearchParamType.URI);
break;
case SPECIAL:
confSp.setType(SearchParamType.SPECIAL);
break;
case HAS:
// Shouldn't happen
break;
@ -171,6 +175,10 @@ public class JpaConformanceProviderR4 extends org.hl7.fhir.r4.hapi.rest.server.S
return myIncludeResourceCounts;
}
public void setIncludeResourceCounts(boolean theIncludeResourceCounts) {
myIncludeResourceCounts = theIncludeResourceCounts;
}
/**
* Subclasses may override
*/
@ -187,10 +195,6 @@ public class JpaConformanceProviderR4 extends org.hl7.fhir.r4.hapi.rest.server.S
myImplementationDescription = theImplDesc;
}
public void setIncludeResourceCounts(boolean theIncludeResourceCounts) {
myIncludeResourceCounts = theIncludeResourceCounts;
}
@Override
public void setRestfulServer(RestfulServer theRestfulServer) {
this.myRestfulServer = theRestfulServer;

11
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/provider/r5/JpaConformanceProviderR5.java
View File

@ -140,6 +140,9 @@ public class JpaConformanceProviderR5 extends org.hl7.fhir.r5.hapi.rest.server.S
case URI:
confSp.setType(SearchParamType.URI);
break;
case SPECIAL:
confSp.setType(SearchParamType.SPECIAL);
break;
case HAS:
// Shouldn't happen
break;
@ -170,6 +173,10 @@ public class JpaConformanceProviderR5 extends org.hl7.fhir.r5.hapi.rest.server.S
return myIncludeResourceCounts;
}
public void setIncludeResourceCounts(boolean theIncludeResourceCounts) {
myIncludeResourceCounts = theIncludeResourceCounts;
}
/**
* Subclasses may override
*/
@ -186,10 +193,6 @@ public class JpaConformanceProviderR5 extends org.hl7.fhir.r5.hapi.rest.server.S
myImplementationDescription = theImplDesc;
}
public void setIncludeResourceCounts(boolean theIncludeResourceCounts) {
myIncludeResourceCounts = theIncludeResourceCounts;
}
@Override
public void setRestfulServer(RestfulServer theRestfulServer) {
this.myRestfulServer = theRestfulServer;

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

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

46
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/term/BaseTermReadSvcImpl.java
View File

