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Merge remote-tracking branch 'origin/master' into im_20200728_term_multi_version_support

This commit is contained in:
ianmarshall 2020-09-23 16:43:22 -04:00
parent ceb5ec6384 ecc09889cb
commit 640ee94c5c
25 changed files with 477 additions and 107 deletions
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5
hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/5_2_0/2097-avoid-crash-on-double-chained-date.yaml Normal file
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@ -0,0 +1,5 @@
---
type: fix
issue: 2097
title: "A crash in the JPA server was fixed when performing a search containined two chained search parameters to
date target types."

6
hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/5_2_0/2099-dont-install-draft-package-contents.yaml Normal file
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@ -0,0 +1,6 @@
---
type: fix
issue: 2099
title: "When using an NPM package spec in STORE_AND_INSTALL mode, conformance resources will only be stored if they
have a status of `active`. This fixes a bug wgere installing the US Core IG caused searches to stop working due to
draft Search Parameters."

6
hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/5_2_0/2099-dont-override-sps-with-draft.yaml Normal file
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@ -0,0 +1,6 @@
---
type: add
issue: 2099
title: "Stored SearchParameter resources with a status of DRAFT will no longer override and disable existing built-in
search parameters. This is done in order to avoid issues caused by uploading NPM packages such as US Core that
contain a large number of draft parameters."

5
hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/5_2_0/2101-avoid-dupe-params-in-cs.yaml Normal file
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@ -0,0 +1,5 @@
---
type: fix
issue: 2101
title: "In some circumstances when using a Plain Server, the generated CapabilityStatement could have duplciate
Search Parameter definitions. This has been corrected."

15
hapi-fhir-jpaserver-api/src/main/java/ca/uhn/fhir/jpa/api/model/DaoMethodOutcome.java
View File

@ -28,6 +28,7 @@ public class DaoMethodOutcome extends MethodOutcome {
private IBasePersistedResource myEntity;
private IBaseResource myPreviousResource;
private boolean myNop;
/**
* Constructor
@ -36,6 +37,20 @@ public class DaoMethodOutcome extends MethodOutcome {
super();
}
/**
* Was this a NO-OP - Typically because of an update to a resource that already matched the contents provided
*/
public boolean isNop() {
return myNop;
}
/**
* Was this a NO-OP - Typically because of an update to a resource that already matched the contents provided
*/
public void setNop(boolean theNop) {
myNop = theNop;
}
public IBasePersistedResource getEntity() {
return myEntity;
}

7
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/BaseStorageDao.java
View File

@ -29,6 +29,7 @@ import ca.uhn.fhir.interceptor.api.Pointcut;
import ca.uhn.fhir.jpa.api.config.DaoConfig;
import ca.uhn.fhir.jpa.api.model.DaoMethodOutcome;
import ca.uhn.fhir.jpa.model.cross.IBasePersistedResource;
import ca.uhn.fhir.jpa.model.entity.ResourceTable;
import ca.uhn.fhir.jpa.searchparam.SearchParameterMap;
import ca.uhn.fhir.jpa.searchparam.registry.ISearchParamRegistry;
import ca.uhn.fhir.jpa.util.JpaInterceptorBroadcaster;
@ -128,6 +129,12 @@ public abstract class BaseStorageDao {
protected DaoMethodOutcome toMethodOutcome(RequestDetails theRequest, @Nonnull final IBasePersistedResource theEntity, @Nonnull IBaseResource theResource) {
DaoMethodOutcome outcome = new DaoMethodOutcome();
if (theEntity instanceof ResourceTable) {
if (((ResourceTable) theEntity).isUnchangedInCurrentOperation()) {
outcome.setNop(true);
}
}
IIdType id = null;
if (theResource.getIdElement().getValue() != null) {
id = theResource.getIdElement();

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

@ -49,7 +49,6 @@ import java.util.Map;
public class PredicateBuilderDate extends BasePredicateBuilder implements IPredicateBuilder {
private static final Logger ourLog = LoggerFactory.getLogger(PredicateBuilderDate.class);
private Map<String, From<?, ResourceIndexedSearchParamDate>> myJoinMap;
PredicateBuilderDate(SearchBuilder theSearchBuilder) {
super(theSearchBuilder);
@ -64,15 +63,15 @@ public class PredicateBuilderDate extends BasePredicateBuilder implements IPredi
String paramName = theSearchParam.getName();
boolean newJoin = false;
if (myJoinMap == null) {
myJoinMap = new HashMap<>();
}
Map<String, From<?, ResourceIndexedSearchParamDate>> joinMap = myQueryStack.getJoinMap();
String key = theResourceName + " " + paramName;
From<?, ResourceIndexedSearchParamDate> join = myJoinMap.get(key);
From<?, ResourceIndexedSearchParamDate> join = joinMap.get(key);
if (join == null) {
join = myQueryStack.createJoin(SearchBuilderJoinEnum.DATE, paramName);
myJoinMap.put(key, join);
joinMap.put(key, join);
newJoin = true;
}

13
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/predicate/querystack/QueryRootEntry.java
View File

@ -23,6 +23,7 @@ package ca.uhn.fhir.jpa.dao.predicate.querystack;
import ca.uhn.fhir.jpa.dao.predicate.IndexJoins;
import ca.uhn.fhir.jpa.dao.predicate.SearchBuilderJoinEnum;
import ca.uhn.fhir.jpa.dao.predicate.SearchBuilderJoinKey;
import ca.uhn.fhir.jpa.model.entity.ResourceIndexedSearchParamDate;
import javax.persistence.criteria.AbstractQuery;
import javax.persistence.criteria.CriteriaBuilder;
@ -37,7 +38,9 @@ import javax.persistence.criteria.Subquery;
import java.util.ArrayList;
import java.util.Collections;
import java.util.Date;
import java.util.HashMap;
import java.util.List;
import java.util.Map;
import java.util.Optional;
abstract class QueryRootEntry {
@ -45,6 +48,7 @@ abstract class QueryRootEntry {
private final IndexJoins myIndexJoins = new IndexJoins();
private final CriteriaBuilder myCriteriaBuilder;
private boolean myHasImplicitTypeSelection;
private Map<String, From<?, ResourceIndexedSearchParamDate>> myJoinMap;
QueryRootEntry(CriteriaBuilder theCriteriaBuilder) {
myCriteriaBuilder = theCriteriaBuilder;
@ -108,6 +112,15 @@ abstract class QueryRootEntry {
return getQueryRoot();
}
public Map<String, From<?, ResourceIndexedSearchParamDate>> getJoinMap() {
Map<String, From<?, ResourceIndexedSearchParamDate>> retVal = myJoinMap;
if (retVal==null) {
retVal = new HashMap<>();
myJoinMap = retVal;
}
return retVal;
}
abstract void orderBy(List<Order> theOrders);
abstract Expression<Date> getLastUpdatedColumn();

