Skip to content

Commit

Permalink
fixing some failing tests in dao/impl
Browse files Browse the repository at this point in the history
  • Loading branch information
@mherman22
mherman22 committed Dec 20, 2023
1 parent 06850a9 commit 3160a80
Show file tree
Hide file tree
Showing 10 changed files with 188 additions and 167 deletions.
24 changes: 8 additions & 16 deletions api/src/main/java/org/openmrs/module/fhir2/api/dao/impl/BaseDao.java
View file
Original file line number Diff line number Diff line change
Expand Up @@ -1041,23 +1041,19 @@ protected <T> Predicate generateSystemQuery(OpenmrsFhirCriteriaContext<T> criter

protected <T> Predicate generateActiveOrderQuery(OpenmrsFhirCriteriaContext<T> criteriaContext, String path,
Date onDate) {
if (StringUtils.isNotBlank(path)) {
path = path + ".";
}

// ACTIVE = date activated null or less than or equal to current datetime, date stopped null or in the future, auto expire date null or in the future
return criteriaContext.getCriteriaBuilder().and(
criteriaContext.getCriteriaBuilder().or(
criteriaContext.getCriteriaBuilder().isNull(criteriaContext.getRoot().get(path + "dateActivated")),
criteriaContext.getCriteriaBuilder().lessThan(criteriaContext.getRoot().get(path + "dateActivated"),
criteriaContext.getCriteriaBuilder().isNull(criteriaContext.getRoot().join(path).get("dateActivated")),
criteriaContext.getCriteriaBuilder().lessThan(criteriaContext.getRoot().join(path).get("dateActivated"),
onDate)),
criteriaContext.getCriteriaBuilder().or(
criteriaContext.getCriteriaBuilder().isNull(criteriaContext.getRoot().get(path + "dateStopped")),
criteriaContext.getCriteriaBuilder().greaterThan(criteriaContext.getRoot().get(path + "dateStopped"),
criteriaContext.getCriteriaBuilder().isNull(criteriaContext.getRoot().join(path).get("dateStopped")),
criteriaContext.getCriteriaBuilder().greaterThan(criteriaContext.getRoot().join(path).get("dateStopped"),
onDate)),
criteriaContext.getCriteriaBuilder().or(
criteriaContext.getCriteriaBuilder().isNull(criteriaContext.getRoot().get(path + "autoExpireDate")),
criteriaContext.getCriteriaBuilder().greaterThan(criteriaContext.getRoot().get(path + "autoExpireDate"),
criteriaContext.getCriteriaBuilder().isNull(criteriaContext.getRoot().join(path).get("autoExpireDate")),
criteriaContext.getCriteriaBuilder().greaterThan(criteriaContext.getRoot().join(path).get("autoExpireDate"),
onDate)));
}

Expand All @@ -1078,15 +1074,11 @@ protected <T> Predicate generateNotCancelledOrderQuery(OpenmrsFhirCriteriaContex
}

protected <T> Predicate generateNotCancelledOrderQuery(OpenmrsFhirCriteriaContext<T> criteriaContext, String path) {
if (StringUtils.isNotBlank(path)) {
path = path + ".";
}

Date now = new Date();

return criteriaContext.getCriteriaBuilder().or(
criteriaContext.getCriteriaBuilder().isNull(criteriaContext.getRoot().get(path + "dateStopped")),
criteriaContext.getCriteriaBuilder().greaterThan(criteriaContext.getRoot().get(path + "dateStopped"), now));
criteriaContext.getCriteriaBuilder().isNull(criteriaContext.getRoot().join(path).get("dateStopped")),
criteriaContext.getCriteriaBuilder().greaterThan(criteriaContext.getRoot().join(path).get("dateStopped"), now));
}

protected TokenOrListParam convertStringStatusToBoolean(TokenOrListParam statusParam) {
Expand Down
20 changes: 10 additions & 10 deletions api/src/main/java/org/openmrs/module/fhir2/api/dao/impl/BaseEncounterDao.java
View file
Original file line number Diff line number Diff line change
Expand Up @@ -11,6 +11,7 @@

import static org.openmrs.module.fhir2.FhirConstants.ENCOUNTER_TYPE_REFERENCE_SEARCH_HANDLER;

import javax.persistence.criteria.Join;
import javax.persistence.criteria.JoinType;
import javax.persistence.criteria.Predicate;

