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FM2-347:Add support for _has and _has:...:not for ServiceRequest and …
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…Observation
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@gitcliff
gitcliff committed Mar 29, 2021
1 parent 976880c commit 453e3cd
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Showing 25 changed files with 475 additions and 243 deletions.
4 changes: 3 additions & 1 deletion api/src/main/java/org/openmrs/module/fhir2/FhirConstants.java
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Expand Up @@ -50,7 +50,7 @@ public class FhirConstants {
+ "/condition-ver-status";

public static final String CLINICAL_FINDINGS_SYSTEM_URI = HL7_FHIR_CODE_SYSTEM_PREFIX + "/clinical-findings";

public static final String TASK_STATUS_VALUE_SET_URI = "http://hl7.org/fhir/task-status";

public static final String OBSERVATION_REFERENCE_RANGE_SYSTEM_URI = HL7_FHIR_CODE_SYSTEM_PREFIX
Expand Down Expand Up @@ -255,6 +255,8 @@ public class FhirConstants {

public static final String COMMON_SEARCH_HANDLER = "common.search.handler";

public static final String HAS_PROPERTY = "_has";

public static final String ID_PROPERTY = "_id.property";

public static final String LAST_UPDATED_PROPERTY = "_lastUpdated.property";
Expand Down
8 changes: 4 additions & 4 deletions api/src/main/java/org/openmrs/module/fhir2/api/FhirObservationService.java
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Expand Up @@ -29,8 +29,8 @@ public interface FhirObservationService extends FhirService<Observation> {
Observation get(@Nonnull String uuid);

IBundleProvider searchForObservations(ReferenceAndListParam encounterReference, ReferenceAndListParam patientReference,
ReferenceAndListParam hasMemberReference, TokenAndListParam valueConcept, DateRangeParam valueDateParam,
QuantityAndListParam valueQuantityParam, StringAndListParam valueStringParam, DateRangeParam date,
TokenAndListParam code, TokenAndListParam category, TokenAndListParam id, DateRangeParam lastUpdated,
SortSpec sort, HashSet<Include> includes, HashSet<Include> revIncludes);
ReferenceAndListParam hasMemberReference, ReferenceAndListParam basedOnReference, TokenAndListParam valueConcept,
DateRangeParam valueDateParam, QuantityAndListParam valueQuantityParam, StringAndListParam valueStringParam,
DateRangeParam date, TokenAndListParam code, TokenAndListParam category, TokenAndListParam id,
DateRangeParam lastUpdated, SortSpec sort, HashSet<Include> includes, HashSet<Include> revIncludes);
}
3 changes: 2 additions & 1 deletion api/src/main/java/org/openmrs/module/fhir2/api/FhirServiceRequestService.java
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Expand Up @@ -14,6 +14,7 @@
import ca.uhn.fhir.model.api.Include;
import ca.uhn.fhir.rest.api.server.IBundleProvider;
import ca.uhn.fhir.rest.param.DateRangeParam;
import ca.uhn.fhir.rest.param.HasAndListParam;
import ca.uhn.fhir.rest.param.ReferenceAndListParam;
import ca.uhn.fhir.rest.param.TokenAndListParam;
import org.hl7.fhir.r4.model.ServiceRequest;
Expand All @@ -22,5 +23,5 @@ public interface FhirServiceRequestService extends FhirService<ServiceRequest> {

