honeymoose
/
hapi-fhir
mirror of https://github.com/hapifhir/hapi-fhir.git
1
0
Fork 0
Code Issues Packages Projects Releases Wiki Activity

Fix _has then chain then _has searches (#5735) 

* Add SQL logging:  Attempt to add test.

* Small fix.

* moar tests

* Tweak unit tests to be parameterized.

* Enhance tests and more logging.

* Better tests.  More logging.  More TODOs.

* Better tests.  More logging.  More TODOs.

* Changes

* Changes

* Updates to tests.  More logging and experimental code.

* Introduce fix along with more logging and TODOs and tweaks to tests.

* Cleanup solution.  Get rid of logs and todos.  Rename test class, test methods and clean up unnecessary code.

* Add changelog.

* Implement simpler chain algorithm without conditional logic and leave a long comment explaining why.

* Implement simpler chain algorithm without conditional logic and leave a long comment explaining why.

* Fix comment.

---------

Co-authored-by: Ken Stevens <khstevens@gmail.com>
This commit is contained in:
Luke deGruchy 2024-03-04 10:52:04 -05:00 committed by GitHub
parent 9ec8882457
commit 4570c28cb6
No known key found for this signature in database
GPG Key ID: B5690EEEBB952194
3 changed files with 390 additions and 3 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

7
hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/7_2_0/5735-has-then-chain-has-searches-not-working.yaml Normal file
View File

@ -0,0 +1,7 @@
---
type: fix
issue: 5735
jira: SMILE-7592
title: "Previously, complex _has then chain then _has searches would fail to return results when expected
(ex: 'Practitioner?_has:ExplanationOfBenefit:care-team:coverage.payor._has:List:item:_id=list1')
This has been fixed."

20
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/search/builder/QueryStack.java
View File

@ -119,6 +119,7 @@ import java.util.Objects;
import java.util.Optional;
import java.util.Set;
import java.util.function.Supplier;
import java.util.regex.Pattern;
import java.util.stream.Collectors;
import static ca.uhn.fhir.jpa.search.builder.QueryStack.SearchForIdsParams.with;
@ -139,6 +140,7 @@ public class QueryStack {
private static final Logger ourLog = LoggerFactory.getLogger(QueryStack.class);
public static final String LOCATION_POSITION = "Location.position";
private static final Pattern PATTERN_DOT_AND_ALL_AFTER = Pattern.compile("\\..*");
private final FhirContext myFhirContext;
private final SearchQueryBuilder mySqlBuilder;
@ -1118,7 +1120,7 @@ public class QueryStack {
targetResourceType = next.getTargetResourceType();
paramReference = next.getReferenceFieldName();
parameterName = next.getParameterName();
paramName = parameterName.replaceAll("\\..*", "");
paramName = PATTERN_DOT_AND_ALL_AFTER.matcher(parameterName).replaceAll("");
parameters.add(QualifiedParamList.singleton(null, next.getValueAsQueryToken(myFhirContext)));
}
@ -1175,11 +1177,23 @@ public class QueryStack {
// Handle internal chain inside the has.
if (parameterName.contains(".")) {
String chainedPartOfParameter = getChainedPart(parameterName);
// Previously, for some unknown reason, we were calling getChainedPart() twice. This broke the _has
// then chain, then _has use case by effectively cutting off the second part of the chain and
// missing one iteration of the recursive call to build the query.
// So, for example, for
// Practitioner?_has:ExplanationOfBenefit:care-team:coverage.payor._has:List:item:_id=list1
// instead of passing " payor._has:List:item:_id=list1" to the next recursion, the second call to
// getChainedPart() was wrongly removing "payor." and passing down "_has:List:item:_id=list1" instead.
// This resulted in running incorrect SQL with nonsensical join that resulted in 0 results.
// However, after running the pipeline, I've concluded there's no use case at all for the
// double call to "getChainedPart()", which is why there's no conditional logic at all to make a double
// call to getChainedPart().
final String chainedPart = getChainedPart(parameterName);
orValues.stream()
.filter(qp -> qp instanceof ReferenceParam)
.map(qp -> (ReferenceParam) qp)
.forEach(rp -> rp.setChain(getChainedPart(chainedPartOfParameter)));
.forEach(rp -> rp.setChain(chainedPart));
parameterName = parameterName.substring(0, parameterName.indexOf('.'));
}