Expand Down Expand Up @@ -111,14 +112,13 @@ protected void handleHasAndListParam(OpenmrsFhirCriteriaContext<T> criteriaConte
criteriaContext.addJoin("en.orders", "orders");
}
}
Join<DrugOrder,Order> join = criteriaContext.getRoot().join("orders");
// Constrain only on non-voided Drug Orders
criteriaContext.addPredicate(criteriaContext.getCriteriaBuilder()
.equal(criteriaContext.getRoot().get("orders.class"), DrugOrder.class));
// TODO Do these criteria still work?
criteriaContext.addPredicate(criteriaContext.getCriteriaBuilder()
.equal(criteriaContext.getRoot().get("orders.voided"), false));
.equal(join.get("voided"), false));
criteriaContext.addPredicate(criteriaContext.getCriteriaBuilder()
.notEqual(criteriaContext.getRoot().get("orders.action"), Order.Action.DISCONTINUE));
.notEqual(join.get("action"), Order.Action.DISCONTINUE));

String paramName = hasParam.getParameterName();
String paramValue = hasParam.getParameterValue();
Expand Down Expand Up @@ -146,7 +146,7 @@ protected void handleHasAndListParam(OpenmrsFhirCriteriaContext<T> criteriaConte
}
if (MedicationRequest.MedicationRequestStatus.COMPLETED.toString()
.equalsIgnoreCase(paramValue)) {
Predicate notCompletedCriterion = generateNotCompletedOrderQuery("orders");
Predicate notCompletedCriterion = generateNotCompletedOrderQuery(criteriaContext,"orders");
if (notCompletedCriterion != null) {
criteriaContext.getCriteriaBuilder().and(notCompletedCriterion);
}
Expand All @@ -156,12 +156,12 @@ protected void handleHasAndListParam(OpenmrsFhirCriteriaContext<T> criteriaConte
} else if ((FhirConstants.SP_FULFILLER_STATUS).equalsIgnoreCase(paramName)) {
if (paramValue != null) {
criteriaContext.getCriteriaBuilder()
.and(generateFulfillerStatusRestriction("orders", paramValue));
.and(generateFulfillerStatusRestriction(criteriaContext,"orders", paramValue));
}
} else if ((FhirConstants.SP_FULFILLER_STATUS + ":not").equalsIgnoreCase(paramName)) {
if (paramValue != null) {
criteriaContext.getCriteriaBuilder()
.and(generateNotFulfillerStatusRestriction("orders", paramValue));
.and(generateNotFulfillerStatusRestriction(criteriaContext,"orders", paramValue));
}
}
criteriaContext.finalizeQuery();
Expand All @@ -184,17 +184,17 @@ protected abstract void handleEncounterType(OpenmrsFhirCriteriaContext<T> criter
protected abstract void handleParticipant(OpenmrsFhirCriteriaContext<T> criteriaContext,
ReferenceAndListParam referenceAndListParam);

protected Predicate generateNotCompletedOrderQuery(String path) {
protected <T> Predicate generateNotCompletedOrderQuery(OpenmrsFhirCriteriaContext<T> criteriaContext, String path) {
// not implemented in Core until 2.2; see override in FhirEncounterDaoImpl_2_2
return null;
}

protected Predicate generateFulfillerStatusRestriction(String path, String fulfillerStatus) {
protected <T> Predicate generateFulfillerStatusRestriction(OpenmrsFhirCriteriaContext<T> criteriaContext, String path, String fulfillerStatus) {
// not implemented in Core until 2.2; see override in FhirEncounterDaoImpl_2_2
return null;
}