IBundleProvider searchForServiceRequests(ReferenceAndListParam patientReference, TokenAndListParam code,
ReferenceAndListParam encounterReference, ReferenceAndListParam participantReference, DateRangeParam occurrence,
TokenAndListParam uuid, DateRangeParam lastUpdated, HashSet<Include> includes);
TokenAndListParam uuid, DateRangeParam lastUpdated, HasAndListParam has, HashSet<Include> includes);
}
53 changes: 53 additions & 0 deletions api/src/main/java/org/openmrs/module/fhir2/api/dao/impl/BaseDao.java
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Expand Up @@ -52,13 +52,17 @@
import java.util.stream.Stream;
import java.util.stream.StreamSupport;

import ca.uhn.fhir.context.FhirContext;
import ca.uhn.fhir.model.api.IQueryParameterAnd;
import ca.uhn.fhir.model.api.IQueryParameterOr;
import ca.uhn.fhir.model.api.IQueryParameterType;
import ca.uhn.fhir.rest.api.QualifiedParamList;
import ca.uhn.fhir.rest.api.SortOrderEnum;
import ca.uhn.fhir.rest.api.SortSpec;
import ca.uhn.fhir.rest.param.DateParam;
import ca.uhn.fhir.rest.param.DateRangeParam;
import ca.uhn.fhir.rest.param.HasAndListParam;
import ca.uhn.fhir.rest.param.HasParam;
import ca.uhn.fhir.rest.param.ParamPrefixEnum;
import ca.uhn.fhir.rest.param.QuantityAndListParam;
import ca.uhn.fhir.rest.param.QuantityParam;
Expand All @@ -82,6 +86,7 @@
import org.hibernate.internal.CriteriaImpl;
import org.hl7.fhir.exceptions.FHIRException;
import org.hl7.fhir.r4.model.Location;
import org.hl7.fhir.r4.model.Observation;
import org.hl7.fhir.r4.model.Patient;
import org.hl7.fhir.r4.model.Practitioner;
import org.hl7.fhir.r4.model.codesystems.AdministrativeGender;
Expand All @@ -90,6 +95,7 @@
import org.openmrs.module.fhir2.api.util.LocalDateTimeFactory;
import org.openmrs.module.fhir2.model.FhirConceptSource;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.beans.factory.annotation.Qualifier;

/**
* <p>
Expand Down Expand Up @@ -171,6 +177,10 @@ public abstract class BaseDao {
@Autowired
private LocalDateTimeFactory localDateTimeFactory;

@Autowired
@Qualifier("fhirR4")
private FhirContext fhirContext;

/**
* Converts an {@link Iterable} to a {@link Stream}
*
Expand Down Expand Up @@ -443,6 +453,49 @@ protected Optional<Criterion> handleDate(String propertyName, DateParam datePara
return Optional.empty();
}

/**
* A handler for a {@link HasParam}
*
* @param propertyName the name of the property in the query to use
* @param hasParam the {@link HasParam} to handle
* @return a {@link Criterion} to be added to the query for the indicate has param
*/
protected Optional<Criterion> handleHas(String propertyName, HasParam hasParam) {
if (hasParam == null) {
return Optional.empty();
}
ArrayList<IQueryParameterType> orValues = new ArrayList<>();
String targetResourceType = null;
String paramReference = null;
String parameterName = null;

String paramName = null;
targetResourceType = hasParam.getTargetResourceType();

if (targetResourceType.getClass().equals(Observation.class)) {
paramReference = hasParam.getReferenceFieldName();
parameterName = hasParam.getParameterName();
paramName = parameterName.replaceAll("\\..*", "");
hasParam = new HasParam(targetResourceType, paramReference, parameterName, hasParam.getParameterValue());
orValues.add(hasParam);
orValues.add(
(IQueryParameterType) QualifiedParamList.singleton(null, hasParam.getValueAsQueryToken(fhirContext)));
}
String qualifier = paramName.substring(4);
hasParam.setValueAsQueryToken(fhirContext, FhirConstants.HAS_PROPERTY, qualifier,
hasParam.getValueAsQueryToken(fhirContext));
orValues.add(hasParam);
return Optional.of(eq(propertyName, orValues));
}

protected Optional<Criterion> handleHasParam(@Nonnull String propertyName, HasAndListParam hasAndListParam) {
if (hasAndListParam == null) {
return Optional.empty();
}

return handleAndListParam(hasAndListParam, hasParam -> handleHas(propertyName, hasParam));
}