@ -424,13 +424,13 @@ public abstract class BaseTermReadSvcImpl implements ITermReadSvc, ApplicationCo
private void logConceptsExpanded(String theLogDescriptionPrefix, TermValueSet theTermValueSet, int theConceptsExpanded) {
if (theConceptsExpanded > 0) {
ourLog.info("{}Have expanded {} concepts in ValueSet[{}]", theLogDescriptionPrefix, theConceptsExpanded, theTermValueSet.getUrl());
ourLog.debug("{}Have expanded {} concepts in ValueSet[{}]", theLogDescriptionPrefix, theConceptsExpanded, theTermValueSet.getUrl());
}
}
private void logDesignationsExpanded(String theLogDescriptionPrefix, TermValueSet theTermValueSet, int theDesignationsExpanded) {
if (theDesignationsExpanded > 0) {
ourLog.info("{}Have expanded {} designations in ValueSet[{}]", theLogDescriptionPrefix, theDesignationsExpanded, theTermValueSet.getUrl());
ourLog.debug("{}Have expanded {} designations in ValueSet[{}]", theLogDescriptionPrefix, theDesignationsExpanded, theTermValueSet.getUrl());
}
}
@ -446,7 +446,7 @@ public abstract class BaseTermReadSvcImpl implements ITermReadSvc, ApplicationCo
StopWatch sw = new StopWatch();
String valueSetInfo = getValueSetInfo(theValueSetToExpand);
ourLog.info("Working with {}", valueSetInfo);
ourLog.debug("Working with {}", valueSetInfo);
// Handle includes
ourLog.debug("Handling includes");
@ -488,7 +488,7 @@ public abstract class BaseTermReadSvcImpl implements ITermReadSvc, ApplicationCo
myTxTemplate.execute(t -> ((ValueSetConceptAccumulator) theValueSetCodeAccumulator).removeGapsFromConceptOrder());
}
ourLog.info("Done working with {} in {}ms", valueSetInfo, sw.getMillis());
ourLog.debug("Done working with {} in {}ms", valueSetInfo, sw.getMillis());
}
private String getValueSetInfo(ValueSet theValueSet) {
@ -553,7 +553,7 @@ public abstract class BaseTermReadSvcImpl implements ITermReadSvc, ApplicationCo
return false;
}
ourLog.info("Starting {} expansion around CodeSystem: {}", (theAdd ? "inclusion" : "exclusion"), system);
ourLog.debug("Starting {} expansion around CodeSystem: {}", (theAdd ? "inclusion" : "exclusion"), system);
TermCodeSystem cs = myCodeSystemDao.findByCodeSystemUri(system);
if (cs != null) {
@ -566,7 +566,7 @@ public abstract class BaseTermReadSvcImpl implements ITermReadSvc, ApplicationCo
* since we're going to do it without the database.
*/
if (myFulltextSearchSvc == null) {
expandWithoutHibernateSearch(theValueSetCodeAccumulator, theAddedCodes, theIncludeOrExclude, system, theAdd, theCodeCounter);
expandWithoutHibernateSearch(theValueSetCodeAccumulator, csv, theAddedCodes, theIncludeOrExclude, system, theAdd, theCodeCounter);
return false;
}
@ -642,7 +642,7 @@ public abstract class BaseTermReadSvcImpl implements ITermReadSvc, ApplicationCo
jpaQuery.setMaxResults(maxResultsPerBatch);
jpaQuery.setFirstResult(theQueryIndex * maxResultsPerBatch);
ourLog.info("Beginning batch expansion for {} with max results per batch: {}", (theAdd ? "inclusion" : "exclusion"), maxResultsPerBatch);
ourLog.debug("Beginning batch expansion for {} with max results per batch: {}", (theAdd ? "inclusion" : "exclusion"), maxResultsPerBatch);
StopWatch swForBatch = new StopWatch();
AtomicInteger countForBatch = new AtomicInteger(0);
@ -661,10 +661,10 @@ public abstract class BaseTermReadSvcImpl implements ITermReadSvc, ApplicationCo
}
}
ourLog.info("Batch expansion for {} with starting index of {} produced {} results in {}ms", (theAdd ? "inclusion" : "exclusion"), firstResult, countForBatch, swForBatch.getMillis());
ourLog.debug("Batch expansion for {} with starting index of {} produced {} results in {}ms", (theAdd ? "inclusion" : "exclusion"), firstResult, countForBatch, swForBatch.getMillis());
if (resultsInBatch < maxResultsPerBatch) {
ourLog.info("Expansion for {} produced {} results in {}ms", (theAdd ? "inclusion" : "exclusion"), count, sw.getMillis());
ourLog.debug("Expansion for {} produced {} results in {}ms", (theAdd ? "inclusion" : "exclusion"), count, sw.getMillis());
return false;
} else {
return true;
@ -675,7 +675,10 @@ public abstract class BaseTermReadSvcImpl implements ITermReadSvc, ApplicationCo
CodeSystem codeSystemFromContext = getCodeSystemFromContext(system);
if (codeSystemFromContext == null) {
throw new InvalidRequestException("Unknown code system: " + system);
String msg = myContext.getLocalizer().getMessage(BaseTermReadSvcImpl.class, "expansionRefersToUnknownCs", system);
ourLog.warn(msg);
theValueSetCodeAccumulator.addMessage(msg);
return false;
}
if (!theIncludeOrExclude.getConcept().isEmpty()) {
@ -709,7 +712,7 @@ public abstract class BaseTermReadSvcImpl implements ITermReadSvc, ApplicationCo
} else if (hasValueSet) {
for (CanonicalType nextValueSet : theIncludeOrExclude.getValueSet()) {
ourLog.info("Starting {} expansion around ValueSet: {}", (theAdd ? "inclusion" : "exclusion"), nextValueSet.getValueAsString());