366
hapi-fhir-jpaserver-test-r4/src/test/java/ca/uhn/fhir/jpa/provider/r4/ResourceProviderR4SearchVariousScenariosTest.java Normal file
View File

@ -0,0 +1,366 @@
package ca.uhn.fhir.jpa.provider.r4;
import ca.uhn.fhir.jpa.provider.BaseResourceProviderR4Test;
import ca.uhn.fhir.jpa.searchparam.SearchParameterMap;
import ca.uhn.fhir.rest.api.server.IBundleProvider;
import ca.uhn.fhir.rest.param.HasParam;
import org.hl7.fhir.instance.model.api.IIdType;
import org.hl7.fhir.r4.model.Bundle;
import org.hl7.fhir.r4.model.CarePlan;
import org.hl7.fhir.r4.model.Coverage;
import org.hl7.fhir.r4.model.Encounter;
import org.hl7.fhir.r4.model.Enumerations;
import org.hl7.fhir.r4.model.ExplanationOfBenefit;
import org.hl7.fhir.r4.model.Group;
import org.hl7.fhir.r4.model.ListResource;
import org.hl7.fhir.r4.model.Observation;
import org.hl7.fhir.r4.model.Organization;
import org.hl7.fhir.r4.model.Patient;
import org.hl7.fhir.r4.model.Practitioner;
import org.hl7.fhir.r4.model.Reference;
import org.hl7.fhir.r4.model.SearchParameter;
import org.junit.jupiter.api.BeforeEach;
import org.junit.jupiter.api.Nested;
import org.junit.jupiter.api.Test;
import org.junit.jupiter.params.ParameterizedTest;
import org.junit.jupiter.params.provider.ValueSource;
import static org.junit.jupiter.api.Assertions.assertFalse;
public class ResourceProviderR4SearchVariousScenariosTest extends BaseResourceProviderR4Test {
private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(ResourceProviderR4SearchVariousScenariosTest.class);
@Nested
class HasMultipleNoChains {
private static final String PAT_ID = "pat1";
private static final String OBSERVATION_ID = "obs1";
private static final String ENCOUNTER_ID = "enc1";
private static final String CARE_PLAN_ID = "cp1";
@BeforeEach
void beforeEach() {
final Patient patient = new Patient();
patient.setId(PAT_ID);
final IIdType patientId = myPatientDao.update(patient, mySrd).getId().toUnqualifiedVersionless();
final Observation observation = new Observation();
observation.setId(OBSERVATION_ID);
observation.setSubject(new Reference(patientId.getValue()));
final IIdType observationId = myObservationDao.update(observation, mySrd).getId().toUnqualifiedVersionless();
final Encounter encounter = new Encounter();
encounter.setId(ENCOUNTER_ID);
encounter.addReasonReference(new Reference(observationId.getValue()));
final IIdType encounterId = myEncounterDao.update(encounter, mySrd).getId().toUnqualifiedVersionless();
final CarePlan carePlan = new CarePlan();
carePlan.setId(CARE_PLAN_ID);
carePlan.setEncounter(new Reference(encounterId.getValue()));
myCarePlanDao.update(carePlan, mySrd);
}
@ParameterizedTest
@ValueSource(strings = {
"Patient?_has:Observation:subject:_has:Encounter:reason-reference:_id="+ENCOUNTER_ID,
})
void doubleHas(String theQueryString) {
runAndAssert(theQueryString);
}
@ParameterizedTest
@ValueSource(strings = {
"Patient?_has:Observation:subject:_has:Encounter:reason-reference:_has:CarePlan:encounter:_id="+CARE_PLAN_ID
})
void tripleHas(String theQueryString) {
runAndAssert(theQueryString);
}
}
@Nested
class PractitionerEobCoveragePractitionerListNoCustomSearchParam {
private static final String PAT_ID = "pat1";
private static final String ORG_ID = "org1";
private static final String ORG_NAME = "myOrg";
private static final String PRACTITIONER_ID = "pra1";
private static final String COVERAGE_ID = "cov1";
private static final String LIST_ID = "list1";
private static final String EOB_ID = "eob1";
@BeforeEach
void beforeEach() {