protected Optional<Criterion> handleQuantity(String propertyName, QuantityParam quantityParam) {
if (quantityParam == null) {
return Optional.empty();
Expand Down
30 changes: 30 additions & 0 deletions api/src/main/java/org/openmrs/module/fhir2/api/dao/impl/FhirObservationDaoImpl.java
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Original file line number Diff line number Diff line change
Expand Up @@ -9,15 +9,19 @@
*/
package org.openmrs.module.fhir2.api.dao.impl;

import static org.hibernate.criterion.Restrictions.and;
import static org.hibernate.criterion.Restrictions.eq;

import javax.annotation.Nonnull;

import java.util.ArrayList;
import java.util.List;
import java.util.Optional;

import ca.uhn.fhir.rest.param.DateRangeParam;
import ca.uhn.fhir.rest.param.QuantityAndListParam;
import ca.uhn.fhir.rest.param.ReferenceAndListParam;
import ca.uhn.fhir.rest.param.ReferenceParam;
import ca.uhn.fhir.rest.param.StringAndListParam;
import ca.uhn.fhir.rest.param.TokenAndListParam;
import ca.uhn.fhir.rest.param.TokenParam;
Expand Down Expand Up @@ -59,6 +63,10 @@ protected void setupSearchParams(Criteria criteria, SearchParameterMap theParams
entry.getValue()
.forEach(category -> handleConceptClass(criteria, (TokenAndListParam) category.getParam()));
break;
case FhirConstants.BASED_ON_REFERENCE_SEARCH_HANDLER:
entry.getValue().forEach(param -> handleReference(criteria, (ReferenceAndListParam) param.getParam(),
"basedOnReferences", "bo"));
break;
case FhirConstants.VALUE_CODED_SEARCH_HANDLER:
entry.getValue().forEach(
valueCoded -> handleValueCodedConcept(criteria, (TokenAndListParam) valueCoded.getParam()));
Expand All @@ -71,6 +79,7 @@ protected void setupSearchParams(Criteria criteria, SearchParameterMap theParams
entry.getValue().forEach(hasMemberReference -> handleHasMemberReference(criteria,
(ReferenceAndListParam) hasMemberReference.getParam()));
break;

case FhirConstants.QUANTITY_SEARCH_HANDLER:
entry.getValue().forEach(
quantity -> handleQuantity(quantity.getPropertyName(), (QuantityAndListParam) quantity.getParam())
Expand Down Expand Up @@ -160,6 +169,27 @@ private void handleValueCodedConcept(Criteria criteria, TokenAndListParam valueC
}
}

private Boolean validReferenceParam(ReferenceParam ref) {
return (ref != null && ref.getIdPart() != null && ref.getResourceType() != null);
}

private void handleReference(Criteria criteria, ReferenceAndListParam reference, String property, String alias) {
handleAndListParam(reference, param -> {
if (validReferenceParam(param)) {
if (lacksAlias(criteria, alias)) {
criteria.createAlias(property, alias);
}

List<Optional<Criterion>> criterionList = new ArrayList<>();
criterionList.add(Optional.of(eq(String.format("%s.reference", alias), param.getIdPart())));
criterionList.add(Optional.of(eq(String.format("%s.type", alias), param.getResourceType())));
return Optional.of(and(toCriteriaArray(criterionList)));
}

return Optional.empty();
}).ifPresent(criteria::add);
}

@Override
protected String paramToProp(@Nonnull String paramName) {
if (Observation.SP_DATE.equals(paramName)) {
Expand Down
12 changes: 12 additions & 0 deletions api/src/main/java/org/openmrs/module/fhir2/api/dao/impl/FhirServiceRequestDaoImpl.java
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Expand Up @@ -15,7 +15,9 @@
import java.util.Optional;
import java.util.stream.Stream;

import ca.uhn.fhir.context.FhirContext;
import ca.uhn.fhir.rest.param.DateRangeParam;
import ca.uhn.fhir.rest.param.HasAndListParam;
import ca.uhn.fhir.rest.param.ReferenceAndListParam;
import ca.uhn.fhir.rest.param.TokenAndListParam;
import lombok.AccessLevel;
Expand All @@ -26,12 +28,18 @@
import org.openmrs.module.fhir2.FhirConstants;
import org.openmrs.module.fhir2.api.dao.FhirServiceRequestDao;
import org.openmrs.module.fhir2.api.search.param.SearchParameterMap;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.beans.factory.annotation.Qualifier;
import org.springframework.stereotype.Component;