ourLog.debug("Starting {} expansion around ValueSet: {}", (theAdd ? "inclusion" : "exclusion"), nextValueSet.getValueAsString());
List<VersionIndependentConcept> expanded = expandValueSet(nextValueSet.getValueAsString());
Map<String, TermCodeSystem> uriToCodeSystem = new HashMap<>();
@ -845,7 +848,7 @@ public abstract class BaseTermReadSvcImpl implements ITermReadSvc, ApplicationCo
.orElseThrow(() -> new InvalidRequestException("Invalid filter criteria - code does not exist: {" + theSystem + "}" + theFilter.getValue()));
if (theFilter.getOp() == ValueSet.FilterOperator.ISA) {
ourLog.info(" * Filtering on codes with a parent of {}/{}/{}", code.getId(), code.getCode(), code.getDisplay());
ourLog.debug(" * Filtering on codes with a parent of {}/{}/{}", code.getId(), code.getCode(), code.getDisplay());
theBool.must(theQb.keyword().onField("myParentPids").matching("" + code.getId()).createQuery());
} else {
throw new InvalidRequestException("Don't know how to handle op=" + theFilter.getOp() + " on property " + theFilter.getProperty());
@ -1012,7 +1015,7 @@ public abstract class BaseTermReadSvcImpl implements ITermReadSvc, ApplicationCo
}
private void logFilteringValueOnProperty(String theValue, String theProperty) {
ourLog.info(" * Filtering with value={} on property {}", theValue, theProperty);
ourLog.debug(" * Filtering with value={} on property {}", theValue, theProperty);
}
private void throwInvalidRequestForOpOnProperty(ValueSet.FilterOperator theOp, String theProperty) {
@ -1057,7 +1060,7 @@ public abstract class BaseTermReadSvcImpl implements ITermReadSvc, ApplicationCo
}
}
private void expandWithoutHibernateSearch(IValueSetConceptAccumulator theValueSetCodeAccumulator, Set<String> theAddedCodes, ValueSet.ConceptSetComponent theInclude, String theSystem, boolean theAdd, AtomicInteger theCodeCounter) {
private void expandWithoutHibernateSearch(IValueSetConceptAccumulator theValueSetCodeAccumulator, TermCodeSystemVersion theVersion, Set<String> theAddedCodes, ValueSet.ConceptSetComponent theInclude, String theSystem, boolean theAdd, AtomicInteger theCodeCounter) {
ourLog.trace("Hibernate search is not enabled");
if (theValueSetCodeAccumulator instanceof ValueSetExpansionComponentWithConceptAccumulator) {
Validate.isTrue(((ValueSetExpansionComponentWithConceptAccumulator) theValueSetCodeAccumulator).getParameter().isEmpty(), "Can not expand ValueSet with parameters - Hibernate Search is not enabled on this server.");
@ -1065,12 +1068,21 @@ public abstract class BaseTermReadSvcImpl implements ITermReadSvc, ApplicationCo
Validate.isTrue(theInclude.getFilter().isEmpty(), "Can not expand ValueSet with filters - Hibernate Search is not enabled on this server.");
Validate.isTrue(isNotBlank(theSystem), "Can not expand ValueSet without explicit system - Hibernate Search is not enabled on this server.");
if (theInclude.getConcept().isEmpty()) {
for (TermConcept next : theVersion.getConcepts()) {
addCodeIfNotAlreadyAdded(theValueSetCodeAccumulator, theAddedCodes, null, theAdd, theCodeCounter, theSystem, next.getCode(), next.getDisplay());
}
}
for (ValueSet.ConceptReferenceComponent next : theInclude.getConcept()) {
if (!theSystem.equals(theInclude.getSystem())) {
continue;
}
addCodeIfNotAlreadyAdded(theValueSetCodeAccumulator, theAddedCodes, null, theAdd, theCodeCounter, theSystem, next.getCode(), next.getDisplay());
}
}
@Override
@ -1212,7 +1224,7 @@ public abstract class BaseTermReadSvcImpl implements ITermReadSvc, ApplicationCo
fetchParents(concept.get(), retVal);
ourLog.info("Fetched {} codes above code {} in {}ms", retVal.size(), theCode, stopwatch.getMillis());
ourLog.debug("Fetched {} codes above code {} in {}ms", retVal.size(), theCode, stopwatch.getMillis());
return retVal;
}
@ -1243,7 +1255,7 @@ public abstract class BaseTermReadSvcImpl implements ITermReadSvc, ApplicationCo
fetchChildren(concept.get(), retVal);
ourLog.info("Fetched {} codes below code {} in {}ms", retVal.size(), theCode, stopwatch.elapsed(TimeUnit.MILLISECONDS));
ourLog.debug("Fetched {} codes below code {} in {}ms", retVal.size(), theCode, stopwatch.elapsed(TimeUnit.MILLISECONDS));
return retVal;
}
@ -1292,7 +1304,7 @@ public abstract class BaseTermReadSvcImpl implements ITermReadSvc, ApplicationCo
@Override
@Transactional
public void storeTermConceptMapAndChildren(ResourceTable theResourceTable, ConceptMap theConceptMap) {
ourLog.info("Storing TermConceptMap for {}", theConceptMap.getIdElement().toVersionless().getValueAsString());
ourLog.debug("Storing TermConceptMap for {}", theConceptMap.getIdElement().toVersionless().getValueAsString());
ValidateUtil.isTrueOrThrowInvalidRequest(theResourceTable != null, "No resource supplied");
ValidateUtil.isNotBlankOrThrowUnprocessableEntity(theConceptMap.getUrl(), "ConceptMap has no value for ConceptMap.url");

