FM2-347:Add support for _has and _has:...:not for ServiceRequest and …

…Observation

api/src/main/java/org/openmrs/module/fhir2/FhirConstants.java

@@ -303,6 +303,8 @@ private FhirConstants() {
 	public static final String CONDITION_OBSERVATION_CONCEPT_UUID = "1284AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA";
 
 	public static final String MAX_SEARCH_HANDLER = "max.search.handler";
+
+	public static final String HAS_PROPERTY = "_has";
 
 	public static final String LASTN_OBSERVATION_SEARCH_HANDLER = "lastn.observation.search.handler";
 

api/src/main/java/org/openmrs/module/fhir2/api/FhirObservationService.java

@@ -30,7 +30,7 @@ public interface FhirObservationService extends FhirService<Observation> {
 	Observation get(@Nonnull String uuid);
 
 	IBundleProvider searchForObservations(ReferenceAndListParam encounterReference, ReferenceAndListParam patientReference,
-	        ReferenceAndListParam hasMemberReference, TokenAndListParam valueConcept, DateRangeParam valueDateParam,
+	        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);

api/src/main/java/org/openmrs/module/fhir2/api/FhirServiceRequestService.java

@@ -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;
@@ -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);
 }

api/src/main/java/org/openmrs/module/fhir2/api/dao/impl/BaseDao.java

@@ -27,6 +27,9 @@
 
 import javax.annotation.Nonnull;
 
+import java.lang.invoke.MethodHandle;
+import java.lang.invoke.MethodHandles;
+
 import java.math.BigDecimal;
 import java.time.Duration;
 import java.time.LocalDateTime;
@@ -71,6 +74,8 @@
 import lombok.Builder;
 import lombok.Data;
 import lombok.EqualsAndHashCode;
+import lombok.SneakyThrows;
+import lombok.extern.slf4j.Slf4j;
 import org.apache.commons.lang3.StringUtils;
 import org.apache.commons.lang3.math.NumberUtils;
 import org.apache.commons.lang3.time.DateUtils;
@@ -164,9 +169,24 @@
  * }</pre>
  * </p>
  */
+@Slf4j
 public abstract class BaseDao {
 
 	private static final BigDecimal APPROX_RANGE = new BigDecimal("0.1");
+
+	private static final MethodHandle detachedCriteria_getCriteriaImpl;
+
+	static {
+		MethodHandle temporaryHandle;
+		try {
+			temporaryHandle = MethodHandles.lookup().findGetter(DetachedCriteria.class, "impl", CriteriaImpl.class);
+		}
+		catch (NoSuchFieldException | IllegalAccessException e) {
+			log.error("Could not find method handle to get impl field from DetachedCriteria", e);
+			temporaryHandle = null;
+		}
+		detachedCriteria_getCriteriaImpl = temporaryHandle;
+	}
 
 	@Autowired
 	private LocalDateTimeFactory localDateTimeFactory;
@@ -230,6 +250,20 @@ protected boolean lacksAlias(@Nonnull Criteria criteria, @Nonnull String alias)
 
 		return subcriteria.filter(subcriteriaIterator -> containsAlias(subcriteriaIterator, alias)).isPresent();
 	}
+
+	/**
+	 * Determines whether or not the given criteria object already has a given alias. This is useful to
+	 * determine whether a mapping has already been made or whether a given alias is already in use.
+	 *
+	 * @param criteria the {@link DetachedCriteria} object to examine
+	 * @param alias the alias to look for
+	 * @return true if the alias exists in this criteria object, false otherwise
+	 */
+	protected boolean lacksAlias(@Nonnull DetachedCriteria criteria, @Nonnull String alias) {
+		Optional<Iterator<CriteriaImpl.Subcriteria>> subcriteria = asImpl(criteria).map(CriteriaImpl::iterateSubcriteria);
+
+		return subcriteria.filter(subcriteriaIterator -> containsAlias(subcriteriaIterator, alias)).isPresent();
+	}
 
 	/**
 	 * Determines whether any of the {@link CriteriaImpl.Subcriteria} objects returned by a given
@@ -1007,6 +1041,15 @@ protected List<String> tokensToList(List<TokenParam> tokens) {
 	protected Stream<String> tokensToParams(List<TokenParam> tokens) {
 		return tokens.stream().map(TokenParam::getValue);
 	}
+
+	@SneakyThrows
+	protected Optional<CriteriaImpl> asImpl(DetachedCriteria criteria) {
+		if (detachedCriteria_getCriteriaImpl == null) {
+			return Optional.empty();
+		}
+		return asImpl((CriteriaImpl) detachedCriteria_getCriteriaImpl.invokeExact(criteria));
+	}
+
 
 	private String groupBySystem(@Nonnull TokenParam token) {
 		return StringUtils.trimToEmpty(token.getSystem());

api/src/main/java/org/openmrs/module/fhir2/api/dao/impl/FhirObservationDaoImpl.java