@Component
@Setter(AccessLevel.PACKAGE)
public class FhirServiceRequestDaoImpl extends BaseFhirDao<TestOrder> implements FhirServiceRequestDao<TestOrder> {

@Autowired
@Qualifier("fhirR4")
private FhirContext fhirContext;

@Override
protected void setupSearchParams(Criteria criteria, SearchParameterMap theParams) {
theParams.getParameters().forEach(entry -> {
Expand All @@ -51,6 +59,10 @@ protected void setupSearchParams(Criteria criteria, SearchParameterMap theParams
entry.getValue().forEach(participantReference -> handleProviderReference(criteria,
(ReferenceAndListParam) participantReference.getParam()));
break;
case FhirConstants.HAS_PROPERTY:
entry.getValue().forEach(hasParameter -> handleHasParam(hasParameter.getPropertyName(),
(HasAndListParam) hasParameter.getParam()).ifPresent(criteria::add));
break;
case FhirConstants.DATE_RANGE_SEARCH_HANDLER:
entry.getValue().forEach(dateRangeParam -> handleDateRange((DateRangeParam) dateRangeParam.getParam())
.ifPresent(criteria::add));
Expand Down
10 changes: 6 additions & 4 deletions api/src/main/java/org/openmrs/module/fhir2/api/impl/FhirObservationServiceImpl.java
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Original file line number Diff line number Diff line change
Expand Up @@ -56,10 +56,11 @@ public class FhirObservationServiceImpl extends BaseFhirService<Observation, org
@Override
@Transactional(readOnly = true)
public IBundleProvider searchForObservations(ReferenceAndListParam encounterReference,
ReferenceAndListParam patientReference, ReferenceAndListParam hasMemberReference, TokenAndListParam valueConcept,
DateRangeParam valueDateParam, QuantityAndListParam valueQuantityParam, StringAndListParam valueStringParam,
DateRangeParam date, TokenAndListParam code, TokenAndListParam category, TokenAndListParam id,
DateRangeParam lastUpdated, SortSpec sort, HashSet<Include> includes, HashSet<Include> revIncludes) {
ReferenceAndListParam patientReference, ReferenceAndListParam hasMemberReference,
ReferenceAndListParam basedOnReference, TokenAndListParam valueConcept, DateRangeParam valueDateParam,
QuantityAndListParam valueQuantityParam, StringAndListParam valueStringParam, DateRangeParam date,
TokenAndListParam code, TokenAndListParam category, TokenAndListParam id, DateRangeParam lastUpdated,
SortSpec sort, HashSet<Include> includes, HashSet<Include> revIncludes) {