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

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

26
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/term/TermCodeSystemStorageSvcImpl.java
View File

@ -335,7 +335,7 @@ public class TermCodeSystemStorageSvcImpl implements ITermCodeSystemStorageSvc {
populateCodeSystemVersionProperties(persCs, theCodeSystem, theResourceEntity);
persCs.getConcepts().addAll(BaseTermReadSvcImpl.toPersistedConcepts(theCodeSystem.getConcept(), persCs));
ourLog.info("Code system has {} concepts", persCs.getConcepts().size());
ourLog.debug("Code system has {} concepts", persCs.getConcepts().size());
storeNewCodeSystemVersion(codeSystemResourcePid, codeSystemUrl, theCodeSystem.getName(), theCodeSystem.getVersion(), persCs, theResourceEntity);
}
@ -366,7 +366,7 @@ public class TermCodeSystemStorageSvcImpl implements ITermCodeSystemStorageSvc {
@Override
@Transactional(propagation = Propagation.REQUIRED)
public void storeNewCodeSystemVersion(Long theCodeSystemResourcePid, String theSystemUri, String theSystemName, String theSystemVersionId, TermCodeSystemVersion theCodeSystemVersion, ResourceTable theCodeSystemResourceTable) {
ourLog.info("Storing code system");
ourLog.debug("Storing code system");
ValidateUtil.isTrueOrThrowInvalidRequest(theCodeSystemVersion.getResource() != null, "No resource supplied");
ValidateUtil.isNotBlankOrThrowInvalidRequest(theSystemUri, "No system URI supplied");
@ -378,15 +378,15 @@ public class TermCodeSystemStorageSvcImpl implements ITermCodeSystemStorageSvc {
* For now we always delete old versions. At some point it would be nice to allow configuration to keep old versions.
*/
ourLog.info("Deleting old code system versions");
for (TermCodeSystemVersion next : existing) {
ourLog.info("Deleting old code system version {}", next.getPid());
Long codeSystemVersionPid = next.getPid();
deleteCodeSystemVersion(codeSystemVersionPid);
}
ourLog.info("Flushing...");
ourLog.debug("Flushing...");
myConceptDao.flush();
ourLog.info("Done flushing");
ourLog.debug("Done flushing");
/*
* Do the upload
@ -399,7 +399,7 @@ public class TermCodeSystemStorageSvcImpl implements ITermCodeSystemStorageSvc {
theCodeSystemVersion.setCodeSystemDisplayName(theSystemName);
theCodeSystemVersion.setCodeSystemVersionId(theSystemVersionId);
ourLog.info("Validating all codes in CodeSystem for storage (this can take some time for large sets)");
ourLog.debug("Validating all codes in CodeSystem for storage (this can take some time for large sets)");
// Validate the code system
ArrayList<String> conceptsStack = new ArrayList<>();
@ -409,35 +409,33 @@ public class TermCodeSystemStorageSvcImpl implements ITermCodeSystemStorageSvc {
totalCodeCount += validateConceptForStorage(next, theCodeSystemVersion, conceptsStack, allConcepts);
}
ourLog.info("Saving version containing {} concepts", totalCodeCount);
ourLog.debug("Saving version containing {} concepts", totalCodeCount);
TermCodeSystemVersion codeSystemVersion = myCodeSystemVersionDao.saveAndFlush(theCodeSystemVersion);
ourLog.info("Saving code system");
ourLog.debug("Saving code system");
codeSystem.setCurrentVersion(theCodeSystemVersion);
codeSystem = myCodeSystemDao.saveAndFlush(codeSystem);
ourLog.info("Setting CodeSystemVersion[{}] on {} concepts...", codeSystem.getPid(), totalCodeCount);
ourLog.debug("Setting CodeSystemVersion[{}] on {} concepts...", codeSystem.getPid(), totalCodeCount);
for (TermConcept next : theCodeSystemVersion.getConcepts()) {
populateVersion(next, codeSystemVersion);
}
ourLog.info("Saving {} concepts...", totalCodeCount);
ourLog.debug("Saving {} concepts...", totalCodeCount);
IdentityHashMap<TermConcept, Object> conceptsStack2 = new IdentityHashMap<>();
for (TermConcept next : theCodeSystemVersion.getConcepts()) {
persistChildren(next, codeSystemVersion, conceptsStack2, totalCodeCount);
}
ourLog.info("Done saving concepts, flushing to database");
ourLog.debug("Done saving concepts, flushing to database");
myConceptDao.flush();
myConceptParentChildLinkDao.flush();
ourLog.info("Done deleting old code system versions");
if (myDeferredStorageSvc.isStorageQueueEmpty() == false) {
ourLog.info("Note that some concept saving has been deferred");
}
@ -612,7 +610,7 @@ public class TermCodeSystemStorageSvcImpl implements ITermCodeSystemStorageSvc {
return;
}
if (theConceptsStack.size() == 1 || theConceptsStack.size() % 10000 == 0) {
if ((theConceptsStack.size() + 1) % 10000 == 0) {
float pct = (float) theConceptsStack.size() / (float) theTotalConcepts;
ourLog.info("Have processed {}/{} concepts ({}%)", theConceptsStack.size(), theTotalConcepts, (int) (pct * 100.0f));
}

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

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

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

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

27
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/dstu3/FhirResourceDaoDstu3ValidateTest.java
View File

@ -89,6 +89,33 @@ public class FhirResourceDaoDstu3ValidateTest extends BaseJpaDstu3Test {
}
@Test
public void testValidateQuestionnaireResponseWithValueSetIncludingCompleteCodeSystem() throws IOException {
CodeSystem cs = loadResourceFromClasspath(CodeSystem.class, "/dstu3/iar/CodeSystem-iar-citizenship-status.xml");
myCodeSystemDao.create(cs);
ValueSet vs = loadResourceFromClasspath(ValueSet.class, "/dstu3/iar/ValueSet-iar-citizenship-status.xml");
myValueSetDao.create(vs);
ValueSet expansion = myValueSetDao.expandByIdentifier("http://ccim.on.ca/fhir/iar/ValueSet/iar-citizenship-status", null);
ourLog.info(myFhirCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(expansion));
// Questionnaire q = loadResourceFromClasspath(Questionnaire.class,"/dstu3/iar/Questionnaire-iar-test.xml" );
// myQuestionnaireDao.create(q);
//
//
//
// Bundle bundleForValidation = loadResourceFromClasspath(Bundle.class, "/dstu3/iar/Bundle-for-validation.xml");
// try {
// MethodOutcome outcome = myBundleDao.validate(bundleForValidation, null, null, null, null, null, null);
// ourLog.info(myFhirCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(outcome.getOperationOutcome()));
// } catch (PreconditionFailedException e) {
// ourLog.info(myFhirCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(e.getOperationOutcome()));
// }
}
@After
public void after() {
FhirInstanceValidator val = AopTestUtils.getTargetObject(myValidatorModule);

