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Jr 20211021 chained references 3 (#3107) 

* Create index entries for outbound references of contained resources

* build query for chained reference

* fix case where the contained reference is an explicit id rather than a continued chain

* fix contained index to use path names not search param names

* make qualified search work

* cleanup and changelog

* recurse while creating indexes on contained resources

* double link both contained

* longer contained subchains

* adding some failing test cases to illustrate the limitations of qualified searches

* clean up merge cruft

* changelog

* create recursive resource links

* add test coverage for a more complicated case

* changelog

* remove unnecessary check for _contained flag

* fix broken tests
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JasonRoberts-smile 2021-10-25 10:16:10 -04:00 committed by GitHub
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8 changed files with 165 additions and 44 deletions
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5
hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/5_6_0/3106-chained-search-multi-contained-resource-to-outbound-ref.yaml Normal file
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@ -0,0 +1,5 @@
---
type: add
issue: 3106
jira: SMILE-3151
title: "Further enhances the features added by issue 3100 to allow chained searches across any combination of discrete and contained references."

8
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/search/builder/QueryStack.java
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@ -1139,13 +1139,7 @@ public class QueryStack {
break;
case REFERENCE:
for (List<? extends IQueryParameterType> nextAnd : theAndOrParams) {
if (theSearchContainedMode.equals(SearchContainedModeEnum.TRUE)) {
// TODO: The _contained parameter is not intended to control search chain interpretation like this.
// See SMILE-2898 for details.
// For now, leave the incorrect implementation alone, just in case someone is relying on it,
// until the complete fix is available.
andPredicates.add(createPredicateReferenceForContainedResource(null, theResourceName, theParamName, new ArrayList<>(), nextParamDef, nextAnd, null, theRequest, theRequestPartitionId));
} else if (isEligibleForContainedResourceSearch(nextAnd)) {
if (isEligibleForContainedResourceSearch(nextAnd)) {
andPredicates.add(toOrPredicate(
createPredicateReference(theSourceJoinColumn, theResourceName, theParamName, new ArrayList<>(), nextAnd, null, theRequest, theRequestPartitionId),
createPredicateReferenceForContainedResource(theSourceJoinColumn, theResourceName, theParamName, new ArrayList<>(), nextParamDef, nextAnd, null, theRequest, theRequestPartitionId)

3
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/search/builder/predicate/ResourceLinkPredicateBuilder.java
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@ -61,6 +61,7 @@ import ca.uhn.fhir.rest.param.SpecialParam;
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.param.UriParam;
import ca.uhn.fhir.rest.server.exceptions.InternalErrorException;
import ca.uhn.fhir.rest.server.exceptions.InvalidRequestException;
import ca.uhn.fhir.rest.server.servlet.ServletRequestDetails;
@ -656,6 +657,8 @@ public class ResourceLinkPredicateBuilder extends BaseJoiningPredicateBuilder {
}
throw new InternalErrorException("Don't know how to convert param type: " + theParam.getParamType());
case URI:
qp = new UriParam();
break;
case HAS:
default:
throw new InternalErrorException("Don't know how to convert param type: " + theParam.getParamType());

42
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/r4/ChainingR4SearchTest.java
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@ -769,6 +769,48 @@ public class ChainingR4SearchTest extends BaseJpaR4Test {
assertThat(oids, contains(oid1.getIdPart()));
}
@Test
public void testShouldResolveAFourLinkChainWhereTheFirstTwoReferencesAreContained() throws Exception {
// setup
myModelConfig.setIndexOnContainedResourcesRecursively(true);
IIdType oid1;
{
Organization org = new Organization();
org.setId(IdType.newRandomUuid());
org.setName("HealthCo");
myOrganizationDao.create(org, mySrd);
Organization partOfOrg = new Organization();
partOfOrg.setId("child");
partOfOrg.getPartOf().setReference(org.getId());
Patient p = new Patient();
p.setId("pat");
p.addName().setFamily("Smith").addGiven("John");
p.getManagingOrganization().setReference("#child");
Observation obs = new Observation();
obs.getContained().add(org);
obs.getContained().add(partOfOrg);
obs.getContained().add(p);
obs.getCode().setText("Observation 1");
obs.getSubject().setReference("#pat");
oid1 = myObservationDao.create(obs, mySrd).getId().toUnqualifiedVersionless();
}
String url = "/Observation?subject.organization.partof.name=HealthCo";
// execute
List<String> oids = searchAndReturnUnqualifiedVersionlessIdValues(url);
// validate
assertEquals(1L, oids.size());
assertThat(oids, contains(oid1.getIdPart()));
}
@Test
public void testShouldResolveAFourLinkChainWhereAllReferencesAreContained() throws Exception {

