Ks 20230324 include prov (#4685)

* fix test

* fixed

* changelog

* add another test

* improve docs

* fix change log

* fix test

* fix test

---------

Co-authored-by: Ken Stevens <ken@smilecdr.com>

hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/6_6_0/4685-patient-everything-skips-other-patients.yaml

@@ -0,0 +1,5 @@
+---
+type: change
+issue: 4685
+title: "When calling $everything on a Patient instance, the jpa server no longer traverses into other patients.
+Previously it was possible to pull in data from another patient for example, via a Provenance resource."

hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/search/builder/SearchBuilder.java

@@ -125,7 +125,6 @@ import java.util.Optional;
 import java.util.Set;
 import java.util.stream.Collectors;
 
-import static org.apache.commons.lang3.StringUtils.countMatches;
 import static org.apache.commons.lang3.StringUtils.defaultString;
 import static org.apache.commons.lang3.StringUtils.isBlank;
 import static org.apache.commons.lang3.StringUtils.isNotBlank;
@@ -1173,6 +1172,11 @@ public class SearchBuilder implements ISearchBuilder<JpaPid> {
 					} else {
 						wantResourceType = null;
 					}
+					// When calling $everything on a Patient instance, we don't want to recurse into new Patient resources
+					// (e.g. via Provenance, List, or Group) when in an $everything operation
+					if (myParams != null && myParams.getEverythingMode() == SearchParameterMap.EverythingModeEnum.PATIENT_INSTANCE) {
+						sqlBuilder.append(" AND r.myTargetResourceType != 'Patient'");
+					}
 
 					String sql = sqlBuilder.toString();
 					List<Collection<JpaPid>> partitions = partition(nextRoundMatches, getMaximumPageSize());

hapi-fhir-jpaserver-test-dstu3/src/test/java/ca/uhn/fhir/jpa/provider/dstu3/PatientEverythingDstu3Test.java

@@ -10,6 +10,7 @@ import org.apache.http.client.methods.CloseableHttpResponse;
 import org.apache.http.client.methods.HttpGet;
 import org.hl7.fhir.dstu3.model.Bundle;
 import org.hl7.fhir.dstu3.model.Bundle.BundleEntryComponent;
+import org.hl7.fhir.dstu3.model.CarePlan;
 import org.hl7.fhir.dstu3.model.Encounter;
 import org.hl7.fhir.dstu3.model.Encounter.EncounterStatus;
 import org.hl7.fhir.dstu3.model.Observation;
@@ -142,16 +143,17 @@ public class PatientEverythingDstu3Test extends BaseResourceProviderDstu3Test {
 
 	@Test
 	public void testEverythingHandlesCircularReferences() throws Exception {
-		Patient linkedPatient1 = new Patient();
+		CarePlan cp1 = new CarePlan();
-		linkedPatient1.addLink().setOther(new Reference(myPatientId));
+		cp1.setSubject(new Reference(myPatientId));
-		String linkedPatient1Id = myClient.create().resource(linkedPatient1).execute().getId().toUnqualifiedVersionless().getValue();
+		String cp1Id = myClient.create().resource(cp1).execute().getId().toUnqualifiedVersionless().getValue();
 
-		Patient linkedPatient2 = new Patient();
+		CarePlan cp2 = new CarePlan();
-		linkedPatient2.addLink().setOther(new Reference(linkedPatient1Id));
+		cp2.addBasedOn(new Reference(cp1Id));
-		String linkedPatient2Id = myClient.create().resource(linkedPatient2).execute().getId().toUnqualifiedVersionless().getValue();
+		String cp2Id = myClient.create().resource(cp2).execute().getId().toUnqualifiedVersionless().getValue();
 
-		myPatient.addLink().setOther(new Reference(linkedPatient2Id));
+		cp1.addBasedOn(new Reference(cp2Id));
-		myClient.update().resource(myPatient).execute();
+		cp1.setId(cp1Id);
+		myClient.update().resource(cp1).execute();
 
 		Bundle bundle = fetchBundle(myServerBase + "/" + myPatientId + "/$everything?_format=json&_count=100", EncodingEnum.JSON);
 
@@ -165,8 +167,8 @@ public class PatientEverythingDstu3Test extends BaseResourceProviderDstu3Test {
 		ourLog.info("Found IDs: {}", actual);
 
 		assertThat(actual, hasItem(myPatientId));
-		assertThat(actual, hasItem(linkedPatient1Id));
+		assertThat(actual, hasItem(cp1Id));
-		assertThat(actual, hasItem(linkedPatient2Id));
+		assertThat(actual, hasItem(cp2Id));
 		assertThat(actual, hasItem(encId1));
 		assertThat(actual, hasItem(encId2));
 		assertThat(actual, hasItem(myOrgId));

hapi-fhir-jpaserver-test-r4/src/test/java/ca/uhn/fhir/jpa/provider/r4/ResourceProviderR4Test.java