44
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/r4/FhirResourceDaoR4SearchWithLuceneDisabledTest.java
View File

@ -4,17 +4,21 @@ import ca.uhn.fhir.context.FhirContext;
import ca.uhn.fhir.jpa.bulk.IBulkDataExportSvc;
import ca.uhn.fhir.jpa.config.TestR4WithLuceneDisabledConfig;
import ca.uhn.fhir.jpa.dao.*;
import ca.uhn.fhir.jpa.dao.dstu2.FhirResourceDaoDstu2SearchNoFtTest;
import ca.uhn.fhir.jpa.search.ISearchCoordinatorSvc;
import ca.uhn.fhir.jpa.search.reindex.IResourceReindexingSvc;
import ca.uhn.fhir.jpa.searchparam.registry.ISearchParamRegistry;
import ca.uhn.fhir.jpa.searchparam.SearchParameterMap;
import ca.uhn.fhir.jpa.searchparam.registry.ISearchParamRegistry;
import ca.uhn.fhir.jpa.sp.ISearchParamPresenceSvc;
import ca.uhn.fhir.parser.IParser;
import ca.uhn.fhir.rest.api.EncodingEnum;
import ca.uhn.fhir.rest.api.server.IBundleProvider;
import ca.uhn.fhir.rest.param.StringParam;
import ca.uhn.fhir.rest.param.TokenParam;
import ca.uhn.fhir.rest.param.TokenParamModifier;
import ca.uhn.fhir.rest.server.exceptions.InvalidRequestException;
import ca.uhn.fhir.util.TestUtil;
import org.apache.commons.io.IOUtils;
import org.hl7.fhir.instance.model.api.IBaseResource;
import org.hl7.fhir.instance.model.api.IIdType;
import org.hl7.fhir.r4.hapi.ctx.IValidationSupport;
@ -31,11 +35,13 @@ import org.springframework.transaction.PlatformTransactionManager;
import org.springframework.transaction.annotation.Transactional;
import javax.persistence.EntityManager;
import java.io.IOException;
import java.io.InputStream;
import java.nio.charset.StandardCharsets;
import java.util.List;
import static org.junit.Assert.*;
import static org.mockito.ArgumentMatchers.any;
import static org.junit.Assert.assertEquals;
import static org.junit.Assert.fail;
@RunWith(SpringJUnit4ClassRunner.class)
@ContextConfiguration(classes = {TestR4WithLuceneDisabledConfig.class})
@ -71,7 +77,7 @@ public class FhirResourceDaoR4SearchWithLuceneDisabledTest extends BaseJpaTest {
private IFhirResourceDao<CodeSystem> myCodeSystemDao;
@Autowired
@Qualifier("myValueSetDaoR4")
private IFhirResourceDao<ValueSet> myValueSetDao;
private IFhirResourceDaoValueSet<ValueSet, ?, ?> myValueSetDao;
@Autowired
@Qualifier("myObservationDaoR4")
private IFhirResourceDao<Observation> myObservationDao;
@ -219,6 +225,34 @@ public class FhirResourceDaoR4SearchWithLuceneDisabledTest extends BaseJpaTest {
}
protected <T extends IBaseResource> T loadResourceFromClasspath(Class<T> type, String resourceName) throws IOException {
InputStream stream = FhirResourceDaoDstu2SearchNoFtTest.class.getResourceAsStream(resourceName);
if (stream == null) {
fail("Unable to load resource: " + resourceName);
}
String string = IOUtils.toString(stream, StandardCharsets.UTF_8);
IParser newJsonParser = EncodingEnum.detectEncodingNoDefault(string).newParser(myFhirCtx);
return newJsonParser.parseResource(type, string);
}
/**
* A valueset that includes a whole system (i.e. no properties) should expand
*/
@Test
public void testExpandValueSetContainingSystemIncludeWithNoCodes() throws IOException {
CodeSystem cs = loadResourceFromClasspath(CodeSystem.class, "/dstu3/iar/CodeSystem-iar-citizenship-status.xml");
myCodeSystemDao.create(cs);
ValueSet vs = loadResourceFromClasspath(ValueSet.class, "/dstu3/iar/ValueSet-iar-citizenship-status.xml");
myValueSetDao.create(vs);
ValueSet expansion = myValueSetDao.expandByIdentifier("http://ccim.on.ca/fhir/iar/ValueSet/iar-citizenship-status", null);
ourLog.info(myFhirCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(expansion));
assertEquals(4, expansion.getExpansion().getContains().size());
}
@AfterClass

2
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/r4/FhirResourceDaoR4ValidateTest.java
View File

@ -730,6 +730,8 @@ public class FhirResourceDaoR4ValidateTest extends BaseJpaR4Test {
assertEquals("The questionnaire \"Questionnaire/DOES_NOT_EXIST\" could not be resolved, so no validation can be performed against the base questionnaire", oo.getIssueFirstRep().getDiagnostics());
}
private IBaseResource findResourceByIdInBundle(Bundle vss, String name) {
IBaseResource retVal = null;
for (BundleEntryComponent next : vss.getEntry()) {

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

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

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

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

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

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

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

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

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

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

36
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/subscription/resthook/RestHookTestDstu3Test.java
View File

