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>
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Ken Stevens
GitHub
parent
7d26a7a38d
commit
47262f5bd5
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@ -0,0 +1,5 @@
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---
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type: change
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issue: 4685
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title: "When calling $everything on a Patient instance, the jpa server no longer traverses into other patients.
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Previously it was possible to pull in data from another patient for example, via a Provenance resource."
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@ -125,7 +125,6 @@ import java.util.Optional;
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import java.util.Set;
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import java.util.stream.Collectors;
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import static org.apache.commons.lang3.StringUtils.countMatches;
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import static org.apache.commons.lang3.StringUtils.defaultString;
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import static org.apache.commons.lang3.StringUtils.isBlank;
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import static org.apache.commons.lang3.StringUtils.isNotBlank;
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@ -1173,6 +1172,11 @@ public class SearchBuilder implements ISearchBuilder<JpaPid> {
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} else {
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wantResourceType = null;
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}
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// When calling $everything on a Patient instance, we don't want to recurse into new Patient resources
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// (e.g. via Provenance, List, or Group) when in an $everything operation
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if (myParams != null && myParams.getEverythingMode() == SearchParameterMap.EverythingModeEnum.PATIENT_INSTANCE) {
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sqlBuilder.append(" AND r.myTargetResourceType != 'Patient'");
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}
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String sql = sqlBuilder.toString();
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List<Collection<JpaPid>> partitions = partition(nextRoundMatches, getMaximumPageSize());
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@ -10,6 +10,7 @@ import org.apache.http.client.methods.CloseableHttpResponse;
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import org.apache.http.client.methods.HttpGet;
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import org.hl7.fhir.dstu3.model.Bundle;
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import org.hl7.fhir.dstu3.model.Bundle.BundleEntryComponent;
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import org.hl7.fhir.dstu3.model.CarePlan;
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import org.hl7.fhir.dstu3.model.Encounter;
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import org.hl7.fhir.dstu3.model.Encounter.EncounterStatus;
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import org.hl7.fhir.dstu3.model.Observation;
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@ -142,16 +143,17 @@ public class PatientEverythingDstu3Test extends BaseResourceProviderDstu3Test {
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@Test
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public void testEverythingHandlesCircularReferences() throws Exception {
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Patient linkedPatient1 = new Patient();
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linkedPatient1.addLink().setOther(new Reference(myPatientId));
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String linkedPatient1Id = myClient.create().resource(linkedPatient1).execute().getId().toUnqualifiedVersionless().getValue();
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CarePlan cp1 = new CarePlan();
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cp1.setSubject(new Reference(myPatientId));
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String cp1Id = myClient.create().resource(cp1).execute().getId().toUnqualifiedVersionless().getValue();
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Patient linkedPatient2 = new Patient();
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linkedPatient2.addLink().setOther(new Reference(linkedPatient1Id));
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String linkedPatient2Id = myClient.create().resource(linkedPatient2).execute().getId().toUnqualifiedVersionless().getValue();
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CarePlan cp2 = new CarePlan();
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cp2.addBasedOn(new Reference(cp1Id));
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String cp2Id = myClient.create().resource(cp2).execute().getId().toUnqualifiedVersionless().getValue();
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myPatient.addLink().setOther(new Reference(linkedPatient2Id));
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myClient.update().resource(myPatient).execute();
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cp1.addBasedOn(new Reference(cp2Id));
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cp1.setId(cp1Id);
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myClient.update().resource(cp1).execute();
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Bundle bundle = fetchBundle(myServerBase + "/" + myPatientId + "/$everything?_format=json&_count=100", EncodingEnum.JSON);
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@ -165,8 +167,8 @@ public class PatientEverythingDstu3Test extends BaseResourceProviderDstu3Test {
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ourLog.info("Found IDs: {}", actual);
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assertThat(actual, hasItem(myPatientId));
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assertThat(actual, hasItem(linkedPatient1Id));
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assertThat(actual, hasItem(linkedPatient2Id));
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assertThat(actual, hasItem(cp1Id));
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assertThat(actual, hasItem(cp2Id));
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assertThat(actual, hasItem(encId1));
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assertThat(actual, hasItem(encId2));
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assertThat(actual, hasItem(myOrgId));
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@ -16,6 +16,7 @@ import ca.uhn.fhir.jpa.searchparam.SearchParameterMap;
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import ca.uhn.fhir.jpa.term.ZipCollectionBuilder;
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import ca.uhn.fhir.jpa.test.config.TestR4Config;
