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

This commit is contained in:
James Agnew 2019-09-05 14:49:29 -04:00
parent 7d162c50db 01015bc435
commit 7105890d2f
6 changed files with 191 additions and 4 deletions
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46
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/stresstest/StressTestR4Test.java
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@ -7,6 +7,7 @@ import ca.uhn.fhir.jpa.search.DatabaseBackedPagingProvider;
import ca.uhn.fhir.jpa.search.ISearchCoordinatorSvc;
import ca.uhn.fhir.jpa.search.SearchCoordinatorSvcImpl;
import ca.uhn.fhir.jpa.searchparam.SearchParameterMap;
import ca.uhn.fhir.model.primitive.IdDt;
import ca.uhn.fhir.rest.api.SortSpec;
import ca.uhn.fhir.rest.client.api.IGenericClient;
import ca.uhn.fhir.test.utilities.UnregisterScheduledProcessor;
@ -31,10 +32,8 @@ import org.hl7.fhir.r4.hapi.validation.FhirInstanceValidator;
import org.hl7.fhir.r4.model.*;
import org.hl7.fhir.r4.model.Bundle.BundleType;
import org.hl7.fhir.r4.model.Bundle.HTTPVerb;
import org.junit.After;
import org.junit.AfterClass;
import org.junit.Before;
import org.junit.Test;
import org.hl7.fhir.r4.model.codesystems.HttpVerb;
import org.junit.*;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.test.context.TestPropertySource;
import org.springframework.test.util.AopTestUtils;
@ -337,6 +336,45 @@ public class StressTestR4Test extends BaseResourceProviderR4Test {
assertEquals(1202, resultsAndIncludes.size());
}
@Ignore
@Test
public void testUpdateListWithLargeNumberOfEntries() {
int numPatients = 3000;
ListResource lr = new ListResource();
lr.setId(IdType.newRandomUuid());
{
Bundle bundle = new Bundle();
for (int i = 0; i < numPatients; ++i) {
Patient patient = new Patient();
patient.setId(IdType.newRandomUuid());
bundle.addEntry().setFullUrl(patient.getId()).setResource(patient).getRequest().setMethod(HTTPVerb.POST).setUrl("Patient");
lr.addEntry().setItem(new Reference(patient.getId()));
}
bundle.addEntry().setFullUrl(lr.getId()).setResource(lr).getRequest().setMethod(HTTPVerb.POST).setUrl("List");
StopWatch sw = new StopWatch();
ourLog.info("Saving list with {} entries", lr.getEntry().size());
mySystemDao.transaction(null, bundle);
ourLog.info("Saved {} resources in {}", bundle.getEntry().size(), sw);
}
{
Bundle bundle = new Bundle();
Patient newPatient = new Patient();
newPatient.setId(IdType.newRandomUuid());
bundle.addEntry().setFullUrl(newPatient.getId()).setResource(newPatient).getRequest().setMethod(HTTPVerb.POST).setUrl("Patient");
lr.addEntry().setItem(new Reference(newPatient.getId()));
bundle.addEntry().setFullUrl(lr.getId()).setResource(lr).getRequest().setMethod(HTTPVerb.PUT).setUrl(lr.getIdElement().toUnqualifiedVersionless().getValue());
StopWatch sw = new StopWatch();
ourLog.info("Updating list with {} entries", lr.getEntry().size());
mySystemDao.transaction(null, bundle);
ourLog.info("Updated {} resources in {}", bundle.getEntry().size(), sw);
}
}
@Test
public void testMultithreadedSearch() throws Exception {

5
hapi-fhir-jpaserver-model/pom.xml
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@ -46,6 +46,11 @@
<artifactId>hapi-fhir-structures-r4</artifactId>
<version>${project.version}</version>
</dependency>
<dependency>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-fhir-structures-r5</artifactId>
<version>${project.version}</version>
</dependency>
<dependency>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-fhir-structures-hl7org-dstu2</artifactId>