@ -18,6 +18,7 @@ import ca.uhn.fhir.rest.server.IResourceProvider;
import ca.uhn.fhir.rest.server.RestfulServer;
import ca.uhn.fhir.rest.server.exceptions.UnprocessableEntityException;
import ca.uhn.fhir.test.utilities.JettyUtil;
import ca.uhn.fhir.util.MetaUtil;
import com.google.common.collect.Lists;
import org.eclipse.jetty.server.Server;
import org.eclipse.jetty.servlet.ServletContextHandler;
@ -242,6 +243,33 @@ public class RestHookTestDstu3Test extends BaseResourceProviderDstu3Test {
assertEquals(Constants.CT_FHIR_JSON_NEW, ourContentTypes.get(0));
}
@Test
public void testRestHookSubscriptionSource() throws Exception {
String payload = "application/fhir+json";
String source = "foosource";
String criteria = "Observation?_source=" + source;
Subscription subscription = newSubscription(criteria, payload, ourListenerServerBase, null);
MethodOutcome methodOutcome = ourClient.create().resource(subscription).execute();
Subscription savedSub = (Subscription) methodOutcome.getResource();
assertInMemoryTag(savedSub);
mySubscriptionIds.add(methodOutcome.getId());
waitForQueueToDrain();
Observation observation = new Observation();
MetaUtil.setSource(myFhirCtx, observation, source);
ourClient.create().resource(observation).execute();
// Should see 1 subscription notification
waitForQueueToDrain();
waitForSize(0, ourCreatedObservations);
waitForSize(1, ourUpdatedObservations);
assertEquals(Constants.CT_FHIR_JSON_NEW, ourContentTypes.get(0));
}
@Test
public void testRestHookSubscriptionApplicationJson() throws Exception {
String payload = "application/json";
@ -478,7 +506,13 @@ public class RestHookTestDstu3Test extends BaseResourceProviderDstu3Test {
Subscription subscriptionActivated = ourClient.read().resource(Subscription.class).withId(subscriptionId.toUnqualifiedVersionless()).execute();
assertEquals(Subscription.SubscriptionStatus.ACTIVE, subscriptionActivated.getStatus());
tags = subscriptionActivated.getMeta().getTag();
assertInMemoryTag(subscriptionActivated);
}
private void assertInMemoryTag(Subscription theSubscription) {
List<Coding> tags;
Coding tag;
tags = theSubscription.getMeta().getTag();
assertEquals(1, tags.size());
tag = tags.get(0);
assertEquals(JpaConstants.EXT_SUBSCRIPTION_MATCHING_STRATEGY, tag.getSystem());

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

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

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

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

34
hapi-fhir-jpaserver-base/src/test/resources/dstu3/iar/CodeSystem-iar-citizenship-status.xml Normal file
View File

@ -0,0 +1,34 @@
<?xml version="1.0" encoding="UTF-8"?>
<CodeSystem xmlns="http://hl7.org/fhir">
<id value="iar-citizenship-status"/>
<url value="http://ccim.on.ca/fhir/iar/CodeSystem/iar-citizenship-status"/>
<version value="0.1"/>
<name value="Citizenship Status"/>
<status value="draft"/>
<date value="2019-08-22"/>
<publisher value="CCIM"/>
<contact>
<telecom>
<system value="other"/>
<value value="https://www.ccim.on.ca"/>
</telecom>
</contact>
<compositional value="false"/>
<content value="complete"/>
<concept>
<code value="CDN"/>
<display value="Canadian Citizen"/>
</concept>
<concept>
<code value="PR"/>
<display value="Permanent Resident"/>
</concept>
<concept>
<code value="TR"/>
<display value="Temporary Resident "/>
</concept>
<concept>
<code value="REF"/>
<display value="Refugee"/>
</concept>
</CodeSystem>

36
hapi-fhir-jpaserver-base/src/test/resources/dstu3/iar/ValueSet-iar-citizenship-status.xml Normal file
View File

@ -0,0 +1,36 @@
<?xml version="1.0" encoding="UTF-8"?>
<ValueSet xmlns="http://hl7.org/fhir">
<id value="iar-citizenship-status"/>
<url value="http://ccim.on.ca/fhir/iar/ValueSet/iar-citizenship-status"/>
<version value="0.1"/>
<name value="Citizenship Status"/>
<status value="draft"/>
<date value="2019-08-08"/>
<publisher value="CCIM"/>
<contact>
<telecom>
<system value="other"/>
<value value="https://www.ccim.on.ca"/>
</telecom>
</contact>
<compose>
<include>
<system value="http://ccim.on.ca/fhir/iar/CodeSystem/iar-citizenship-status"/>
<version value="0.1"/>
</include>
<include>
<system value="http://hl7.org/fhir/v3/NullFlavor"/>
<concept>
<code value="UNK"/>
<display value="unknown"/>
</concept>
</include>
<include>
<system value="http://hl7.org/fhir/v3/NullFlavor"/>
<concept>
<code value="ASKU"/>
<display value="asked but unknown"/>
</concept>
</include>
</compose>
</ValueSet>

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

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

12
hapi-fhir-jpaserver-subscription/src/test/java/ca/uhn/fhir/jpa/subscription/module/cache/SubscriptionLoaderTest.java vendored
View File