SearchParameterMap theParams = new SearchParameterMap()
.addParameter(FhirConstants.ENCOUNTER_REFERENCE_SEARCH_HANDLER, encounterReference)
Expand All @@ -68,6 +69,7 @@ public IBundleProvider searchForObservations(ReferenceAndListParam encounterRefe
.addParameter(FhirConstants.CATEGORY_SEARCH_HANDLER, category)
.addParameter(FhirConstants.VALUE_CODED_SEARCH_HANDLER, valueConcept)
.addParameter(FhirConstants.HAS_MEMBER_SEARCH_HANDLER, hasMemberReference)
.addParameter(FhirConstants.BASED_ON_REFERENCE_SEARCH_HANDLER, basedOnReference)
.addParameter(FhirConstants.VALUE_STRING_SEARCH_HANDLER, "valueText", valueStringParam)
.addParameter(FhirConstants.QUANTITY_SEARCH_HANDLER, "valueNumeric", valueQuantityParam)
.addParameter(FhirConstants.DATE_RANGE_SEARCH_HANDLER, "obsDatetime", date)
Expand Down
6 changes: 4 additions & 2 deletions api/src/main/java/org/openmrs/module/fhir2/api/impl/FhirServiceRequestServiceImpl.java
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Original file line number Diff line number Diff line change
Expand Up @@ -14,6 +14,7 @@
import ca.uhn.fhir.model.api.Include;
import ca.uhn.fhir.rest.api.server.IBundleProvider;
import ca.uhn.fhir.rest.param.DateRangeParam;
import ca.uhn.fhir.rest.param.HasAndListParam;
import ca.uhn.fhir.rest.param.ReferenceAndListParam;
import ca.uhn.fhir.rest.param.TokenAndListParam;
import lombok.AccessLevel;
Expand Down Expand Up @@ -53,11 +54,12 @@ public class FhirServiceRequestServiceImpl extends BaseFhirService<ServiceReques
@Override
public IBundleProvider searchForServiceRequests(ReferenceAndListParam patientReference, TokenAndListParam code,
ReferenceAndListParam encounterReference, ReferenceAndListParam participantReference, DateRangeParam occurrence,
TokenAndListParam uuid, DateRangeParam lastUpdated, HashSet<Include> includes) {
TokenAndListParam uuid, DateRangeParam lastUpdated, HasAndListParam has, HashSet<Include> includes) {

SearchParameterMap theParams = new SearchParameterMap()
.addParameter(FhirConstants.PATIENT_REFERENCE_SEARCH_HANDLER, patientReference)
.addParameter(FhirConstants.CODED_SEARCH_HANDLER, code)
.addParameter(FhirConstants.CODED_SEARCH_HANDLER, code)
.addParameter(FhirConstants.HAS_PROPERTY, has)
.addParameter(FhirConstants.ENCOUNTER_REFERENCE_SEARCH_HANDLER, encounterReference)
.addParameter(FhirConstants.PARTICIPANT_REFERENCE_SEARCH_HANDLER, participantReference)
.addParameter(FhirConstants.DATE_RANGE_SEARCH_HANDLER, occurrence)
Expand Down
15 changes: 9 additions & 6 deletions api/src/main/java/org/openmrs/module/fhir2/api/search/SearchQueryInclude.java
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Original file line number Diff line number Diff line change
Expand Up @@ -210,7 +210,7 @@ private IBundleProvider handleObservationReverseInclude(ReferenceAndListParam pa
switch (targetType) {
case FhirConstants.OBSERVATION:
return observationService.searchForObservations(null, null, params, null, null, null, null, null, null, null,
null, null, null, null, null);
null, null, null, null, null, null);
case FhirConstants.DIAGNOSTIC_REPORT:
return diagnosticReportService.searchForDiagnosticReports(null, null, null, null, params, null, null, null,
null);
Expand All @@ -228,7 +228,8 @@ private IBundleProvider handlePractitionerReverseInclude(ReferenceAndListParam p
null);
case FhirConstants.PROCEDURE_REQUEST:
case FhirConstants.SERVICE_REQUEST:
return serviceRequestService.searchForServiceRequests(null, null, null, params, null, null, null, null);
return serviceRequestService.searchForServiceRequests(null, null, null, params, null, null, null, null,
null);
}