protected Predicate generateNotFulfillerStatusRestriction(String path, String fulfillerStatus) {
protected <V> Predicate generateNotFulfillerStatusRestriction(OpenmrsFhirCriteriaContext<V> criteriaContext, String path, String fulfillerStatus) {
// not implemented in Core until 2.2; see override in FhirEncounterDaoImpl_2_2
return null;
}
Expand Down
45 changes: 23 additions & 22 deletions api/src/main/java/org/openmrs/module/fhir2/api/dao/impl/BaseFhirDao.java
View file
Original file line number Diff line number Diff line change
Expand Up @@ -32,6 +32,7 @@
import org.hibernate.proxy.HibernateProxy;
import org.hl7.fhir.r4.model.DomainResource;
import org.openmrs.Auditable;
import org.openmrs.Encounter;
import org.openmrs.Obs;
import org.openmrs.OpenmrsObject;
import org.openmrs.Order;
Expand Down Expand Up @@ -157,30 +158,30 @@ protected OpenmrsFhirCriteriaContext<T> getSearchResultCriteria(SearchParameterM
@Override
public List<T> getSearchResults(@Nonnull SearchParameterMap theParams) {
OpenmrsFhirCriteriaContext<T> criteriaContext = getSearchResultCriteria(theParams);

handleSort(criteriaContext, theParams.getSortSpec());
criteriaContext.addOrder(criteriaContext.getCriteriaBuilder().asc(criteriaContext.getRoot().get("id")));

criteriaContext.getEntityManager().createQuery(criteriaContext.getCriteriaQuery())
.setFirstResult(theParams.getFromIndex());
if (theParams.getToIndex() != Integer.MAX_VALUE) {
int maxResults = theParams.getToIndex() - theParams.getFromIndex();
criteriaContext.getEntityManager().createQuery(criteriaContext.getCriteriaQuery()).setMaxResults(maxResults);
}

List<T> results;
if (hasDistinctResults()) {
results = criteriaContext.getEntityManager().createQuery(criteriaContext.getCriteriaQuery()).getResultList();
} else {

OpenmrsFhirCriteriaContext<Long> longOpenmrsFhirCriteriaContext = createCriteriaContext(Long.class);
longOpenmrsFhirCriteriaContext.getCriteriaQuery().subquery(Long.class).select(longOpenmrsFhirCriteriaContext
.getCriteriaBuilder().countDistinct(longOpenmrsFhirCriteriaContext.getRoot().get("id")));
handleSort(criteriaContext, theParams.getSortSpec());
criteriaContext.addOrder(criteriaContext.getCriteriaBuilder().asc(criteriaContext.getRoot().get("id")));

criteriaContext.getEntityManager().createQuery(criteriaContext.getCriteriaQuery())
.setFirstResult(theParams.getFromIndex());
if (theParams.getToIndex() != Integer.MAX_VALUE) {
int maxResults = theParams.getToIndex() - theParams.getFromIndex();
criteriaContext.getEntityManager().createQuery(criteriaContext.getCriteriaQuery()).setMaxResults(maxResults);
}

longOpenmrsFhirCriteriaContext.getCriteriaQuery().select(longOpenmrsFhirCriteriaContext.getRoot())
.where(longOpenmrsFhirCriteriaContext.getCriteriaBuilder()
.in(longOpenmrsFhirCriteriaContext.getRoot().get("id"))
.value(longOpenmrsFhirCriteriaContext.getCriteriaQuery().subquery(Long.class)));
List<T> results;
if (hasDistinctResults()) {
results = criteriaContext.getEntityManager().createQuery(criteriaContext.getCriteriaQuery()).getResultList();
} else {