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

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

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

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

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

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

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

19
hapi-fhir-structures-dstu3/src/test/java/ca/uhn/fhir/util/MetaUtilTest.java Normal file
View File

@ -0,0 +1,19 @@
package ca.uhn.fhir.util;
import ca.uhn.fhir.context.FhirContext;
import org.hl7.fhir.dstu3.model.Observation;
import org.junit.Test;
import static org.junit.Assert.assertEquals;
public class MetaUtilTest {
FhirContext ourFhirContext = FhirContext.forDstu3();
@Test
public void testSetGetDstu3() {
String source = "testSource";
Observation observation = new Observation();
MetaUtil.setSource(ourFhirContext, observation, source);
assertEquals(source, MetaUtil.getSource(ourFhirContext, observation.getMeta()));
}
}

69
hapi-fhir-structures-r4/src/main/java/org/hl7/fhir/r4/hapi/rest/server/ServerCapabilityStatementProvider.java
View File

@ -9,7 +9,10 @@ import ca.uhn.fhir.rest.annotation.Metadata;
import ca.uhn.fhir.rest.annotation.Read;
import ca.uhn.fhir.rest.api.Constants;
import ca.uhn.fhir.rest.api.server.RequestDetails;
import ca.uhn.fhir.rest.server.*;
import ca.uhn.fhir.rest.server.Bindings;
import ca.uhn.fhir.rest.server.IServerConformanceProvider;
import ca.uhn.fhir.rest.server.RestfulServer;
import ca.uhn.fhir.rest.server.RestfulServerConfiguration;
import ca.uhn.fhir.rest.server.exceptions.ResourceNotFoundException;
import ca.uhn.fhir.rest.server.method.*;
import ca.uhn.fhir.rest.server.method.SearchParameter;
@ -113,7 +116,6 @@ public class ServerCapabilityStatementProvider extends BaseServerCapabilityState
}
private DateTimeType conformanceDate(RequestDetails theRequestDetails) {
IPrimitiveType<Date> buildDate = getServerConfiguration(theRequestDetails).getConformanceDate();
if (buildDate != null && buildDate.getValue() != null) {
@ -127,7 +129,6 @@ public class ServerCapabilityStatementProvider extends BaseServerCapabilityState
}
/**
* Gets the value of the "publisher" that will be placed in the generated conformance statement. As this is a mandatory element, the value should not be null (although this is not enforced). The
* value defaults to "Not provided" but may be set to null, which will cause this element to be omitted.
@ -194,7 +195,7 @@ public class ServerCapabilityStatementProvider extends BaseServerCapabilityState
// Map<String, CapabilityStatement.RestResourceSearchParam> nameToSearchParam = new HashMap<String,
// CapabilityStatement.RestResourceSearchParam>();
for (BaseMethodBinding<?> nextMethodBinding : nextEntry.getValue()) {
if (nextMethodBinding.getRestOperationType() != null) {
nextMethodBinding.getRestOperationType();
String resOpCode = nextMethodBinding.getRestOperationType().getCode();
if (resOpCode != null) {
TypeRestfulInteraction resOp;
@ -238,7 +239,6 @@ public class ServerCapabilityStatementProvider extends BaseServerCapabilityState
}
}
}
}
checkBindingForSystemOps(rest, systemOps, nextMethodBinding);
@ -315,28 +315,18 @@ public class ServerCapabilityStatementProvider extends BaseServerCapabilityState
}
sortSearchParameters(searchParameters);
if (!searchParameters.isEmpty()) {
// boolean allOptional = searchParameters.get(0).isRequired() == false;
//
// OperationDefinition query = null;
// if (!allOptional) {
// RestOperation operation = rest.addOperation();
// query = new OperationDefinition();
// operation.setDefinition(new ResourceReferenceDt(query));
// query.getDescriptionElement().setValue(searchMethodBinding.getDescription());
// query.addUndeclaredExtension(false, ExtensionConstants.QUERY_RETURN_TYPE, new CodeDt(resourceName));
// for (String nextInclude : searchMethodBinding.getIncludes()) {
// query.addUndeclaredExtension(false, ExtensionConstants.QUERY_ALLOWED_INCLUDE, new StringDt(nextInclude));
// }
// }
for (SearchParameter nextParameter : searchParameters) {
if (nextParameter.getParamType() == null) {
ourLog.warn("SearchParameter {}:{} does not declare a type - Not exporting in CapabilityStatement", def.getName(), nextParameter.getName());
continue;
}
String nextParamName = nextParameter.getName();
String chain = null;
String nextParamUnchainedName = nextParamName;
if (nextParamName.contains(".")) {
chain = nextParamName.substring(nextParamName.indexOf('.') + 1);
nextParamUnchainedName = nextParamName.substring(0, nextParamName.indexOf('.'));
}
@ -352,43 +342,16 @@ public class ServerCapabilityStatementProvider extends BaseServerCapabilityState
}
}
CapabilityStatementRestResourceSearchParamComponent param = resource.addSearchParam();
String typeCode = nextParameter.getParamType().getCode();
param.getTypeElement().setValueAsString(typeCode);
param.setName(nextParamUnchainedName);
// if (StringUtils.isNotBlank(chain)) {
// param.addChain(chain);
// }
//
// if (nextParameter.getParamType() == RestSearchParameterTypeEnum.REFERENCE) {
// for (String nextWhitelist : new TreeSet<String>(nextParameter.getQualifierWhitelist())) {
// if (nextWhitelist.startsWith(".")) {
// param.addChain(nextWhitelist.substring(1));
// }
// }
// }
param.setDocumentation(nextParamDescription);
if (nextParameter.getParamType() != null) {
param.getTypeElement().setValueAsString(nextParameter.getParamType().getCode());
}
for (Class<? extends IBaseResource> nextTarget : nextParameter.getDeclaredTypes()) {
RuntimeResourceDefinition targetDef = getServerConfiguration(theRequestDetails).getFhirContext().getResourceDefinition(nextTarget);
if (targetDef != null) {
ResourceType code;
try {
code = ResourceType.fromCode(targetDef.getName());
} catch (FHIRException e) {
code = null;
}
// if (code != null) {
// param.addTarget(targetDef.getName());
// }
}
}
}
}
}
}
}
}
@Read(type = OperationDefinition.class)