32
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/r4/FhirResourceDaoR4ContainedTest.java
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@ -77,7 +77,6 @@ public class FhirResourceDaoR4ContainedTest extends BaseJpaR4Test {
map = new SearchParameterMap();
map.add("subject", new ReferenceParam("name", "Smith"));
map.setSearchContainedMode(SearchContainedModeEnum.TRUE);
assertThat(toUnqualifiedVersionlessIdValues(myObservationDao.search(map)), containsInAnyOrder(toValues(id)));
}
@ -112,7 +111,6 @@ public class FhirResourceDaoR4ContainedTest extends BaseJpaR4Test {
map = new SearchParameterMap();
map.add("subject", new ReferenceParam("name", "Smith"));
map.setSearchContainedMode(SearchContainedModeEnum.TRUE);
map.setLoadSynchronous(true);
assertThat(toUnqualifiedVersionlessIdValues(myObservationDao.search(map)), containsInAnyOrder(toValues(id)));
@ -183,8 +181,7 @@ public class FhirResourceDaoR4ContainedTest extends BaseJpaR4Test {
map = new SearchParameterMap();
map.add("general-practitioner", new ReferenceParam("family", "Smith"));
map.setSearchContainedMode(SearchContainedModeEnum.TRUE);
assertThat(toUnqualifiedVersionlessIdValues(myPatientDao.search(map)), containsInAnyOrder(toValues(id)));
}
@ -268,30 +265,10 @@ public class FhirResourceDaoR4ContainedTest extends BaseJpaR4Test {
map = new SearchParameterMap();
map.add("based-on", new ReferenceParam("authored", "2021-02-23"));
map.setSearchContainedMode(SearchContainedModeEnum.TRUE);
assertThat(toUnqualifiedVersionlessIdValues(myEncounterDao.search(map)), containsInAnyOrder(toValues(id)));
}
@Test
public void testSearchWithNotSupportedSearchType() {
SearchParameterMap map;
map = new SearchParameterMap();
map.add("subject", new ReferenceParam("near", "toronto"));
map.setSearchContainedMode(SearchContainedModeEnum.TRUE);
try {
IBundleProvider outcome = myObservationDao.search(map);
outcome.getResources(0, 1).get(0);
fail();
} catch (InvalidRequestException e) {
assertEquals(e.getMessage(), "The search type: SPECIAL is not supported.");
}
}
@Test
public void testSearchWithNotSupportedSearchParameter() {
@ -299,14 +276,13 @@ public class FhirResourceDaoR4ContainedTest extends BaseJpaR4Test {
map = new SearchParameterMap();
map.add("subject", new ReferenceParam("marital-status", "M"));
map.setSearchContainedMode(SearchContainedModeEnum.TRUE);
try {
IBundleProvider outcome = myObservationDao.search(map);
outcome.getResources(0, 1).get(0);
fail();
} catch (InvalidRequestException e) {
assertEquals(e.getMessage(), "Unknown search parameter name: subject.marital-status.");
assertEquals("Invalid parameter chain: subject.marital-status", e.getMessage());
}
}