7
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/predicate/querystack/QueryStack.java
View File

@ -23,6 +23,7 @@ package ca.uhn.fhir.jpa.dao.predicate.querystack;
import ca.uhn.fhir.interceptor.model.RequestPartitionId;
import ca.uhn.fhir.jpa.dao.predicate.SearchBuilderJoinEnum;
import ca.uhn.fhir.jpa.dao.predicate.SearchBuilderJoinKey;
import ca.uhn.fhir.jpa.model.entity.ResourceIndexedSearchParamDate;
import ca.uhn.fhir.jpa.searchparam.SearchParameterMap;
import org.apache.commons.lang3.Validate;
@ -38,6 +39,7 @@ import javax.persistence.criteria.Root;
import javax.persistence.criteria.Subquery;
import java.util.Date;
import java.util.List;
import java.util.Map;
import java.util.Optional;
import java.util.Stack;
@ -281,4 +283,9 @@ public class QueryStack {
public Predicate addNeverMatchingPredicate() {
return top().addNeverMatchingPredicate();
}
public Map<String, From<?, ResourceIndexedSearchParamDate>> getJoinMap() {
return top().getJoinMap();
}
}

20
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/packages/PackageInstallerSvcImpl.java
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@ -26,6 +26,7 @@ import ca.uhn.fhir.context.support.IValidationSupport;
import ca.uhn.fhir.context.support.ValidationSupportContext;
import ca.uhn.fhir.jpa.api.dao.DaoRegistry;
import ca.uhn.fhir.jpa.api.dao.IFhirResourceDao;
import ca.uhn.fhir.jpa.api.model.DaoMethodOutcome;
import ca.uhn.fhir.jpa.dao.data.INpmPackageVersionDao;
import ca.uhn.fhir.jpa.model.entity.NpmPackageVersionEntity;
import ca.uhn.fhir.jpa.searchparam.SearchParameterMap;
@ -35,7 +36,6 @@ import ca.uhn.fhir.rest.param.StringParam;
import ca.uhn.fhir.rest.param.TokenParam;
import ca.uhn.fhir.rest.param.UriParam;
import ca.uhn.fhir.rest.server.exceptions.InternalErrorException;
import ca.uhn.fhir.rest.server.exceptions.PreconditionFailedException;
import ca.uhn.fhir.util.FhirTerser;
import ca.uhn.fhir.util.SearchParameterUtil;
import com.google.common.annotations.VisibleForTesting;
@ -208,6 +208,7 @@ public class PackageInstallerSvcImpl implements IPackageInstallerSvc {
count[i] = resources.size();
for (IBaseResource next : resources) {
try {
next = isStructureDefinitionWithoutSnapshot(next) ? generateSnapshot(next) : next;
create(next, theOutcome);
@ -215,6 +216,7 @@ public class PackageInstallerSvcImpl implements IPackageInstallerSvc {
ourLog.warn("Failed to upload resource of type {} with ID {} - Error: {}", myFhirContext.getResourceType(next), next.getIdElement().getValue(), e.toString());
throw new ImplementationGuideInstallationException(String.format("Error installing IG %s#%s: %s", name, version, e.toString()), e);
}
}
}
@ -321,10 +323,11 @@ public class PackageInstallerSvcImpl implements IPackageInstallerSvc {
} else {
ourLog.info("Updating existing resource matching {}", map.toNormalizedQueryString(myFhirContext));
theOutcome.incrementResourcesInstalled(myFhirContext.getResourceType(theResource));
theResource.setId(searchResult.getResources(0,1).get(0).getIdElement().toUnqualifiedVersionless());
dao.update(theResource);
theResource.setId(searchResult.getResources(0, 1).get(0).getIdElement().toUnqualifiedVersionless());
DaoMethodOutcome outcome = dao.update(theResource);
if (!outcome.isNop()) {
theOutcome.incrementResourcesInstalled(myFhirContext.getResourceType(theResource));
}
}
}
@ -349,6 +352,13 @@ public class PackageInstallerSvcImpl implements IPackageInstallerSvc {
}
}
List<IPrimitiveType> statusTypes = myFhirContext.newFhirPath().evaluate(theResource, "status", IPrimitiveType.class);
if (statusTypes.size() > 0) {
if (!statusTypes.get(0).getValueAsString().equals("active")) {
return false;
}
}
return true;
}

19
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/r4/FhirResourceDaoR4SearchCustomSearchParamTest.java
View File

@ -1,6 +1,7 @@
package ca.uhn.fhir.jpa.dao.r4;
import ca.uhn.fhir.context.FhirContext;
import ca.uhn.fhir.context.RuntimeSearchParam;
import ca.uhn.fhir.interceptor.api.HookParams;
import ca.uhn.fhir.interceptor.api.IAnonymousInterceptor;
import ca.uhn.fhir.interceptor.api.Pointcut;
@ -462,6 +463,24 @@ public class FhirResourceDaoR4SearchCustomSearchParamTest extends BaseJpaR4Test
}
@Test
public void testBuiltInSearchParameterNotReplacedByDraftSearchParameter() {
myModelConfig.setDefaultSearchParamsCanBeOverridden(true);
SearchParameter memberSp = new SearchParameter();
memberSp.setCode("family");
memberSp.addBase("Patient");
memberSp.setType(Enumerations.SearchParamType.STRING);
memberSp.setExpression("Patient.name.family");
memberSp.setStatus(Enumerations.PublicationStatus.DRAFT);
mySearchParameterDao.create(memberSp, mySrd);
mySearchParamRegistry.forceRefresh();
RuntimeSearchParam sp = mySearchParamRegistry.getActiveSearchParam("Patient", "family");
assertEquals(RuntimeSearchParam.RuntimeSearchParamStatusEnum.ACTIVE, sp.getStatus());
}
@Test