35
hapi-fhir-testpage-overlay/src/main/java/ca/uhn/fhir/to/Controller.java
View File

@ -294,6 +294,9 @@ public class Controller extends BaseController {
case R4:
haveSearchParams = extractSearchParamsR4CapabilityStatement(conformance, resourceName, includes, revIncludes, sortParams, haveSearchParams, queryIncludes);
break;
case R5:
haveSearchParams = extractSearchParamsR5CapabilityStatement(conformance, resourceName, includes, revIncludes, sortParams, haveSearchParams, queryIncludes);
break;
default:
throw new IllegalStateException("Unknown FHIR version: " + theRequest.getFhirVersion(myConfig));
}
@ -758,6 +761,38 @@ public class Controller extends BaseController {
return haveSearchParams;
}
private boolean extractSearchParamsR5CapabilityStatement(IBaseResource theConformance, String resourceName, TreeSet<String> includes, TreeSet<String> theRevIncludes, TreeSet<String> sortParams,
boolean haveSearchParams, List<List<String>> queryIncludes) {
org.hl7.fhir.r5.model.CapabilityStatement conformance = (org.hl7.fhir.r5.model.CapabilityStatement) theConformance;
for (org.hl7.fhir.r5.model.CapabilityStatement.CapabilityStatementRestComponent nextRest : conformance.getRest()) {
for (org.hl7.fhir.r5.model.CapabilityStatement.CapabilityStatementRestResourceComponent nextRes : nextRest.getResource()) {
if (nextRes.getTypeElement().getValue().equals(resourceName)) {
for (org.hl7.fhir.r5.model.StringType next : nextRes.getSearchInclude()) {
if (next.isEmpty() == false) {
includes.add(next.getValue());
}
}
for (org.hl7.fhir.r5.model.CapabilityStatement.CapabilityStatementRestResourceSearchParamComponent next : nextRes.getSearchParam()) {
if (next.getTypeElement().getValue() != org.hl7.fhir.r5.model.Enumerations.SearchParamType.COMPOSITE) {
sortParams.add(next.getNameElement().getValue());
}
}
if (nextRes.getSearchParam().size() > 0) {
haveSearchParams = true;
}
} else {
// It's a different resource from the one we're searching, so
// scan for revinclude candidates
for (org.hl7.fhir.r5.model.CapabilityStatement.CapabilityStatementRestResourceSearchParamComponent next : nextRes.getSearchParam()) {
if (next.getTypeElement().getValue() == org.hl7.fhir.r5.model.Enumerations.SearchParamType.REFERENCE) {
}
}
}
}
}
return haveSearchParams;
}
private boolean handleSearchParam(String paramIdxString, HttpServletRequest theReq, IQuery theQuery, JsonWriter theClientCodeJsonWriter) throws IOException {
String nextName = theReq.getParameter("param." + paramIdxString + ".name");
if (isBlank(nextName)) {

4
pom.xml
View File

@ -567,6 +567,10 @@
<id>jelmerterwal</id>
<name>Jelmer ter Wal</name>
</developer>
<developer>
<id>jiaola</id>
<name>Dazhi Jiao</name>
</developer>
</developers>
<licenses>

13
src/changes/changes.xml
View File

@ -476,6 +476,19 @@
<action type="fix">
Search parameters of type URI did not work in the hapi-fhir-testpage-overlay. This has been corrected.
</action>
<action type="fix" issue="1568">
JPA servers accidentally stripped the type attribute from the server-exported CapabilityStatement
when search parameters of type "special" were found. This has been corrected.
</action>
<action type="fix">
When running the JPA server without Lucene indexing enabled and performing ValueSet expansion,
the server would incorrectly ignore inclusion rules that specified a system but no codes (i.e.
include the whole system). This has been corrected.
</action>
<action type="fix" issue="1538">
The hapi-fhir-testpage-overlay has been updated to support R5 endpoints. Thanks to Dazhi Jiao
for the pull request!
</action>
</release>
<release version="4.0.3" date="2019-09-03" description="Igloo (Point Release)">
<action type="fix">