88
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/r4/FhirResourceDaoR4CreateTest.java
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@ -135,7 +135,7 @@ public class FhirResourceDaoR4CreateTest extends BaseJpaR4Test {
p.getNameFirstRep().setFamily("Smith");
Observation containedObs = new Observation();
containedObs.setId("#obs");
containedObs.setId("obs");
containedObs.setSubject(new Reference("#pat"));
Encounter enc = new Encounter();
@ -172,7 +172,7 @@ public class FhirResourceDaoR4CreateTest extends BaseJpaR4Test {
org2.setPartOf(new Reference("#org1"));
Observation containedObs = new Observation();
containedObs.setId("#obs");
containedObs.setId("obs");
containedObs.addPerformer(new Reference("#org1"));
Encounter enc = new Encounter();
@ -206,6 +206,90 @@ public class FhirResourceDaoR4CreateTest extends BaseJpaR4Test {
});
}
@Test
public void testCreateLinkCreatesAppropriatePaths_ContainedResourceRecursive_ToOutboundReference() {
myModelConfig.setIndexOnContainedResources(true);
myModelConfig.setIndexOnContainedResourcesRecursively(true);
Organization org = new Organization();
org.setId("Organization/ABC");
myOrganizationDao.update(org);
Patient p = new Patient();
p.setId("pat");
p.setActive(true);
p.setManagingOrganization(new Reference("Organization/ABC"));
Observation containedObs = new Observation();
containedObs.setId("#cont");
containedObs.setSubject(new Reference("#pat"));
Encounter enc = new Encounter();
enc.getContained().add(p);
enc.getContained().add(containedObs);
enc.addReasonReference(new Reference("#cont"));
myEncounterDao.create(enc, mySrd);
runInTransaction(() ->{
List<ResourceLink> allLinks = myResourceLinkDao.findAll();
Optional<ResourceLink> link = allLinks
.stream()
.filter(t -> "Encounter.reasonReference.subject.managingOrganization".equals(t.getSourcePath()))
.findFirst();
assertTrue(link.isPresent());
assertEquals("Organization", link.get().getTargetResourceType());
assertEquals("ABC", link.get().getTargetResourceId());
});
}
@Test
public void testCreateLinkCreatesAppropriatePaths_ContainedResourceRecursive_ToOutboundReference_NoLoops() {
myModelConfig.setIndexOnContainedResources(true);
myModelConfig.setIndexOnContainedResourcesRecursively(true);
Organization org = new Organization();
org.setId("Organization/ABC");
myOrganizationDao.update(org);
Patient p = new Patient();
p.setId("pat");
p.setActive(true);
p.setManagingOrganization(new Reference("Organization/ABC"));
Observation obs1 = new Observation();
obs1.setId("obs1");
obs1.setSubject(new Reference("#pat"));
obs1.addPartOf(new Reference("#obs2"));
Observation obs2 = new Observation();
obs2.setId("obs2");
obs2.addPartOf(new Reference("#obs1"));
Encounter enc = new Encounter();
enc.getContained().add(p);
enc.getContained().add(obs1);
enc.getContained().add(obs2);
enc.addReasonReference(new Reference("#obs2"));
myEncounterDao.create(enc, mySrd);
runInTransaction(() ->{
List<ResourceLink> allLinks = myResourceLinkDao.findAll();
Optional<ResourceLink> link = allLinks
.stream()
.filter(t -> "Encounter.reasonReference.partOf.subject.managingOrganization".equals(t.getSourcePath()))
.findFirst();
assertTrue(link.isPresent());
assertEquals("Organization", link.get().getTargetResourceType());
assertEquals("ABC", link.get().getTargetResourceId());
Optional<ResourceLink> noLink = allLinks
.stream()
.filter(t -> "Encounter.reasonReference.partOf.partOf.partOf.subject.managingOrganization".equals(t.getSourcePath()))
.findFirst();
assertFalse(noLink.isPresent());
});
}
@Test
public void testConditionalCreateWithPlusInUrl() {
Observation obs = new Observation();

6
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/provider/r4/ResourceProviderR4SearchContainedTest.java
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@ -823,20 +823,20 @@ public class ResourceProviderR4SearchContainedTest extends BaseResourceProviderR
}
//-- Search by uri
String uri = ourServerBase + "/Observation?based-on.instantiates-uri=http://www.hl7.com&_contained=true";
String uri = ourServerBase + "/Observation?based-on.instantiates-uri=http://www.hl7.com";
List<String> oids = searchAndReturnUnqualifiedVersionlessIdValues(uri);
assertEquals(1L, oids.size());
assertThat(oids, contains(oid1.getValue()));
//-- Search by uri more than 1 results
uri = ourServerBase + "/Observation?based-on.instantiates-uri=http://www2.hl7.com&_contained=true";
uri = ourServerBase + "/Observation?based-on.instantiates-uri=http://www2.hl7.com";
oids = searchAndReturnUnqualifiedVersionlessIdValues(uri);
assertEquals(2L, oids.size());
//-- Search by uri with 'or'
uri = ourServerBase + "/Observation?based-on.instantiates-uri=http://www.hl7.com,http://www2.hl7.com&_contained=true";
uri = ourServerBase + "/Observation?based-on.instantiates-uri=http://www.hl7.com,http://www2.hl7.com";
oids = searchAndReturnUnqualifiedVersionlessIdValues(uri);
assertEquals(3L, oids.size());