85
hapi-fhir-jpaserver-model/src/main/java/ca/uhn/fhir/jpa/model/any/AnyListResource.java
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@ -43,6 +43,8 @@ public class AnyListResource {
return new AnyListResource(new org.hl7.fhir.dstu3.model.ListResource());
case R4:
return new AnyListResource(new org.hl7.fhir.r4.model.ListResource());
case R5:
return new AnyListResource(new org.hl7.fhir.r5.model.ListResource());
default:
throw new UnsupportedOperationException(version + " not supported");
}
@ -63,6 +65,11 @@ public class AnyListResource {
myListResource = theListResourceR4;
}
public AnyListResource(org.hl7.fhir.r5.model.ListResource theListResourceR5) {
myFhirVersion = FhirVersionEnum.R5;
myListResource = theListResourceR5;
}
public static AnyListResource fromResource(IBaseResource theListResource) {
if (theListResource instanceof ca.uhn.fhir.model.dstu2.resource.ListResource) {
return new AnyListResource((ca.uhn.fhir.model.dstu2.resource.ListResource) theListResource);
@ -70,6 +77,8 @@ public class AnyListResource {
return new AnyListResource((org.hl7.fhir.dstu3.model.ListResource) theListResource);
} else if (theListResource instanceof org.hl7.fhir.r4.model.ListResource) {
return new AnyListResource((org.hl7.fhir.r4.model.ListResource) theListResource);
} else if (theListResource instanceof org.hl7.fhir.r5.model.ListResource) {
return new AnyListResource((org.hl7.fhir.r5.model.ListResource) theListResource);
} else {
throw new UnsupportedOperationException("Cannot convert " + theListResource.getClass().getName() + " to AnyList");
}
@ -94,6 +103,11 @@ public class AnyListResource {
return (org.hl7.fhir.r4.model.ListResource) get();
}
public org.hl7.fhir.r5.model.ListResource getR5() {
Validate.isTrue(myFhirVersion == FhirVersionEnum.R5);
return (org.hl7.fhir.r5.model.ListResource) get();
}
public FhirVersionEnum getFhirVersion() {
return myFhirVersion;
}
@ -106,6 +120,9 @@ public class AnyListResource {
case R4:
getR4().getCode().addCoding().setSystem(theSystem).setCode(theCode);
break;
case R5:
getR5().getCode().addCoding().setSystem(theSystem).setCode(theCode);
break;
default:
throw new UnsupportedOperationException(myFhirVersion + " not supported");
}
@ -119,6 +136,9 @@ public class AnyListResource {
case R4:
getR4().getIdentifier().add(new org.hl7.fhir.r4.model.Identifier().setSystem(theSystem).setValue(theValue));
break;
case R5:
getR5().getIdentifier().add(new org.hl7.fhir.r5.model.Identifier().setSystem(theSystem).setValue(theValue));
break;
default:
throw new UnsupportedOperationException(myFhirVersion + " not supported");
}
@ -132,6 +152,9 @@ public class AnyListResource {
case R4:
getR4().addExtension().setUrl(theUrl).setValue(new org.hl7.fhir.r4.model.StringType(theValue));
break;
case R5:
getR5().addExtension().setUrl(theUrl).setValue(new org.hl7.fhir.r5.model.StringType(theValue));
break;
default:
throw new UnsupportedOperationException(myFhirVersion + " not supported");
}
@ -143,6 +166,8 @@ public class AnyListResource {
return getStringExtensionValueOrNullDstu3(theUrl);
case R4:
return getStringExtensionValueOrNullR4(theUrl);
case R5:
return getStringExtensionValueOrNullR5(theUrl);
default:
throw new UnsupportedOperationException(myFhirVersion + " not supported");
}
@ -166,6 +191,15 @@ public class AnyListResource {
return targetType.getValue();
}
private String getStringExtensionValueOrNullR5(String theUrl) {
List<org.hl7.fhir.r5.model.Extension> targetTypes = getR5().getExtensionsByUrl(theUrl);
if (targetTypes.size() < 1) {
return null;
}
org.hl7.fhir.r5.model.StringType targetType = (org.hl7.fhir.r5.model.StringType) targetTypes.get(0).getValue();
return targetType.getValue();
}
public void addReference(IBaseReference theReference) {
switch (myFhirVersion) {
case DSTU3:
@ -174,6 +208,9 @@ public class AnyListResource {
case R4:
getR4().addEntry().setItem((org.hl7.fhir.r4.model.Reference) theReference);
break;
case R5:
getR5().addEntry().setItem((org.hl7.fhir.r5.model.Reference) theReference);
break;
default:
throw new UnsupportedOperationException(myFhirVersion + " not supported");
}
@ -187,6 +224,9 @@ public class AnyListResource {
case R4:
getR4().addEntry().setItem(new org.hl7.fhir.r4.model.Reference(theReferenceId));
break;
case R5:
getR5().addEntry().setItem(new org.hl7.fhir.r5.model.Reference(theReferenceId));
break;
default:
throw new UnsupportedOperationException(myFhirVersion + " not supported");
}
@ -202,6 +242,10 @@ public class AnyListResource {
return getR4().getEntry().stream()
.map(entry -> entry.getItem().getReference())
.map(reference -> new org.hl7.fhir.r4.model.IdType(reference).toUnqualifiedVersionless().getValue());
case R5:
return getR5().getEntry().stream()
.map(entry -> entry.getItem().getReference())
.map(reference -> new org.hl7.fhir.r5.model.IdType(reference).toUnqualifiedVersionless().getValue());
default:
throw new UnsupportedOperationException(myFhirVersion + " not supported");
}
@ -213,6 +257,8 @@ public class AnyListResource {
return removeItemDstu3(theReferenceId);
case R4:
return removeItemR4(theReferenceId);
case R5:
return removeItemR5(theReferenceId);
default:
throw new UnsupportedOperationException(myFhirVersion + " not supported");
}
@ -250,6 +296,22 @@ public class AnyListResource {
return removed;
}
private boolean removeItemR5(String theReferenceId) {
boolean removed = false;
for (org.hl7.fhir.r5.model.ListResource.ListEntryComponent entry : getR5().getEntry()) {
if (theReferenceId.equals(entry.getItem().getReference()) && !entry.getDeleted()) {
entry.setDeleted(true);
removed = true;
break;
}
}
if (removed) {
getR5().getEntry().removeIf(entry -> entry.getDeleted());
}
return removed;
}
public TokenParam getCodeFirstRep() {
switch (myFhirVersion) {
case DSTU3:
@ -258,17 +320,40 @@ public class AnyListResource {
case R4:
org.hl7.fhir.r4.model.Coding codingR4 = getR4().getCode().getCodingFirstRep();
return new TokenParam(codingR4.getSystem(), codingR4.getCode());
case R5:
org.hl7.fhir.r5.model.Coding codingR5 = getR5().getCode().getCodingFirstRep();
return new TokenParam(codingR5.getSystem(), codingR5.getCode());
default:
throw new UnsupportedOperationException(myFhirVersion + " not supported");
}
}
public TokenParam getIdentifierirstRep() {
switch (myFhirVersion) {
case DSTU3:
org.hl7.fhir.dstu3.model.Identifier identDstu3 = getDstu3().getIdentifierFirstRep();
return new TokenParam(identDstu3.getSystem(), identDstu3.getValue());
case R4:
org.hl7.fhir.r4.model.Identifier identR4 = getR4().getIdentifierFirstRep();
return new TokenParam(identR4.getSystem(), identR4.getValue());
case R5:
org.hl7.fhir.r5.model.Identifier identR5 = getR5().getIdentifierFirstRep();
return new TokenParam(identR5.getSystem(), identR5.getValue());
default:
throw new UnsupportedOperationException(myFhirVersion + " not supported");
}
}
public boolean isEmpty() {
switch (myFhirVersion) {
case DSTU3:
return getDstu3().getEntry().isEmpty();
case R4:
return getR4().getEntry().isEmpty();
case R5:
return getR5().getEntry().isEmpty();
default:
throw new UnsupportedOperationException(myFhirVersion + " not supported");
}