myStorageSettings.setIndexOnContainedResources(false);
final Patient patient = new Patient();
patient.setId(PAT_ID);
final IIdType patientId = myPatientDao.update(patient, mySrd).getId().toUnqualifiedVersionless();
final Organization organization = new Organization();
organization.setId(ORG_ID);
organization.setName(ORG_NAME);
final IIdType orgId = myOrganizationDao.update(organization, mySrd).getId().toUnqualifiedVersionless();
final Practitioner practitioner = new Practitioner();
practitioner.setId(PRACTITIONER_ID);
final IIdType practitionerId = myPractitionerDao.update(practitioner, mySrd).getId().toUnqualifiedVersionless();
final Coverage coverage = new Coverage();
coverage.setId(COVERAGE_ID);
coverage.addPayor().setReference(orgId.getValue());
final IIdType coverageId = myCoverageDao.update(coverage, mySrd).getId().toUnqualifiedVersionless();
final ListResource list = new ListResource();
list.setId(LIST_ID);
list.addEntry().setItem(new Reference(orgId.getValue()));
myListDao.update(list, mySrd).getId().toUnqualifiedVersionless();
final ExplanationOfBenefit explanationOfBenefit = new ExplanationOfBenefit();
explanationOfBenefit.setId(EOB_ID);
explanationOfBenefit.setPatient(new Reference(patientId.getValue()));
explanationOfBenefit.setInsurer(new Reference(orgId.getValue()));
explanationOfBenefit.setProvider(new Reference(orgId.getValue()));
explanationOfBenefit.addCareTeam().setProvider(new Reference(practitionerId.getValue()));
explanationOfBenefit.addInsurance().setCoverage(new Reference(coverageId.getValue()));
myExplanationOfBenefitDao.update(explanationOfBenefit, mySrd).getId().toUnqualifiedVersionless();
}
@ParameterizedTest
@ValueSource(strings = {
"ExplanationOfBenefit?coverage.payor.name="+ORG_NAME,
})
void chainSimple(String theQueryString) {
runAndAssert(theQueryString);
}
@ParameterizedTest
@ValueSource(strings = {
"Practitioner?_has:ExplanationOfBenefit:care-team:coverage.payor="+ORG_ID, // This is the first half
})
void hasThenChainSimple(String theQueryString) {
runAndAssert(theQueryString);
}
@ParameterizedTest
@ValueSource(strings = {
"ExplanationOfBenefit?coverage.payor:Organization._has:List:item:_id="+LIST_ID
})
void chainThenHasSimple(String theQueryString) {
runAndAssert(theQueryString);
}
@ParameterizedTest
@ValueSource(strings = {
"Coverage?payor._has:List:item:_id="+LIST_ID, // dot _has
"Coverage?payor.name="+ORG_NAME,
"Coverage?payor="+ORG_ID,
"ExplanationOfBenefit?coverage="+COVERAGE_ID,
"ExplanationOfBenefit?coverage.payor.name="+ORG_NAME,
"ExplanationOfBenefit?coverage.payor="+ORG_ID,
"ExplanationOfBenefit?coverage.payor._has:List:item:_id="+LIST_ID,
"ExplanationOfBenefit?coverage.payor:Organization._has:List:item:_id="+LIST_ID,
"Organization?_has:List:item:_id="+LIST_ID, // This the second half of the buggy query
})
void complexQueryFromList(String theQueryString) {
runAndAssert(theQueryString);
}
@ParameterizedTest
@ValueSource(strings = {
"Organization?_has:Coverage:payor:_has:ExplanationOfBenefit:coverage:_id="+EOB_ID, // THIS WORKS!!!!!!!
"Practitioner?_has:ExplanationOfBenefit:care-team:coverage.payor="+ORG_ID, // this works
// "Practitioner?_has:ExplanationOfBenefit:care-team:coverage.payor.name="+ORG_NAME, // this does not work
"Practitioner?_has:ExplanationOfBenefit:care-team:_id="+EOB_ID,
"Practitioner?_has:ExplanationOfBenefit:care-team:coverage="+COVERAGE_ID,
"Practitioner?_has:ExplanationOfBenefit:care-team:coverage.payor="+ORG_ID, // This is the first half