25
hapi-fhir-jpaserver-searchparam/src/main/java/ca/uhn/fhir/jpa/searchparam/extractor/SearchParamExtractorService.java
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@ -137,7 +137,7 @@ public class SearchParamExtractorService {
extractSearchIndexParametersForContainedResources(theRequestDetails, theParams, theResource, theEntity, containedResources, new HashSet<>());
}
private void extractSearchIndexParametersForContainedResources(RequestDetails theRequestDetails, ResourceIndexedSearchParams theParams, IBaseResource theResource, ResourceTable theEntity, Collection<IBaseResource> containedResources, Collection<IBaseResource> theAlreadySeenResources) {
private void extractSearchIndexParametersForContainedResources(RequestDetails theRequestDetails, ResourceIndexedSearchParams theParams, IBaseResource theResource, ResourceTable theEntity, Collection<IBaseResource> theContainedResources, Collection<IBaseResource> theAlreadySeenResources) {
// 2. Find referenced search parameters
ISearchParamExtractor.SearchParamSet<PathAndRef> referencedSearchParamSet = mySearchParamExtractor.extractResourceLinks(theResource, true);
@ -153,7 +153,7 @@ public class SearchParamExtractorService {
continue;
// 3.2 find the contained resource
IBaseResource containedResource = findContainedResource(containedResources, nextPathAndRef.getRef());
IBaseResource containedResource = findContainedResource(theContainedResources, nextPathAndRef.getRef());
if (containedResource == null)
continue;
@ -171,7 +171,7 @@ public class SearchParamExtractorService {
if (myModelConfig.isIndexOnContainedResourcesRecursively()) {
HashSet<IBaseResource> nextAlreadySeenResources = new HashSet<>(theAlreadySeenResources);
nextAlreadySeenResources.add(containedResource);
extractSearchIndexParametersForContainedResources(theRequestDetails, currParams, containedResource, theEntity, containedResources, nextAlreadySeenResources);
extractSearchIndexParametersForContainedResources(theRequestDetails, currParams, containedResource, theEntity, theContainedResources, nextAlreadySeenResources);
}
// 3.5 added reference name as a prefix for the contained resource if any
@ -430,6 +430,11 @@ public class SearchParamExtractorService {
// 1. get all contained resources
Collection<IBaseResource> containedResources = terser.getAllEmbeddedResources(theResource, false);
extractResourceLinksForContainedResources(theRequestPartitionId, theParams, theEntity, theResource, theTransactionDetails, theFailOnInvalidReference, theRequest, containedResources, new HashSet<>());
}
private void extractResourceLinksForContainedResources(RequestPartitionId theRequestPartitionId, ResourceIndexedSearchParams theParams, ResourceTable theEntity, IBaseResource theResource, TransactionDetails theTransactionDetails, boolean theFailOnInvalidReference, RequestDetails theRequest, Collection<IBaseResource> theContainedResources, Collection<IBaseResource> theAlreadySeenResources) {
// 2. Find referenced search parameters
ISearchParamExtractor.SearchParamSet<PathAndRef> referencedSearchParamSet = mySearchParamExtractor.extractResourceLinks(theResource, true);
@ -445,15 +450,27 @@ public class SearchParamExtractorService {
continue;
// 3.2 find the contained resource
IBaseResource containedResource = findContainedResource(containedResources, nextPathAndRef.getRef());
IBaseResource containedResource = findContainedResource(theContainedResources, nextPathAndRef.getRef());
if (containedResource == null)
continue;
// 3.2.1 if we've already processed this resource upstream, do not process it again, to prevent infinite loops
if (theAlreadySeenResources.contains(containedResource)) {
continue;
}
currParams = new ResourceIndexedSearchParams();
// 3.3 create indexes for the current contained resource
extractResourceLinks(theRequestPartitionId, currParams, theEntity, containedResource, theTransactionDetails, theFailOnInvalidReference, theRequest);
// 3.4 recurse to process any other contained resources referenced by this one
if (myModelConfig.isIndexOnContainedResourcesRecursively()) {
HashSet<IBaseResource> nextAlreadySeenResources = new HashSet<>(theAlreadySeenResources);
nextAlreadySeenResources.add(containedResource);
extractResourceLinksForContainedResources(theRequestPartitionId, currParams, theEntity, containedResource, theTransactionDetails, theFailOnInvalidReference, theRequest, theContainedResources, nextAlreadySeenResources);
}
// 3.4 added reference name as a prefix for the contained resource if any
// e.g. for Observation.subject contained reference
// the SP_NAME = subject.family