@@ -109,6 +109,10 @@ protected void setupSearchParams(Criteria criteria, SearchParameterMap theParams
 				case FhirConstants.CODED_SEARCH_HANDLER:
 					entry.getValue().forEach(code -> handleCodedConcept(criteria, (TokenAndListParam) code.getParam()));
 					break;
+				case FhirConstants.BASED_ON_REFERENCE_SEARCH_HANDLER:
+					entry.getValue().forEach(param -> handleReference("ord", (ReferenceAndListParam) param.getParam())
+								.ifPresent(c -> criteria.createAlias("order", "ord").add(c)));
+					break;	
 				case FhirConstants.CATEGORY_SEARCH_HANDLER:
 					entry.getValue()
 					        .forEach(category -> handleConceptClass(criteria, (TokenAndListParam) category.getParam()));
@@ -170,6 +174,14 @@ private void handleHasMemberReference(Criteria criteria, ReferenceAndListParam h
 			}).ifPresent(criteria::add);
 		}
 	}
+
+	private Optional<Criterion> handleReference(@Nonnull String orderAlias, ReferenceAndListParam orderReference) {
+		if (orderReference == null) {
+			return Optional.empty();
+		}
+		return handleAndListParam(orderReference,
+		    param -> Optional.of(eq(String.format("%s.uuid", orderAlias), param.getIdPart())));
+	}
 
 	private Optional<Criterion> handleValueStringParam(@Nonnull String propertyName, StringAndListParam valueStringParam) {
 		return handleAndListParam(valueStringParam, v -> propertyLike(propertyName, v.getValue()));

api/src/main/java/org/openmrs/module/fhir2/api/dao/impl/FhirServiceRequestDaoImpl.java

@@ -9,28 +9,42 @@
  */
 package org.openmrs.module.fhir2.api.dao.impl;
 
+import static org.hibernate.criterion.Projections.property;
 import static org.hibernate.criterion.Restrictions.and;
 import static org.hibernate.criterion.Restrictions.or;
 
 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;
 import lombok.Setter;
 import org.hibernate.Criteria;
 import org.hibernate.criterion.Criterion;
+import org.hibernate.criterion.DetachedCriteria;
+import org.hibernate.criterion.Restrictions;
+import org.hibernate.criterion.Subqueries;
+import org.hl7.fhir.r4.model.Observation;
+import org.openmrs.Obs;
 import org.openmrs.TestOrder;
 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) {
@@ -44,6 +58,9 @@ protected void setupSearchParams(Criteria criteria, SearchParameterMap theParams
 					entry.getValue().forEach(patientReference -> handlePatientReference(criteria,
 					    (ReferenceAndListParam) patientReference.getParam(), "patient"));
 					break;
+				case FhirConstants.HAS_PROPERTY:
+					entry.getValue().forEach(hasParameter -> handleHasAndParam(criteria, (HasAndListParam) hasParameter.getParam()));
+					break;	
 				case FhirConstants.CODED_SEARCH_HANDLER:
 					entry.getValue().forEach(code -> handleCodedConcept(criteria, (TokenAndListParam) code.getParam()));
 					break;
@@ -83,5 +100,47 @@ private Optional<Criterion> handleDateRange(DateRangeParam dateRangeParam) {
 		    Optional.of(or(toCriteriaArray(Stream.of(handleDate("dateStopped", dateRangeParam.getUpperBound()),
 		        handleDate("autoExpireDate", dateRangeParam.getUpperBound())))))))));
 	}
+
+	private void handleHasAndParam(Criteria criteria, HasAndListParam hasAndListParam) {
+		if (hasAndListParam == null || hasAndListParam.size() == 0) {
+			return;
+		}
+
+		DetachedCriteria obsSubquery = DetachedCriteria.forClass(Obs.class, "obs");
+		handleAndListParam(hasAndListParam, hasParam -> {
+			if (!FhirConstants.OBSERVATION.equals(hasParam.getTargetResourceType())) {
+				return Optional.empty();
+			}
+
+			if (hasParam.getParameterName() != null) {
+				switch (hasParam.getParameterName()) {
+					case Observation.SP_ENCOUNTER:
+						obsSubquery.createCriteria("encounter")
+						        .add(Restrictions.eq("uuid", hasParam.getParameterValue().toString()));
+						break;
+					case Observation.SP_PATIENT:
+						obsSubquery.createCriteria("person")
+						        .add(Restrictions.eq("uuid", hasParam.getParameterValue().toString()));
+						break;
+					case Observation.SP_CATEGORY:
+						obsSubquery.createCriteria("concept").createCriteria("conceptClass")
+						        .add(Restrictions.eq("name", hasParam.getValueAsQueryToken(fhirContext).toString()));
+						break;
+					case Observation.SP_CODE:
+						obsSubquery.createCriteria("concept")
+						        .add(Restrictions.eq("id", Integer.parseInt(hasParam.getParameterValue().toString())));
+						break;
+				}
+			} else {
+				return Optional.empty();
+			}
+			return Optional.empty();
+		}).ifPresent(obsSubquery::add);
+
+		obsSubquery.setProjection(property("obs.order"));
+		criteria.add(Subqueries.propertyIn("id", obsSubquery));
+	}
+
+
 