// "Practitioner?_has:ExplanationOfBenefit:care-team:coverage.payor._has:List:item:_id="+LIST_ID, // this doesn't work ... reomoves Organzation
})
void complexQueryFromPractitioner(String theQueryString) {
runAndAssert(theQueryString);
}
@ParameterizedTest
@ValueSource(strings = {
"Practitioner?_has:ExplanationOfBenefit:care-team:coverage.payor._has:List:item:_id="+LIST_ID,
"Practitioner?_has:ExplanationOfBenefit:care-team:coverage.payor:Organization._has:List:item:_id="+LIST_ID // same thing
})
void hasThenChainThenHas(String theQueryString) {
runAndAssert(theQueryString);
}
@Test
void searchWithSearchParameterHasThenChainThenChain() {
final SearchParameterMap searchParameterMap = new SearchParameterMap();
final HasParam hasParam = new HasParam("ExplanationOfBenefit", "care-team", "coverage.payor:Organization._has:List:item:_id", LIST_ID);
searchParameterMap.add("_has", hasParam);
final IBundleProvider search = myPractitionerDao.search(searchParameterMap, mySrd);
assertFalse(search.isEmpty());
}
@Test
void searchWithSearchParameterFirstHalf() {
final SearchParameterMap searchParameterMap = new SearchParameterMap();
// "Practitioner?_has:ExplanationOfBenefit:care-team:coverage.payor:Organization="+ORG_ID // This the first half of the buggy query
final HasParam hasParam = new HasParam("ExplanationOfBenefit", "care-team", "coverage.payor", ORG_ID);
searchParameterMap.add("_has", hasParam);
final IBundleProvider search = myPractitionerDao.search(searchParameterMap, mySrd);
assertFalse(search.isEmpty());
}
@Test
void searchWithSearchParameterSecondHalf() {
final SearchParameterMap searchParameterMap = new SearchParameterMap();
// "Organization?_has:List:item:_id="+LIST_ID, // This the second half of the buggy query
final HasParam hasParam = new HasParam("List", "item", "_id", LIST_ID);
searchParameterMap.add("_has", hasParam);
final IBundleProvider search = myOrganizationDao.search(searchParameterMap, mySrd);
assertFalse(search.isEmpty());
}
}
@Nested
class PractitionerEobCoveragePractitionerGroupYesCustomSearchParam {
private static final String PAT_ID = "pat1";
private static final String ORG_ID = "org1";
private static final String ORG_NAME = "myOrg";
private static final String PRACTITIONER_ID = "pra1";
private static final String COVERAGE_ID = "cov1";
private static final String GROUP_ID = "grp1";
private static final String EOB_ID = "eob1";
@BeforeEach
void beforeEach() {
myStorageSettings.setMarkResourcesForReindexingUponSearchParameterChange(false);
myStorageSettings.setIndexOnContainedResources(false);
// This is not exactly lik the production scenario but create SearchParameter first to create the RES_LINK
// and avoid a call to reindex
final SearchParameter searchParameterGroupValueReference = new SearchParameter();
searchParameterGroupValueReference.setId("group-value-reference");
searchParameterGroupValueReference.setName("group-value-reference");
searchParameterGroupValueReference.addBase("Group");
searchParameterGroupValueReference.setStatus(Enumerations.PublicationStatus.ACTIVE);
searchParameterGroupValueReference.setCode("value-reference");
searchParameterGroupValueReference.setType(Enumerations.SearchParamType.REFERENCE);
searchParameterGroupValueReference.setExpression("Group.characteristic.value.as(Reference)");
searchParameterGroupValueReference.addTarget("Organization");
searchParameterGroupValueReference.setXpathUsage(SearchParameter.XPathUsageType.NORMAL);
mySearchParameterDao.update(searchParameterGroupValueReference, mySrd);
final Patient patient = new Patient();