@@ -16,6 +16,7 @@ import ca.uhn.fhir.jpa.searchparam.SearchParameterMap;
 import ca.uhn.fhir.jpa.term.ZipCollectionBuilder;
 import ca.uhn.fhir.jpa.test.config.TestR4Config;
 import ca.uhn.fhir.jpa.util.QueryParameterUtils;
+import ca.uhn.fhir.model.api.Include;
 import ca.uhn.fhir.model.api.StorageResponseCodeEnum;
 import ca.uhn.fhir.model.api.TemporalPrecisionEnum;
 import ca.uhn.fhir.model.primitive.IdDt;
@@ -138,6 +139,7 @@ import org.hl7.fhir.r4.model.Patient;
 import org.hl7.fhir.r4.model.Period;
 import org.hl7.fhir.r4.model.Practitioner;
 import org.hl7.fhir.r4.model.Procedure;
+import org.hl7.fhir.r4.model.Provenance;
 import org.hl7.fhir.r4.model.Quantity;
 import org.hl7.fhir.r4.model.Questionnaire;
 import org.hl7.fhir.r4.model.Questionnaire.QuestionnaireItemType;
@@ -3763,6 +3765,73 @@ public class ResourceProviderR4Test extends BaseResourceProviderR4Test {
 		assertEquals(null, response.getLink("next"));
 	}
 
+
+	@Test
+	public void testEverythingDoesNotEnterSecondPatient() {
+		Patient goodPatient = new Patient();
+		goodPatient.setActive(true);
+		String goodPid = myPatientDao.create(goodPatient, mySrd).getId().toUnqualifiedVersionless().getValue();
+
+		Patient badPatient = new Patient();
+		badPatient.setActive(true);
+		String badPid = myPatientDao.create(badPatient, mySrd).getId().toUnqualifiedVersionless().getValue();
+
+		Observation o = new Observation();
+		o.getSubject().setReference(goodPid);
+		o.addIdentifier().setSystem("foo").setValue("1");
+		String oid = myObservationDao.create(o, mySrd).getId().toUnqualifiedVersionless().getValue();
+
+		Provenance prov = new Provenance();
+		prov.addTarget().setReference(goodPid);
+		prov.addTarget().setReference(badPid);
+		String provid = myProvenanceDao.create(prov, mySrd).getId().toUnqualifiedVersionless().getValue();
+
+		Bundle response = myClient
+			.operation()
+			.onInstance(new IdType(goodPid))
+			.named("everything")
+			.withNoParameters(Parameters.class)
+			.returnResourceType(Bundle.class)
+			.execute();
+
+		List<String> ids = toUnqualifiedVersionlessIdValues(response);
+		// We should not pick up other resources via the provenance
+		assertThat(ids, containsInAnyOrder(goodPid, oid, provid));
+	}
+
+	@Test
+	public void testIncludeRecurseFromProvenanceDoesTraverse() {
+		Patient goodPatient = new Patient();
+		goodPatient.setActive(true);
+		String goodPid = myPatientDao.create(goodPatient, mySrd).getId().toUnqualifiedVersionless().getValue();
+
+		Practitioner prac = new Practitioner();
+		prac.addName().setFamily("FAM");
+		String pracid = myPractitionerDao.create(prac, mySrd).getId().toUnqualifiedVersionless().getValue();
+
+		Patient otherPatient = new Patient();
+		otherPatient.setActive(true);
+		otherPatient.addGeneralPractitioner().setReference(pracid);
+		String otherPid = myPatientDao.create(otherPatient, mySrd).getId().toUnqualifiedVersionless().getValue();
+
+		Provenance prov = new Provenance();
+		prov.addTarget().setReference(goodPid);
+		prov.addTarget().setReference(otherPid);
+		String provid = myProvenanceDao.create(prov, mySrd).getId().toUnqualifiedVersionless().getValue();
+
+		Bundle response = myClient
+			.search()
+			.forResource("Provenance")
+			.where(Provenance.TARGET.hasId(goodPid))
+			.include(new Include("*", true))
+			.returnBundle(Bundle.class)
+			.execute();
+
+		List<String> ids = toUnqualifiedVersionlessIdValues(response);
+		// We should not pick up other resources via the provenance
+		assertThat(ids, containsInAnyOrder(goodPid, otherPid, pracid, provid));
+	}
+
 	@Test
 	public void testParseAndEncodeExtensionWithValueWithExtension() throws IOException {
 		String input = "<Patient xmlns=\"http://hl7.org/fhir\">\n" +