29
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/r4/FhirResourceDaoR4SearchNoFtTest.java
View File

@ -72,6 +72,7 @@ import org.hl7.fhir.r4.model.CodeSystem;
import org.hl7.fhir.r4.model.CodeType;
import org.hl7.fhir.r4.model.CodeableConcept;
import org.hl7.fhir.r4.model.Coding;
import org.hl7.fhir.r4.model.Communication;
import org.hl7.fhir.r4.model.CommunicationRequest;
import org.hl7.fhir.r4.model.Condition;
import org.hl7.fhir.r4.model.ContactPoint.ContactPointSystem;
@ -5080,6 +5081,34 @@ public class FhirResourceDaoR4SearchNoFtTest extends BaseJpaR4Test {
assertThat(toUnqualifiedVersionlessIdValues(outcome), contains(crId));
}
@Test
public void testSearchWithTwoChainedDates() {
// Matches
Encounter e1 = new Encounter();
e1.setPeriod(new Period().setStartElement(new DateTimeType("2020-09-14T12:00:00Z")).setEndElement(new DateTimeType("2020-09-14T12:00:00Z")));
String e1Id = myEncounterDao.create(e1).getId().toUnqualifiedVersionless().getValue();
Communication c1 = new Communication();
c1.getEncounter().setReference(e1Id);
myCommunicationDao.create(c1);
// Doesn't match
Encounter e2 = new Encounter();
e2.setPeriod(new Period().setStartElement(new DateTimeType("2020-02-14T12:00:00Z")).setEndElement(new DateTimeType("2020-02-14T12:00:00Z")));
String e2Id = myEncounterDao.create(e2).getId().toUnqualifiedVersionless().getValue();
Communication c2 = new Communication();
c2.getEncounter().setReference(e2Id);
myCommunicationDao.create(c2);
SearchParameterMap map = SearchParameterMap.newSynchronous();
map.add(Communication.SP_ENCOUNTER, new ReferenceParam("ge2020-09-14").setChain("date"));
map.add(Communication.SP_ENCOUNTER, new ReferenceParam("le2020-09-15").setChain("date"));
IBundleProvider outcome = myCommunicationDao.search(map);
assertEquals(1, outcome.sizeOrThrowNpe());
}
@Test
public void testCircularReferencesDontBreakRevIncludes() {

44
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/packages/NpmTestR4.java
View File

@ -49,6 +49,7 @@ import javax.servlet.http.HttpServletRequest;
import javax.servlet.http.HttpServletResponse;
import java.io.IOException;
import java.util.HashMap;
import java.util.List;
import java.util.Map;
import java.util.stream.Collectors;
@ -114,6 +115,20 @@ public class NpmTestR4 extends BaseJpaR4Test {
PackageInstallationSpec spec = new PackageInstallationSpec().setName("hl7.fhir.us.core").setVersion("3.1.0").setInstallMode(PackageInstallationSpec.InstallModeEnum.STORE_AND_INSTALL).setFetchDependencies(true);
igInstaller.install(spec);
runInTransaction(()->{
SearchParameterMap map = SearchParameterMap.newSynchronous(SearchParameter.SP_BASE, new TokenParam("NamingSystem"));
IBundleProvider outcome = mySearchParameterDao.search(map);
List<IBaseResource> resources = outcome.getResources(0, outcome.sizeOrThrowNpe());
for (int i = 0; i < resources.size(); i++) {
ourLog.info("**************************************************************************");
ourLog.info("**************************************************************************");
ourLog.info("Res " + i);
ourLog.info(myFhirCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(resources.get(i)));
}
});
igInstaller.install(spec);
}
@ -162,7 +177,8 @@ public class NpmTestR4 extends BaseJpaR4Test {
myFakeNpmServlet.myResponses.put("/hl7.fhir.uv.shorthand/0.12.0", bytes);
PackageInstallationSpec spec = new PackageInstallationSpec().setName("hl7.fhir.uv.shorthand").setVersion("0.12.0").setInstallMode(PackageInstallationSpec.InstallModeEnum.STORE_AND_INSTALL);
igInstaller.install(spec);
PackageInstallOutcomeJson outcome = igInstaller.install(spec);
assertEquals(1, outcome.getResourcesInstalled().get("CodeSystem"));
// Be sure no further communication with the server
JettyUtil.closeServer(myServer);
@ -215,11 +231,25 @@ public class NpmTestR4 extends BaseJpaR4Test {
runInTransaction(() -> {
SearchParameterMap map = SearchParameterMap.newSynchronous();
map.add(StructureDefinition.SP_URL, new UriParam("http://hl7.org/fhir/uv/shorthand/CodeSystem/shorthand-code-system"));
IBundleProvider outcome = myCodeSystemDao.search(map);
assertEquals(1, outcome.sizeOrThrowNpe());
IBundleProvider result = myCodeSystemDao.search(map);
assertEquals(1, result.sizeOrThrowNpe());
});
}
@Test
public void testInstallR4Package_DraftResourcesNotInstalled() throws Exception {
myDaoConfig.setAllowExternalReferences(true);
byte[] bytes = loadClasspathBytes("/packages/test-draft-sample.tgz");
myFakeNpmServlet.myResponses.put("/hl7.fhir.uv.shorthand/0.11.1", bytes);
PackageInstallationSpec spec = new PackageInstallationSpec().setName("hl7.fhir.uv.shorthand").setVersion("0.11.1").setInstallMode(PackageInstallationSpec.InstallModeEnum.STORE_AND_INSTALL);
PackageInstallOutcomeJson outcome = igInstaller.install(spec);
assertEquals(0, outcome.getResourcesInstalled().size(), outcome.getResourcesInstalled().toString());
}
@Test
public void testInstallR4Package_Twice() throws Exception {
myDaoConfig.setAllowExternalReferences(true);
@ -236,6 +266,11 @@ public class NpmTestR4 extends BaseJpaR4Test {
igInstaller.install(spec);
outcome = igInstaller.install(spec);
assertEquals(null, outcome.getResourcesInstalled().get("CodeSystem"));
// Ensure that we loaded the contents
IBundleProvider searchResult = myCodeSystemDao.search(SearchParameterMap.newSynchronous("url", new UriParam("http://hl7.org/fhir/uv/shorthand/CodeSystem/shorthand-code-system")));
assertEquals(1, searchResult.sizeOrThrowNpe());
}
@ -257,9 +292,6 @@ public class NpmTestR4 extends BaseJpaR4Test {
assertEquals(null, pkg.description());
assertEquals("UK.Core.r4", pkg.name());
// Ensure that we loaded the contents
IBundleProvider searchResult = myStructureDefinitionDao.search(SearchParameterMap.newSynchronous("url", new UriParam("https://fhir.nhs.uk/R4/StructureDefinition/UKCore-Patient")));
assertEquals(1, searchResult.sizeOrThrowNpe());
}
@Test