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import ca.uhn.fhir.jpa.util.QueryParameterUtils;
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import ca.uhn.fhir.model.api.Include;
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import ca.uhn.fhir.model.api.StorageResponseCodeEnum;
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import ca.uhn.fhir.model.api.TemporalPrecisionEnum;
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import ca.uhn.fhir.model.primitive.IdDt;
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@ -138,6 +139,7 @@ import org.hl7.fhir.r4.model.Patient;
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import org.hl7.fhir.r4.model.Period;
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import org.hl7.fhir.r4.model.Practitioner;
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import org.hl7.fhir.r4.model.Procedure;
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import org.hl7.fhir.r4.model.Provenance;
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import org.hl7.fhir.r4.model.Quantity;
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import org.hl7.fhir.r4.model.Questionnaire;
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import org.hl7.fhir.r4.model.Questionnaire.QuestionnaireItemType;
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@ -3763,6 +3765,73 @@ public class ResourceProviderR4Test extends BaseResourceProviderR4Test {
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assertEquals(null, response.getLink("next"));
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}
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@Test
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public void testEverythingDoesNotEnterSecondPatient() {
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Patient goodPatient = new Patient();
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goodPatient.setActive(true);
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String goodPid = myPatientDao.create(goodPatient, mySrd).getId().toUnqualifiedVersionless().getValue();
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Patient badPatient = new Patient();
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badPatient.setActive(true);
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String badPid = myPatientDao.create(badPatient, mySrd).getId().toUnqualifiedVersionless().getValue();
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Observation o = new Observation();
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o.getSubject().setReference(goodPid);
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o.addIdentifier().setSystem("foo").setValue("1");
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String oid = myObservationDao.create(o, mySrd).getId().toUnqualifiedVersionless().getValue();
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Provenance prov = new Provenance();
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prov.addTarget().setReference(goodPid);
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prov.addTarget().setReference(badPid);
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String provid = myProvenanceDao.create(prov, mySrd).getId().toUnqualifiedVersionless().getValue();
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Bundle response = myClient
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.operation()
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.onInstance(new IdType(goodPid))
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.named("everything")
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.withNoParameters(Parameters.class)
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.returnResourceType(Bundle.class)
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.execute();
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List<String> ids = toUnqualifiedVersionlessIdValues(response);
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// We should not pick up other resources via the provenance
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assertThat(ids, containsInAnyOrder(goodPid, oid, provid));
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}
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@Test
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public void testIncludeRecurseFromProvenanceDoesTraverse() {
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Patient goodPatient = new Patient();
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goodPatient.setActive(true);
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String goodPid = myPatientDao.create(goodPatient, mySrd).getId().toUnqualifiedVersionless().getValue();
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Practitioner prac = new Practitioner();
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prac.addName().setFamily("FAM");
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String pracid = myPractitionerDao.create(prac, mySrd).getId().toUnqualifiedVersionless().getValue();
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Patient otherPatient = new Patient();
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otherPatient.setActive(true);
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otherPatient.addGeneralPractitioner().setReference(pracid);
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String otherPid = myPatientDao.create(otherPatient, mySrd).getId().toUnqualifiedVersionless().getValue();
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Provenance prov = new Provenance();
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prov.addTarget().setReference(goodPid);
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prov.addTarget().setReference(otherPid);
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String provid = myProvenanceDao.create(prov, mySrd).getId().toUnqualifiedVersionless().getValue();
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Bundle response = myClient
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.search()
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.forResource("Provenance")
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.where(Provenance.TARGET.hasId(goodPid))
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.include(new Include("*", true))
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.returnBundle(Bundle.class)
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.execute();
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List<String> ids = toUnqualifiedVersionlessIdValues(response);
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// We should not pick up other resources via the provenance
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assertThat(ids, containsInAnyOrder(goodPid, otherPid, pracid, provid));
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}
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@Test
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public void testParseAndEncodeExtensionWithValueWithExtension() throws IOException {
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String input = "<Patient xmlns=\"http://hl7.org/fhir\">\n" +
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