return null;
Expand All @@ -238,7 +239,7 @@ private IBundleProvider handleEncounterReverseInclude(ReferenceAndListParam para
switch (targetType) {
case FhirConstants.OBSERVATION:
return observationService.searchForObservations(params, null, null, null, null, null, null, null, null, null,
null, null, null, null, null);
null, null, null, null, null, null);
case FhirConstants.DIAGNOSTIC_REPORT:
return diagnosticReportService.searchForDiagnosticReports(params, null, null, null, null, null, null, null,
null);
Expand All @@ -247,7 +248,8 @@ private IBundleProvider handleEncounterReverseInclude(ReferenceAndListParam para
null);
case FhirConstants.PROCEDURE_REQUEST:
case FhirConstants.SERVICE_REQUEST:
return serviceRequestService.searchForServiceRequests(null, null, params, null, null, null, null, null);
return serviceRequestService.searchForServiceRequests(null, null, params, null, null, null, null, null,
null);
}

return null;
Expand All @@ -267,7 +269,7 @@ private IBundleProvider handlePatientReverseInclude(ReferenceAndListParam params
switch (targetType) {
case FhirConstants.OBSERVATION:
return observationService.searchForObservations(null, params, null, null, null, null, null, null, null, null,
null, null, null, null, null);
null, null, null, null, null, null);
case FhirConstants.DIAGNOSTIC_REPORT:
return diagnosticReportService.searchForDiagnosticReports(null, params, null, null, null, null, null, null,
null);
Expand All @@ -281,7 +283,8 @@ private IBundleProvider handlePatientReverseInclude(ReferenceAndListParam params
null);
case FhirConstants.SERVICE_REQUEST:
case FhirConstants.PROCEDURE_REQUEST:
return serviceRequestService.searchForServiceRequests(params, null, null, null, null, null, null, null);
return serviceRequestService.searchForServiceRequests(params, null, null, null, null, null, null, null,
null);
}

return null;
Expand Down
7 changes: 5 additions & 2 deletions api/src/main/java/org/openmrs/module/fhir2/providers/r3/ObservationFhirResourceProvider.java
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Original file line number Diff line number Diff line change
Expand Up @@ -46,6 +46,7 @@
import org.hl7.fhir.dstu3.model.Patient;
import org.hl7.fhir.dstu3.model.Resource;
import org.hl7.fhir.instance.model.api.IBaseResource;
import org.hl7.fhir.r4.model.ServiceRequest;
import org.openmrs.module.fhir2.api.FhirObservationService;
import org.openmrs.module.fhir2.api.search.SearchQueryBundleProviderR3Wrapper;
import org.openmrs.module.fhir2.providers.util.FhirProviderUtils;
Expand Down Expand Up @@ -112,6 +113,8 @@ public IBundleProvider searchObservations(
Patient.SP_FAMILY, Patient.SP_NAME }, targetTypes = Patient.class) ReferenceAndListParam patientParam,
@OptionalParam(name = Observation.SP_RELATED_TYPE, chainWhitelist = { "",
Observation.SP_CODE }, targetTypes = Observation.class) ReferenceAndListParam hasMemberReference,
@OptionalParam(name = Observation.SP_BASED_ON, chainWhitelist = { "",
ServiceRequest.SP_IDENTIFIER }, targetTypes = ServiceRequest.class) ReferenceAndListParam basedOnReference,
@OptionalParam(name = Observation.SP_VALUE_CONCEPT) TokenAndListParam valueConcept,
@OptionalParam(name = Observation.SP_VALUE_DATE) DateRangeParam valueDateParam,
@OptionalParam(name = Observation.SP_VALUE_QUANTITY) QuantityAndListParam valueQuantityParam,
Expand All @@ -138,8 +141,8 @@ public IBundleProvider searchObservations(
}

return new SearchQueryBundleProviderR3Wrapper(observationService.searchForObservations(encounterReference,
patientReference, hasMemberReference, valueConcept, valueDateParam, valueQuantityParam, valueStringParam, date,
code, category, id, lastUpdated, sort, includes, revIncludes));
patientReference, basedOnReference, hasMemberReference, valueConcept, valueDateParam, valueQuantityParam,
valueStringParam, date, code, category, id, lastUpdated, sort, includes, revIncludes));
}

}
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