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hapi-fhir-jpaserver-base/src/test/resources/packages/test-draft-sample.tgz Normal file
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3
hapi-fhir-jpaserver-searchparam/src/main/java/ca/uhn/fhir/jpa/searchparam/registry/SearchParamRegistryImpl.java
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@ -291,6 +291,9 @@ public class SearchParamRegistryImpl implements ISearchParamRegistry {
if (runtimeSp == null) {
continue;
}
if (runtimeSp.getStatus() == RuntimeSearchParam.RuntimeSearchParamStatusEnum.DRAFT) {
continue;
}
for (String nextBaseName : SearchParameterUtil.getBaseAsStrings(myFhirContext, nextSp)) {
if (isBlank(nextBaseName)) {

2
hapi-fhir-server-empi/src/main/java/ca/uhn/fhir/empi/util/PersonHelper.java
View File

@ -268,7 +268,7 @@ public class PersonHelper {
if (theAllowOverwriting || person.getName().isEmpty()) {
person.setName(patient.getName());
}
if (theAllowOverwriting || person.getName().isEmpty()) {
if (theAllowOverwriting || person.getAddress().isEmpty()) {
person.setAddress(patient.getAddress());
}
if (theAllowOverwriting || person.getTelecom().isEmpty()) {

20
hapi-fhir-server/src/main/java/ca/uhn/fhir/rest/server/messaging/BaseResourceMessage.java
View File

@ -1,5 +1,25 @@
package ca.uhn.fhir.rest.server.messaging;
/*-
* #%L
* HAPI FHIR - Server Framework
* %%
* Copyright (C) 2014 - 2020 University Health Network
* %%
* Licensed under the Apache License, Version 2.0 (the "License");
* you may not use this file except in compliance with the License.
* You may obtain a copy of the License at
*
* http://www.apache.org/licenses/LICENSE-2.0
*
* Unless required by applicable law or agreed to in writing, software
* distributed under the License is distributed on an "AS IS" BASIS,
* WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
* See the License for the specific language governing permissions and
* limitations under the License.
* #L%
*/
import ca.uhn.fhir.model.api.IModelJson;

20
hapi-fhir-server/src/main/java/ca/uhn/fhir/rest/server/messaging/BaseResourceModifiedMessage.java
View File

@ -1,5 +1,25 @@
package ca.uhn.fhir.rest.server.messaging;
/*-
* #%L
* HAPI FHIR - Server Framework
* %%
* Copyright (C) 2014 - 2020 University Health Network
* %%
* Licensed under the Apache License, Version 2.0 (the "License");
* you may not use this file except in compliance with the License.
* You may obtain a copy of the License at
*
* http://www.apache.org/licenses/LICENSE-2.0
*
* Unless required by applicable law or agreed to in writing, software
* distributed under the License is distributed on an "AS IS" BASIS,
* WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
* See the License for the specific language governing permissions and
* limitations under the License.
* #L%
*/
import ca.uhn.fhir.context.FhirContext;
import ca.uhn.fhir.model.api.IModelJson;
import ca.uhn.fhir.parser.IParser;

20
hapi-fhir-server/src/main/java/ca/uhn/fhir/rest/server/messaging/IResourceMessage.java
View File

@ -1,5 +1,25 @@
package ca.uhn.fhir.rest.server.messaging;
/*-
* #%L
* HAPI FHIR - Server Framework
* %%
* Copyright (C) 2014 - 2020 University Health Network
* %%
* Licensed under the Apache License, Version 2.0 (the "License");
* you may not use this file except in compliance with the License.
* You may obtain a copy of the License at
*
* http://www.apache.org/licenses/LICENSE-2.0
*
* Unless required by applicable law or agreed to in writing, software
* distributed under the License is distributed on an "AS IS" BASIS,
* WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
* See the License for the specific language governing permissions and
* limitations under the License.
* #L%
*/
public interface IResourceMessage {

20
hapi-fhir-server/src/main/java/ca/uhn/fhir/rest/server/messaging/ResourceOperationMessage.java
View File

@ -1,5 +1,25 @@
package ca.uhn.fhir.rest.server.messaging;
/*-
* #%L
* HAPI FHIR - Server Framework
* %%
* Copyright (C) 2014 - 2020 University Health Network
* %%
* Licensed under the Apache License, Version 2.0 (the "License");
* you may not use this file except in compliance with the License.
* You may obtain a copy of the License at
*
* http://www.apache.org/licenses/LICENSE-2.0
*
* Unless required by applicable law or agreed to in writing, software
* distributed under the License is distributed on an "AS IS" BASIS,
* WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
* See the License for the specific language governing permissions and
* limitations under the License.
* #L%
*/
import ca.uhn.fhir.context.FhirContext;
import ca.uhn.fhir.rest.api.server.RequestDetails;
import org.hl7.fhir.instance.model.api.IBaseResource;