24
hapi-fhir-jpaserver-model/src/test/java/ca/uhn/fhir/jpa/model/any/AnyListResourceTest.java Normal file
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@ -0,0 +1,24 @@
package ca.uhn.fhir.jpa.model.any;
import org.hl7.fhir.r5.model.ListResource;
import org.junit.Test;
import static org.junit.Assert.assertEquals;
public class AnyListResourceTest {
@Test
public void getCodeFirstRep() {
AnyListResource listResource = AnyListResource.fromResource(new ListResource());
listResource.addCode("foo", "bar");
assertEquals("foo", listResource.getCodeFirstRep().getSystem());
assertEquals("bar", listResource.getCodeFirstRep().getValue());
}
@Test
public void getIdentifierFirstRep() {
AnyListResource listResource = AnyListResource.fromResource(new ListResource());
listResource.addIdentifier("foo", "bar");
assertEquals("foo", listResource.getIdentifierirstRep().getSystem());
assertEquals("bar", listResource.getIdentifierirstRep().getValue());
}
}

9
src/changes/changes.xml
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@ -114,6 +114,15 @@
could be bypassed if a Content Type was not included.
</action>
</release>
<release version="4.0.1" date="2019-09-03" description="Igloo (Point Release)">
<action type="fix">
This release contains no new or updated functionality, but addressed a dependency
version that was left incorrectly requiring a SNAPSHOT maven build of the
org.hl7.fhir.utilities module. Users who are successfully using HAPI FHIR 4.0.0
do not need to upgrade, but any users who were blocked from upgrading due to
snapshot dependency issues are advised to upgrade immediately.
</action>
</release>
<release version="4.0.0" date="2019-08-14" description="Igloo">
<action type="add">
The version of a few dependencies have been bumped to the

26
src/site/xdoc/index.xml
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@ -67,6 +67,32 @@
</section>
<section name="Announcements">
<p>
<b>September 3, 2019 - Community Survey and HAPI FHIR 4.0.1</b> -
It is time for us to do another HAPI FHIR community survey. The survey is a not-quite-annual
tradition that helps us to set priority for the coming year and get a pulse on how people
are using HAPI FHIR.
</p>
<p>
We would very much appreciate if everyone could take a few minutes to fill it out. The
survey is short (2 pages / 5 mins) so it shouldn't be much of a burden.
</p>
<p>
Access the survey here:
<a href="http://bit.ly/33HO4cs">http://bit.ly/33HO4cs</a> (note that this URL was originally posted incorrectly. It is now fixed)
</p>
<p>
In addition, a new HAPI FHIR release (4.0.1) has been uploaded to the
Maven Central repos.
This release contains no new or updated functionality, but addressed a dependency
version that was left incorrectly requiring a SNAPSHOT maven build of the
org.hl7.fhir.utilities module. Users who are successfully using HAPI FHIR 4.0.0
do not need to upgrade, but any users who were blocked from upgrading due to
snapshot dependency issues are advised to upgrade immediately.
</p>
<p>
<b>August 14, 2019 - HAPI FHIR 4.0.0 (Igloo) Released</b> -
The next release of HAPI has now been uploaded to the Maven repos and