OpenmrsFhirCriteriaContext<Long> longOpenmrsFhirCriteriaContext = createCriteriaContext(Long.class);
longOpenmrsFhirCriteriaContext.getCriteriaQuery().subquery(Long.class).select(longOpenmrsFhirCriteriaContext
.getCriteriaBuilder().countDistinct(longOpenmrsFhirCriteriaContext.getRoot().get("id")));

longOpenmrsFhirCriteriaContext.getCriteriaQuery().select(longOpenmrsFhirCriteriaContext.getRoot())
.where(longOpenmrsFhirCriteriaContext.getCriteriaBuilder()
.in(longOpenmrsFhirCriteriaContext.getRoot().get("id"))
.value(longOpenmrsFhirCriteriaContext.getCriteriaQuery().subquery(Long.class)));

//TODO: gonna come back to it later
// handleSort(projectionCriteriaBuilder, theParams.getSortSpec(), this::paramToProps).ifPresent(
Expand Down
77 changes: 21 additions & 56 deletions api/src/main/java/org/openmrs/module/fhir2/api/dao/impl/FhirConceptDaoImpl.java
View file
Original file line number Diff line number Diff line change
Expand Up @@ -50,30 +50,14 @@ public Optional<Concept> getConceptWithSameAsMappingInSource(@Nonnull ConceptSou
@Nonnull String mappingCode) {
OpenmrsFhirCriteriaContext<Concept> criteriaContext = createCriteriaContext(Concept.class);

//TODO: Change back to method
OpenmrsFhirCriteriaContext<ConceptMap> xontext = createCriteriaContext(ConceptMap.class);
xontext.getCriteriaQuery().select(xontext.getRoot().get("concept"));
Join<ConceptReferenceTerm, ConceptMap> termJoin = xontext.getRoot().join("conceptReferenceTerm");
Join<ConceptMap, ConceptMapType> mapTypeJoin = xontext.getRoot().join("conceptMapType");
Join<ConceptMap, Concept> conceptJoin = xontext.getRoot().join("concept");

if (Context.getAdministrationService().isDatabaseStringComparisonCaseSensitive()) {
xontext.addPredicate(xontext.getCriteriaBuilder()
.equal(xontext.getCriteriaBuilder().lower(termJoin.get("code")), mappingCode.toLowerCase()));
} else {
xontext.addPredicate(xontext.getCriteriaBuilder().equal(termJoin.get("code"), mappingCode));
}

xontext.addPredicate(xontext.getCriteriaBuilder().equal(termJoin.get("conceptSource"), conceptSource));
xontext.finalizeQuery();
//TODO: method stops here
createConceptMapCriteriaBuilder(conceptSource,mappingCode);

criteriaContext.addPredicate(criteriaContext.getCriteriaBuilder()
.or(criteriaContext.getCriteriaBuilder().equal(mapTypeJoin.get("uuid"),
.or(criteriaContext.getCriteriaBuilder().equal(criteriaContext.getRoot().join("conceptMapType").get("mapType.uuid"),
ConceptMapType.SAME_AS_MAP_TYPE_UUID),
criteriaContext.getCriteriaBuilder().equal(mapTypeJoin.get("name"), "SAME-AS")));
criteriaContext.getCriteriaBuilder().equal(criteriaContext.getRoot().join("conceptMapType").get("mapType.name"), "SAME-AS")));

criteriaContext.addOrder(criteriaContext.getCriteriaBuilder().asc(conceptJoin.get("retired")));
criteriaContext.addOrder(criteriaContext.getCriteriaBuilder().asc(criteriaContext.getRoot().join("concept").get("retired")));
criteriaContext.finalizeQuery();

return Optional.ofNullable(
Expand All @@ -88,26 +72,9 @@ public List<Concept> getConceptsWithAnyMappingInSource(@Nonnull ConceptSource co
}

OpenmrsFhirCriteriaContext<Concept> criteriaContext = createCriteriaContext(Concept.class);