20
hapi-fhir-server/src/main/java/ca/uhn/fhir/rest/server/messaging/json/BaseJsonMessage.java
View File

@ -1,5 +1,25 @@
package ca.uhn.fhir.rest.server.messaging.json;
/*-
* #%L
* HAPI FHIR - Server Framework
* %%
* Copyright (C) 2014 - 2020 University Health Network
* %%
* Licensed under the Apache License, Version 2.0 (the "License");
* you may not use this file except in compliance with the License.
* You may obtain a copy of the License at
*
* http://www.apache.org/licenses/LICENSE-2.0
*
* Unless required by applicable law or agreed to in writing, software
* distributed under the License is distributed on an "AS IS" BASIS,
* WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
* See the License for the specific language governing permissions and
* limitations under the License.
* #L%
*/
import ca.uhn.fhir.model.api.IModelJson;
import com.fasterxml.jackson.annotation.JsonProperty;

20
hapi-fhir-server/src/main/java/ca/uhn/fhir/rest/server/messaging/json/HapiMessageHeaders.java
View File

@ -1,5 +1,25 @@
package ca.uhn.fhir.rest.server.messaging.json;
/*-
* #%L
* HAPI FHIR - Server Framework
* %%
* Copyright (C) 2014 - 2020 University Health Network
* %%
* Licensed under the Apache License, Version 2.0 (the "License");
* you may not use this file except in compliance with the License.
* You may obtain a copy of the License at
*
* http://www.apache.org/licenses/LICENSE-2.0
*
* Unless required by applicable law or agreed to in writing, software
* distributed under the License is distributed on an "AS IS" BASIS,
* WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
* See the License for the specific language governing permissions and
* limitations under the License.
* #L%
*/
import ca.uhn.fhir.model.api.IModelJson;
import com.fasterxml.jackson.annotation.JsonProperty;
import org.springframework.messaging.MessageHeaders;

20
hapi-fhir-server/src/main/java/ca/uhn/fhir/rest/server/messaging/json/ResourceOperationJsonMessage.java
View File

@ -1,5 +1,25 @@
package ca.uhn.fhir.rest.server.messaging.json;
/*-
* #%L
* HAPI FHIR - Server Framework
* %%
* Copyright (C) 2014 - 2020 University Health Network
* %%
* Licensed under the Apache License, Version 2.0 (the "License");
* you may not use this file except in compliance with the License.
* You may obtain a copy of the License at
*
* http://www.apache.org/licenses/LICENSE-2.0
*
* Unless required by applicable law or agreed to in writing, software
* distributed under the License is distributed on an "AS IS" BASIS,
* WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
* See the License for the specific language governing permissions and
* limitations under the License.
* #L%
*/
import ca.uhn.fhir.rest.server.messaging.ResourceOperationMessage;
import com.fasterxml.jackson.annotation.JsonProperty;
import org.apache.commons.lang3.builder.ToStringBuilder;

7
hapi-fhir-structures-r4/src/main/java/org/hl7/fhir/r4/hapi/rest/server/ServerCapabilityStatementProvider.java
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@ -332,6 +332,7 @@ public class ServerCapabilityStatementProvider extends BaseServerCapabilityState
sortSearchParameters(searchParameters);
if (!searchParameters.isEmpty()) {
Set<String> paramNames = new HashSet<>();
for (SearchParameter nextParameter : searchParameters) {
if (nextParameter.getParamType() == null) {
@ -346,6 +347,10 @@ public class ServerCapabilityStatementProvider extends BaseServerCapabilityState
nextParamUnchainedName = nextParamName.substring(0, nextParamName.indexOf('.'));
}
if (!paramNames.add(nextParamUnchainedName)) {
continue;
}
String nextParamDescription = nextParameter.getDescription();
/*
@ -425,6 +430,8 @@ public class ServerCapabilityStatementProvider extends BaseServerCapabilityState
param.setMin(nextParam.isRequired() ? 1 : 0);
param.setMax("1");
param.setName(nextParam.getName());
}
}

245
hapi-fhir-structures-r4/src/test/java/ca/uhn/fhir/rest/server/ServerCapabilityStatementProviderR4Test.java
View File