patient.setId(PAT_ID);
final IIdType patientId = myPatientDao.update(patient, mySrd).getId().toUnqualifiedVersionless();
final Organization organization = new Organization();
organization.setId(ORG_ID);
organization.setName(ORG_NAME);
final IIdType orgId = myOrganizationDao.update(organization, mySrd).getId().toUnqualifiedVersionless();
final Practitioner practitioner = new Practitioner();
practitioner.setId(PRACTITIONER_ID);
final IIdType practitionerId = myPractitionerDao.update(practitioner, mySrd).getId().toUnqualifiedVersionless();
final Coverage coverage = new Coverage();
coverage.setId(COVERAGE_ID);
coverage.addPayor().setReference(orgId.getValue());
final IIdType coverageId = myCoverageDao.update(coverage, mySrd).getId().toUnqualifiedVersionless();
final Group group = new Group();
group.setId(GROUP_ID);
group.addCharacteristic().getValueReference().setReference(orgId.getValue());
myGroupDao.update(group, mySrd);
final ExplanationOfBenefit explanationOfBenefit = new ExplanationOfBenefit();
explanationOfBenefit.setId(EOB_ID);
explanationOfBenefit.setPatient(new Reference(patientId.getValue()));
explanationOfBenefit.setInsurer(new Reference(orgId.getValue()));
explanationOfBenefit.setProvider(new Reference(orgId.getValue()));
explanationOfBenefit.addCareTeam().setProvider(new Reference(practitionerId.getValue()));
explanationOfBenefit.addInsurance().setCoverage(new Reference(coverageId.getValue()));
myExplanationOfBenefitDao.update(explanationOfBenefit, mySrd).getId().toUnqualifiedVersionless();
}
@ParameterizedTest
@ValueSource(strings = {
"Coverage?payor.name="+ORG_NAME,
"Coverage?payor="+ORG_ID,
"ExplanationOfBenefit?coverage.payor.name="+ORG_NAME,
"ExplanationOfBenefit?coverage.payor="+ORG_ID,
"ExplanationOfBenefit?care-team="+PRACTITIONER_ID,
"ExplanationOfBenefit?coverage="+COVERAGE_ID,
"ExplanationOfBenefit?provider="+ORG_ID,
})
void complexQueryFromGroup(String theQueryString) {
runAndAssert(theQueryString);
}
@ParameterizedTest
@ValueSource(strings = {
"Group?value-reference="+ORG_ID,
"Organization?_has:Group:value-reference:_id="+GROUP_ID, // This the second half of the buggy query
})
void useCustomSearchParam(String theQueryString) {
runAndAssert(theQueryString);
}
@ParameterizedTest
@ValueSource(strings = {
"Practitioner?_has:ExplanationOfBenefit:care-team:coverage.payor:Organization._has:Group:value-reference:_id="+GROUP_ID,
})
void hasThenChainThenHas(String theQueryString) {
runAndAssert(theQueryString);
}
@ParameterizedTest
@ValueSource(strings = {
"Practitioner?_has:ExplanationOfBenefit:care-team:_id="+EOB_ID,
"Practitioner?_has:ExplanationOfBenefit:care-team:coverage="+COVERAGE_ID,
"Practitioner?_has:ExplanationOfBenefit:care-team:coverage.payor="+ORG_ID,
"Practitioner?_has:ExplanationOfBenefit:care-team:coverage.payor:Organization="+ORG_ID, // This the first half of the buggy query
// "Practitioner?_has:ExplanationOfBenefit:care-team:coverage.payor._has:Group:value-reference:_id="+GROUP_ID, // this doesn't work
// "Practitioner?_has:ExplanationOfBenefit:care-team:coverage.payor:Organization.name="+ORG_NAME // This doesn't work
})
void complexQueryFromPractitioner(String theQueryString) {
runAndAssert(theQueryString);
}
}
private void runAndAssert(String theQueryString) {
ourLog.info("queryString:\n{}", theQueryString);
final Bundle outcome = myClient.search()
.byUrl(theQueryString)
.returnBundle(Bundle.class)
.execute();
assertFalse(outcome.getEntry().isEmpty());
ourLog.info("result:\n{}", theQueryString);
}
}