//TODO: Change back to method
OpenmrsFhirCriteriaContext<ConceptMap> xontext = createCriteriaContext(ConceptMap.class);
xontext.getCriteriaQuery().select(xontext.getRoot().get("concept"));
Join<ConceptMap, ConceptReferenceTerm> termJoin = xontext.getRoot().join("conceptReferenceTerm");
Join<ConceptMap, ConceptMapType> mapTypeJoin = xontext.getRoot().join("conceptMapType");
Join<ConceptMap, Concept> conceptJoin = xontext.getRoot().join("concept");

if (Context.getAdministrationService().isDatabaseStringComparisonCaseSensitive()) {
xontext.addPredicate(xontext.getCriteriaBuilder()
.equal(xontext.getCriteriaBuilder().lower(termJoin.get("code")), mappingCode.toLowerCase()));
} else {
xontext.addPredicate(xontext.getCriteriaBuilder().equal(termJoin.get("code"), mappingCode));
}

xontext.addPredicate(xontext.getCriteriaBuilder().equal(termJoin.get("conceptSource"), conceptSource));
xontext.finalizeQuery();
//TODO: method stops here
createConceptMapCriteriaBuilder(conceptSource,mappingCode);

criteriaContext.addOrder(criteriaContext.getCriteriaBuilder().asc(conceptJoin.get("retired")));
criteriaContext.addOrder(criteriaContext.getCriteriaBuilder().asc(criteriaContext.getRoot().join("concept").get("retired")));

return criteriaContext.getEntityManager().createQuery(criteriaContext.getCriteriaQuery()).getResultList();
}
Expand All @@ -132,21 +99,19 @@ protected void handleTitle(OpenmrsFhirCriteriaContext<Concept> criteriaContext,
criteriaContext.finalizeQuery();
}

// protected void createConceptMapCriteriaBuilder(@Nonnull ConceptSource conceptSource, String mappingCode) {
// OpenmrsFhirCriteriaContext<ConceptMap> criteriaContext = createCriteriaContext(ConceptMap.class);
// criteriaContext.getCriteriaQuery().select(criteriaContext.getRoot().get("concept"));
// Join<ConceptMap, ConceptReferenceTerm> termJoin = criteriaContext.getRoot().join("conceptReferenceTerm");
// Join<ConceptMap, ConceptMapType> mapTypeJoin = criteriaContext.getRoot().join("conceptMapType");
// Join<ConceptMap, Concept> conceptJoin = criteriaContext.getRoot().join("concept");
//
// if (Context.getAdministrationService().isDatabaseStringComparisonCaseSensitive()) {
// criteriaContext.addPredicate(criteriaContext.getCriteriaBuilder()
// .equal(criteriaContext.getCriteriaBuilder().lower(termJoin.get("code")), mappingCode.toLowerCase()));
// } else {
// criteriaContext.addPredicate(criteriaContext.getCriteriaBuilder().equal(termJoin.get("code"), mappingCode));
// }
//
// criteriaContext.addPredicate(criteriaContext.getCriteriaBuilder().equal(termJoin.get("conceptSource"), conceptSource));
// criteriaContext.finalizeQuery();
// }
protected void createConceptMapCriteriaBuilder(@Nonnull ConceptSource conceptSource, String mappingCode) {
OpenmrsFhirCriteriaContext<ConceptMap> criteriaContext = createCriteriaContext(ConceptMap.class);
criteriaContext.getCriteriaQuery().select(criteriaContext.getRoot().get("concept"));
Join<ConceptMap, ConceptReferenceTerm> termJoin = criteriaContext.getRoot().join("conceptReferenceTerm");

if (Context.getAdministrationService().isDatabaseStringComparisonCaseSensitive()) {
criteriaContext.addPredicate(criteriaContext.getCriteriaBuilder()
.equal(criteriaContext.getCriteriaBuilder().lower(termJoin.get("code")), mappingCode.toLowerCase()));
} else {
criteriaContext.addPredicate(criteriaContext.getCriteriaBuilder().equal(termJoin.get("code"), mappingCode));
}