@ -5,11 +5,26 @@ import ca.uhn.fhir.model.api.Include;
import ca.uhn.fhir.model.api.annotation.Description;
import ca.uhn.fhir.model.api.annotation.ResourceDef;
import ca.uhn.fhir.model.primitive.InstantDt;
import ca.uhn.fhir.rest.annotation.*;
import ca.uhn.fhir.rest.annotation.ConditionalUrlParam;
import ca.uhn.fhir.rest.annotation.Create;
import ca.uhn.fhir.rest.annotation.Delete;
import ca.uhn.fhir.rest.annotation.History;
import ca.uhn.fhir.rest.annotation.IdParam;
import ca.uhn.fhir.rest.annotation.IncludeParam;
import ca.uhn.fhir.rest.annotation.Operation;
import ca.uhn.fhir.rest.annotation.OperationParam;
import ca.uhn.fhir.rest.annotation.OptionalParam;
import ca.uhn.fhir.rest.annotation.Read;
import ca.uhn.fhir.rest.annotation.RequiredParam;
import ca.uhn.fhir.rest.annotation.ResourceParam;
import ca.uhn.fhir.rest.annotation.Search;
import ca.uhn.fhir.rest.annotation.Update;
import ca.uhn.fhir.rest.annotation.Validate;
import ca.uhn.fhir.rest.api.MethodOutcome;
import ca.uhn.fhir.rest.api.RestSearchParameterTypeEnum;
import ca.uhn.fhir.rest.api.server.IBundleProvider;
import ca.uhn.fhir.rest.api.server.RequestDetails;
import ca.uhn.fhir.rest.param.DateParam;
import ca.uhn.fhir.rest.param.DateRangeParam;
import ca.uhn.fhir.rest.param.QuantityParam;
import ca.uhn.fhir.rest.param.ReferenceAndListParam;
@ -27,7 +42,8 @@ import ca.uhn.fhir.validation.ValidationResult;
import com.google.common.collect.Lists;
import org.hl7.fhir.instance.model.api.IBaseResource;
import org.hl7.fhir.r4.hapi.rest.server.ServerCapabilityStatementProvider;
import org.hl7.fhir.r4.model.*;
import org.hl7.fhir.r4.model.Bundle;
import org.hl7.fhir.r4.model.CapabilityStatement;
import org.hl7.fhir.r4.model.CapabilityStatement.CapabilityStatementRestComponent;
import org.hl7.fhir.r4.model.CapabilityStatement.CapabilityStatementRestResourceComponent;
import org.hl7.fhir.r4.model.CapabilityStatement.CapabilityStatementRestResourceOperationComponent;
@ -35,10 +51,18 @@ import org.hl7.fhir.r4.model.CapabilityStatement.CapabilityStatementRestResource
import org.hl7.fhir.r4.model.CapabilityStatement.ConditionalDeleteStatus;
import org.hl7.fhir.r4.model.CapabilityStatement.SystemRestfulInteraction;
import org.hl7.fhir.r4.model.CapabilityStatement.TypeRestfulInteraction;
import org.hl7.fhir.r4.model.CodeType;
import org.hl7.fhir.r4.model.DateType;
import org.hl7.fhir.r4.model.DiagnosticReport;
import org.hl7.fhir.r4.model.Encounter;
import org.hl7.fhir.r4.model.Enumerations.PublicationStatus;
import org.hl7.fhir.r4.model.IdType;
import org.hl7.fhir.r4.model.OperationDefinition;
import org.hl7.fhir.r4.model.OperationDefinition.OperationDefinitionParameterComponent;
import org.hl7.fhir.r4.model.OperationDefinition.OperationKind;
import org.hl7.fhir.r4.model.OperationDefinition.OperationParameterUse;
import org.hl7.fhir.r4.model.Patient;
import org.hl7.fhir.r4.model.StringType;
import org.junit.jupiter.api.AfterAll;
import org.junit.jupiter.api.Test;
@ -49,6 +73,7 @@ import java.util.Collection;
import java.util.HashSet;
import java.util.List;
import java.util.Set;
import java.util.stream.Collectors;
import static org.hamcrest.MatcherAssert.assertThat;
import static org.hamcrest.Matchers.containsInAnyOrder;
@ -65,8 +90,12 @@ import static org.mockito.Mockito.when;
public class ServerCapabilityStatementProviderR4Test {
private static FhirContext ourCtx;
public static final String PATIENT_SUB = "PatientSub";
public static final String PATIENT_SUB_SUB = "PatientSubSub";
public static final String PATIENT_SUB_SUB_2 = "PatientSubSub2";
public static final String PATIENT_TRIPLE_SUB = "PatientTripleSub";
private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(ServerCapabilityStatementProviderR4Test.class);
private static FhirContext ourCtx;
private static FhirValidator ourValidator;
static {
@ -259,7 +288,9 @@ public class ServerCapabilityStatementProviderR4Test {
assertNull(res.getConditionalUpdateElement().getValue());
}
/** See #379 */
/**
* See #379
*/
@Test
public void testOperationAcrossMultipleTypes() throws Exception {
RestfulServer rs = new RestfulServer(ourCtx);
@ -513,10 +544,10 @@ public class ServerCapabilityStatementProviderR4Test {
for (ResourceBinding resourceBinding : resourceBindings) {
if (resourceBinding.getResourceName().equals("Patient")) {
List<BaseMethodBinding<?>> methodBindings = resourceBinding.getMethodBindings();
SearchMethodBinding binding = (SearchMethodBinding) methodBindings.get(0);
SearchParameter param = (SearchParameter) binding.getParameters().get(25);
assertEquals("The organization at which this person is a patient", param.getDescription());
found = true;
SearchMethodBinding binding = (SearchMethodBinding) methodBindings.get(0);
SearchParameter param = (SearchParameter) binding.getParameters().get(25);
assertEquals("The organization at which this person is a patient", param.getDescription());
found = true;
}
}
assertTrue(found);
@ -569,7 +600,7 @@ public class ServerCapabilityStatementProviderR4Test {
@Test
public void testSearchReferenceParameterWithList() throws Exception {
RestfulServer rsNoType = new RestfulServer(ourCtx){
RestfulServer rsNoType = new RestfulServer(ourCtx) {
@Override
public RestfulServerConfiguration createConfiguration() {
RestfulServerConfiguration retVal = super.createConfiguration();
@ -586,7 +617,7 @@ public class ServerCapabilityStatementProviderR4Test {
String confNoType = ourCtx.newXmlParser().setPrettyPrint(true).encodeResourceToString(conformance);
ourLog.info(confNoType);
RestfulServer rsWithType = new RestfulServer(ourCtx){
RestfulServer rsWithType = new RestfulServer(ourCtx) {
@Override
public RestfulServerConfiguration createConfiguration() {
RestfulServerConfiguration retVal = super.createConfiguration();