 }

api/src/main/java/org/openmrs/module/fhir2/api/impl/FhirObservationServiceImpl.java

@@ -59,7 +59,7 @@ public class FhirObservationServiceImpl extends BaseFhirService<Observation, org
 	@Override
 	@Transactional(readOnly = true)
 	public IBundleProvider searchForObservations(ReferenceAndListParam encounterReference,
-	        ReferenceAndListParam patientReference, ReferenceAndListParam hasMemberReference, TokenAndListParam valueConcept,
+	        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) {
@@ -70,7 +70,8 @@ public IBundleProvider searchForObservations(ReferenceAndListParam encounterRefe
 		        .addParameter(FhirConstants.CODED_SEARCH_HANDLER, code)
 		        .addParameter(FhirConstants.CATEGORY_SEARCH_HANDLER, category)
 		        .addParameter(FhirConstants.VALUE_CODED_SEARCH_HANDLER, valueConcept)
-		        .addParameter(FhirConstants.HAS_MEMBER_SEARCH_HANDLER, hasMemberReference)
+				.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)

api/src/main/java/org/openmrs/module/fhir2/api/impl/FhirServiceRequestServiceImpl.java

@@ -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;
@@ -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)

api/src/main/java/org/openmrs/module/fhir2/api/search/SearchQueryInclude.java

@@ -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);
@@ -228,7 +228,7 @@ 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;
@@ -238,7 +238,7 @@ 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);
@@ -247,7 +247,7 @@ 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;
@@ -267,7 +267,7 @@ 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);
@@ -281,7 +281,7 @@ 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;

api/src/main/java/org/openmrs/module/fhir2/providers/r3/ObservationFhirResourceProvider.java

@@ -50,6 +50,7 @@
 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.annotations.R3Provider;
 import org.openmrs.module.fhir2.api.search.SearchQueryBundleProviderR3Wrapper;
@@ -116,6 +117,8 @@ 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,
@@ -142,8 +145,8 @@ public IBundleProvider searchObservations(
 		}
 
 		return new SearchQueryBundleProviderR3Wrapper(observationService.searchForObservations(encounterReference,
-		    patientReference, hasMemberReference, valueConcept, valueDateParam, valueQuantityParam, valueStringParam, date,
-		    code, category, id, lastUpdated, sort, includes, revIncludes));
+		    patientReference, hasMemberReference, basedOnReference, valueConcept, valueDateParam, valueQuantityParam,
+		    valueStringParam, date, code, category, id, lastUpdated, sort, includes, revIncludes));
 	}
 
 	@Operation(name = "lastn", idempotent = true, type = Observation.class)

api/src/main/java/org/openmrs/module/fhir2/providers/r3/ProcedureRequestFhirResourceProvider.java

@@ -25,6 +25,7 @@
 import ca.uhn.fhir.rest.api.MethodOutcome;
 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 ca.uhn.fhir.rest.server.IResourceProvider;
@@ -114,7 +115,8 @@ public IBundleProvider searchForProcedureRequests(
 	                Practitioner.SP_NAME }, targetTypes = Practitioner.class) ReferenceAndListParam participantReference,
 	        @OptionalParam(name = ProcedureRequest.SP_OCCURRENCE) DateRangeParam occurrence,
 	        @OptionalParam(name = ProcedureRequest.SP_RES_ID) TokenAndListParam uuid,
-	        @OptionalParam(name = "_lastUpdated") DateRangeParam lastUpdated,
+			@OptionalParam(name = "_lastUpdated") DateRangeParam lastUpdated,
+			@OptionalParam(name = "_has") HasAndListParam has,
 	        @IncludeParam(allow = { "ProcedureRequest:" + ProcedureRequest.SP_PATIENT,
 	                "ProcedureRequest:" + ProcedureRequest.SP_REQUESTER,
 	                "ProcedureRequest:" + ProcedureRequest.SP_ENCOUNTER }) HashSet<Include> includes) {
@@ -127,6 +129,6 @@ public IBundleProvider searchForProcedureRequests(
 		}
 
 		return new SearchQueryBundleProviderR3Wrapper(serviceRequestService.searchForServiceRequests(patientReference, code,
-		    encounterReference, participantReference, occurrence, uuid, lastUpdated, includes));
+		    encounterReference, participantReference, occurrence, uuid, lastUpdated,has, includes));
 	}
 }