criteriaContext.addPredicate(criteriaContext.getCriteriaBuilder().equal(termJoin.get("conceptSource"), conceptSource));
criteriaContext.finalizeQuery();
}
}
32 changes: 22 additions & 10 deletions api/src/main/java/org/openmrs/module/fhir2/api/dao/impl/FhirConceptSourceDaoImpl.java
View file
Original file line number Diff line number Diff line change
Expand Up @@ -11,6 +11,7 @@

import javax.annotation.Nonnull;
import javax.persistence.EntityManager;
import javax.persistence.NoResultException;
import javax.persistence.TypedQuery;
import javax.persistence.criteria.CriteriaBuilder;
import javax.persistence.criteria.CriteriaQuery;
Expand Down Expand Up @@ -56,11 +57,17 @@ public Collection<FhirConceptSource> getFhirConceptSources() {
public Optional<FhirConceptSource> getFhirConceptSourceByUrl(@Nonnull String url) {
OpenmrsFhirCriteriaContext<FhirConceptSource> criteriaContext = openmrsFhirCriteriaContext();
criteriaContext.getCriteriaQuery().select(criteriaContext.getRoot());

criteriaContext.addPredicate(criteriaContext.getCriteriaBuilder().and(criteriaContext.getCriteriaBuilder()
.equal(criteriaContext.getRoot().get("url"), url),criteriaContext.getCriteriaBuilder()
.equal(criteriaContext.getRoot().get("retired"), false)));

criteriaContext.addPredicate(criteriaContext.getCriteriaBuilder().equal(criteriaContext.getRoot().get("url"), url));
criteriaContext.addPredicate(criteriaContext.getCriteriaBuilder().equal(criteriaContext.getRoot().get("retired"), false));

return Optional.ofNullable(criteriaContext.getEntityManager().createQuery(criteriaContext.finalizeQuery()).getSingleResult());
try {
return Optional.ofNullable(criteriaContext.getEntityManager().createQuery(criteriaContext.finalizeQuery()).getSingleResult());
}
catch (NoResultException e) {
return Optional.empty();
}
}

@Override
Expand All @@ -70,13 +77,18 @@ public Optional<FhirConceptSource> getFhirConceptSourceByConceptSourceName(@Nonn
criteriaContext.getCriteriaQuery().select(criteriaContext.getRoot());

Join<FhirConceptSource, ConceptSource> conceptSourceJoin = criteriaContext.getRoot().join("conceptSource");

criteriaContext.addPredicate(criteriaContext.getCriteriaBuilder().and(criteriaContext.getCriteriaBuilder()
.equal(conceptSourceJoin.get("name"), sourceName),criteriaContext.getCriteriaBuilder()
.equal(conceptSourceJoin.get("retired"), false),criteriaContext.getCriteriaBuilder()
.equal(criteriaContext.getRoot().get("retired"), false)));

criteriaContext.addPredicate(criteriaContext.getCriteriaBuilder().equal(conceptSourceJoin.get("name"), sourceName));
criteriaContext.addPredicate(criteriaContext.getCriteriaBuilder().equal(conceptSourceJoin.get("voided"), false));

criteriaContext.addPredicate(criteriaContext.getCriteriaBuilder().equal(criteriaContext.getRoot().get("voided"), false));

return Optional.ofNullable(criteriaContext.getEntityManager().createQuery(criteriaContext.finalizeQuery()).getSingleResult());
try {
return Optional.ofNullable(criteriaContext.getEntityManager().createQuery(criteriaContext.finalizeQuery()).getSingleResult());
}
catch (NoResultException e) {
return Optional.empty();
}
}

@Override
Expand Down

0 comments on commit 3160a80

Please sign in to comment.