@ -645,6 +676,46 @@ public class ServerCapabilityStatementProviderR4Test {
assertThat(conf, containsString("<interaction><code value=\"" + TypeRestfulInteraction.HISTORYTYPE.toCode() + "\"/></interaction>"));
}
@Test
public void testStaticIncludeChains() throws Exception {
class MyProvider implements IResourceProvider {
@Override
public Class<DiagnosticReport> getResourceType() {
return DiagnosticReport.class;
}
@Search
public List<IBaseResource> search(@RequiredParam(name = DiagnosticReport.SP_PATIENT + "." + Patient.SP_FAMILY) StringParam lastName,
@RequiredParam(name = DiagnosticReport.SP_PATIENT + "." + Patient.SP_GIVEN) StringParam firstName,
@RequiredParam(name = DiagnosticReport.SP_PATIENT + "." + Patient.SP_BIRTHDATE) DateParam dob,
@OptionalParam(name = DiagnosticReport.SP_DATE) DateRangeParam range) {
return null;
}
}
RestfulServer rs = new RestfulServer(ourCtx);
rs.setProviders(new MyProvider());
ServerCapabilityStatementProvider sc = new ServerCapabilityStatementProvider() {
};
rs.setServerConformanceProvider(sc);
rs.init(createServletConfig());
CapabilityStatement opDef = sc.getServerConformance(createHttpServletRequest(), createRequestDetails(rs));
String conf = ourCtx.newXmlParser().setPrettyPrint(true).encodeResourceToString(opDef);
ourLog.info(conf);
CapabilityStatementRestResourceComponent resource = opDef.getRest().get(0).getResource().get(0);
assertEquals("DiagnosticReport", resource.getType());
List<String> searchParamNames = resource.getSearchParam().stream().map(t -> t.getName()).collect(Collectors.toList());
assertThat(searchParamNames, containsInAnyOrder("patient", "date"));
}
@Test
public void testSystemLevelNamedQueryWithParameters() throws Exception {
RestfulServer rs = new RestfulServer(ourCtx);
@ -729,8 +800,8 @@ public class ServerCapabilityStatementProviderR4Test {
assertThat(param.getUse(), is(OperationParameterUse.IN));
CapabilityStatementRestResourceComponent patientResource = restComponent.getResource().stream()
.filter(r -> patientResourceName.equals(r.getType()))
.findAny().get();
.filter(r -> patientResourceName.equals(r.getType()))
.findAny().get();
assertThat("Named query parameters should not appear in the resource search params", patientResource.getSearchParam(), is(empty()));
}
@ -761,26 +832,26 @@ public class ServerCapabilityStatementProviderR4Test {
assertThat(opDef.getType(), is(true));
assertThat(opDef.getInstance(), is(false));
}
@Test
public void testProfiledResourceStructureDefinitionLinks() throws Exception {
RestfulServer rs = new RestfulServer(ourCtx);
rs.setResourceProviders(new ProfiledPatientProvider(), new MultipleProfilesPatientProvider());
ServerCapabilityStatementProvider sc = new ServerCapabilityStatementProvider();
rs.setServerConformanceProvider(sc);
@Test
public void testProfiledResourceStructureDefinitionLinks() throws Exception {
RestfulServer rs = new RestfulServer(ourCtx);
rs.setResourceProviders(new ProfiledPatientProvider(), new MultipleProfilesPatientProvider());
rs.init(createServletConfig());
ServerCapabilityStatementProvider sc = new ServerCapabilityStatementProvider();
rs.setServerConformanceProvider(sc);
CapabilityStatement conformance = sc.getServerConformance(createHttpServletRequest(), createRequestDetails(rs));
ourLog.info(ourCtx.newXmlParser().setPrettyPrint(true).encodeResourceToString(conformance));
rs.init(createServletConfig());
List<CapabilityStatementRestResourceComponent> resources = conformance.getRestFirstRep().getResource();
CapabilityStatementRestResourceComponent patientResource = resources.stream()
.filter(resource -> "Patient".equals(resource.getType()))
.findFirst().get();
assertThat(patientResource.getProfile(), containsString(PATIENT_SUB));
}
CapabilityStatement conformance = sc.getServerConformance(createHttpServletRequest(), createRequestDetails(rs));
ourLog.info(ourCtx.newXmlParser().setPrettyPrint(true).encodeResourceToString(conformance));
List<CapabilityStatementRestResourceComponent> resources = conformance.getRestFirstRep().getResource();
CapabilityStatementRestResourceComponent patientResource = resources.stream()
.filter(resource -> "Patient".equals(resource.getType()))
.findFirst().get();
assertThat(patientResource.getProfile(), containsString(PATIENT_SUB));
}
private List<String> toOperationIdParts(List<CapabilityStatementRestResourceOperationComponent> theOperation) {
ArrayList<String> retVal = Lists.newArrayList();
@ -817,11 +888,6 @@ public class ServerCapabilityStatementProviderR4Test {
assertTrue(result.isSuccessful(), outcome);
}
@AfterAll
public static void afterClassClearContext() {
TestUtil.clearAllStaticFieldsForUnitTest();
}
@SuppressWarnings("unused")
public static class ConditionalProvider implements IResourceProvider {
@ -866,7 +932,7 @@ public class ServerCapabilityStatementProviderR4Test {
@Search(type = Patient.class)
public Patient findPatient(@Description(shortDefinition = "The patient's identifier") @OptionalParam(name = Patient.SP_IDENTIFIER) TokenParam theIdentifier,
@Description(shortDefinition = "The patient's name") @OptionalParam(name = Patient.SP_NAME) StringParam theName) {
@Description(shortDefinition = "The patient's name") @OptionalParam(name = Patient.SP_NAME) StringParam theName) {
return null;
}
@ -942,7 +1008,7 @@ public class ServerCapabilityStatementProviderR4Test {
@SuppressWarnings("unused")
public static class PlainProviderWithExtendedOperationOnNoType {
@Operation(name = "plain", idempotent = true, returnParameters = { @OperationParam(min = 1, max = 2, name = "out1", type = StringType.class) })
@Operation(name = "plain", idempotent = true, returnParameters = {@OperationParam(min = 1, max = 2, name = "out1", type = StringType.class)})
public IBundleProvider everything(HttpServletRequest theServletRequest, @IdParam IdType theId, @OperationParam(name = "start") DateType theStart,
@OperationParam(name = "end") DateType theEnd) {
return null;
@ -972,8 +1038,8 @@ public class ServerCapabilityStatementProviderR4Test {
@Description(shortDefinition = "This is a search for stuff!")
@Search
public List<DiagnosticReport> findDiagnosticReportsByPatient(@RequiredParam(name = DiagnosticReport.SP_SUBJECT + '.' + Patient.SP_IDENTIFIER) TokenParam thePatientId,
@OptionalParam(name = DiagnosticReport.SP_CODE) TokenOrListParam theNames, @OptionalParam(name = DiagnosticReport.SP_DATE) DateRangeParam theDateRange,
@IncludeParam(allow = { "DiagnosticReport.result" }) Set<Include> theIncludes) throws Exception {
@OptionalParam(name = DiagnosticReport.SP_CODE) TokenOrListParam theNames, @OptionalParam(name = DiagnosticReport.SP_DATE) DateRangeParam theDateRange,
@IncludeParam(allow = {"DiagnosticReport.result"}) Set<Include> theIncludes) throws Exception {
return null;
}
@ -1004,7 +1070,7 @@ public class ServerCapabilityStatementProviderR4Test {
@Search(type = Patient.class)
public Patient findPatient2(
@Description(shortDefinition = "All patients linked to the given patient") @OptionalParam(name = "link", targetTypes = { Patient.class }) ReferenceAndListParam theLink) {
@Description(shortDefinition = "All patients linked to the given patient") @OptionalParam(name = "link", targetTypes = {Patient.class}) ReferenceAndListParam theLink) {
return null;
}
@ -1014,15 +1080,15 @@ public class ServerCapabilityStatementProviderR4Test {
public static class SearchProviderWithWhitelist {
@Search(type = Patient.class)
public Patient findPatient1(@Description(shortDefinition = "The organization at which this person is a patient") @RequiredParam(name = Patient.SP_ORGANIZATION, chainWhitelist = { "foo",
"bar" }) ReferenceAndListParam theIdentifier) {
public Patient findPatient1(@Description(shortDefinition = "The organization at which this person is a patient") @RequiredParam(name = Patient.SP_ORGANIZATION, chainWhitelist = {"foo",
"bar"}) ReferenceAndListParam theIdentifier) {
return null;
}
}
@SuppressWarnings("unused")
public static class SearchProviderWithListNoType implements IResourceProvider {
public static class SearchProviderWithListNoType implements IResourceProvider {
@Override
public Class<? extends IBaseResource> getResourceType() {
@ -1030,7 +1096,6 @@ public class ServerCapabilityStatementProviderR4Test {
}
@Search()
public List<Patient> findPatient1(@Description(shortDefinition = "The organization at which this person is a patient") @RequiredParam(name = Patient.SP_ORGANIZATION) ReferenceAndListParam theIdentifier) {
return null;
@ -1039,7 +1104,7 @@ public class ServerCapabilityStatementProviderR4Test {
}
@SuppressWarnings("unused")
public static class SearchProviderWithListWithType implements IResourceProvider {
public static class SearchProviderWithListWithType implements IResourceProvider {
@Override
public Class<? extends IBaseResource> getResourceType() {
@ -1047,15 +1112,13 @@ public class ServerCapabilityStatementProviderR4Test {
}
@Search(type=Patient.class)
@Search(type = Patient.class)
public List<Patient> findPatient1(@Description(shortDefinition = "The organization at which this person is a patient") @RequiredParam(name = Patient.SP_ORGANIZATION) ReferenceAndListParam theIdentifier) {
return null;
}
}
public static class SystemHistoryProvider {
@History
@ -1093,7 +1156,7 @@ public class ServerCapabilityStatementProviderR4Test {
}
}
public static class TypeLevelOperationProvider implements IResourceProvider {
public static final String OPERATION_NAME = "op";
@ -1139,49 +1202,53 @@ public class ServerCapabilityStatementProviderR4Test {
}
}
public static class ProfiledPatientProvider implements IResourceProvider {
@Override
public Class<? extends IBaseResource> getResourceType() {
return PatientSubSub2.class;
}
@Search
public List<PatientSubSub2> find() {
return null;
}
}
public static class MultipleProfilesPatientProvider implements IResourceProvider {
public static class ProfiledPatientProvider implements IResourceProvider {
@Override
public Class<? extends IBaseResource> getResourceType() {
return PatientSubSub.class;
}
@Read(type = PatientTripleSub.class)
public PatientTripleSub read(@IdParam IdType theId) {
return null;
}
}
public static final String PATIENT_SUB = "PatientSub";
public static final String PATIENT_SUB_SUB = "PatientSubSub";
public static final String PATIENT_SUB_SUB_2 = "PatientSubSub2";
public static final String PATIENT_TRIPLE_SUB = "PatientTripleSub";
@ResourceDef(id = PATIENT_SUB)
public static class PatientSub extends Patient {}
@ResourceDef(id = PATIENT_SUB_SUB)
public static class PatientSubSub extends PatientSub {}
@ResourceDef(id = PATIENT_SUB_SUB_2)
public static class PatientSubSub2 extends PatientSub {}
@ResourceDef(id = PATIENT_TRIPLE_SUB)
public static class PatientTripleSub extends PatientSubSub {}
@Override
public Class<? extends IBaseResource> getResourceType() {
return PatientSubSub2.class;
}
@Search
public List<PatientSubSub2> find() {
return null;
}
}
public static class MultipleProfilesPatientProvider implements IResourceProvider {
@Override
public Class<? extends IBaseResource> getResourceType() {
return PatientSubSub.class;
}
@Read(type = PatientTripleSub.class)
public PatientTripleSub read(@IdParam IdType theId) {
return null;
}
}
@ResourceDef(id = PATIENT_SUB)
public static class PatientSub extends Patient {
}
@ResourceDef(id = PATIENT_SUB_SUB)
public static class PatientSubSub extends PatientSub {
}
@ResourceDef(id = PATIENT_SUB_SUB_2)
public static class PatientSubSub2 extends PatientSub {
}
@ResourceDef(id = PATIENT_TRIPLE_SUB)
public static class PatientTripleSub extends PatientSubSub {
}
@AfterAll
public static void afterClassClearContext() {
TestUtil.clearAllStaticFieldsForUnitTest();
}
}