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

…Observation

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

@@ -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
@@ -255,6 +255,8 @@ public class FhirConstants {
 
 	public static final String COMMON_SEARCH_HANDLER = "common.search.handler";
 
+	public static final String HAS_SEARCH_HANDLER = "_has";
+
 	public static final String ID_PROPERTY = "_id.property";
 
 	public static final String LAST_UPDATED_PROPERTY = "_lastUpdated.property";

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

@@ -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);
 }

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

@@ -14,13 +14,14 @@
 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.HasParam;
 import ca.uhn.fhir.rest.param.ReferenceAndListParam;
 import ca.uhn.fhir.rest.param.TokenAndListParam;
 import org.hl7.fhir.r4.model.ServiceRequest;
 
 public interface FhirServiceRequestService extends FhirService<ServiceRequest> {
 
-	IBundleProvider searchForServiceRequests(ReferenceAndListParam patientReference, TokenAndListParam code,
+	IBundleProvider searchForServiceRequests(ReferenceAndListParam patientReference, TokenAndListParam code, HasParam has,
 	        ReferenceAndListParam encounterReference, ReferenceAndListParam participantReference, DateRangeParam occurrence,
 	        TokenAndListParam uuid, DateRangeParam lastUpdated, HashSet<Include> includes);
 }

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

@@ -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)
@@ -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)

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.HasParam;
 import ca.uhn.fhir.rest.param.ReferenceAndListParam;
 import ca.uhn.fhir.rest.param.TokenAndListParam;
 import lombok.AccessLevel;
@@ -52,12 +53,12 @@ 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) {
+	        HasParam has, ReferenceAndListParam encounterReference, ReferenceAndListParam participantReference,
+	        DateRangeParam occurrence, TokenAndListParam uuid, DateRangeParam lastUpdated, 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_SEARCH_HANDLER, 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 +228,8 @@ 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, null, params, null, null, null,
+				    null);
 		}
 
 		return null;
@@ -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);
@@ -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, null, params, null, null, null, null,
+				    null);
 		}
 
 		return null;
@@ -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);
@@ -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;

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

@@ -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;
@@ -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,
@@ -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));
 	}
 
 }

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

@@ -23,6 +23,7 @@
 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.HasParam;
 import ca.uhn.fhir.rest.param.ReferenceAndListParam;
 import ca.uhn.fhir.rest.param.TokenAndListParam;
 import ca.uhn.fhir.rest.server.IResourceProvider;
@@ -113,7 +114,7 @@ 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") HasParam has,
 	        @IncludeParam(allow = { "ProcedureRequest:" + ProcedureRequest.SP_PATIENT,
 	                "ProcedureRequest:" + ProcedureRequest.SP_REQUESTER,
 	                "ProcedureRequest:" + ProcedureRequest.SP_ENCOUNTER }) HashSet<Include> includes) {
@@ -126,6 +127,6 @@ public IBundleProvider searchForProcedureRequests(
 		}
 
 		return new SearchQueryBundleProviderR3Wrapper(serviceRequestService.searchForServiceRequests(patientReference, code,
-		    encounterReference, participantReference, occurrence, uuid, lastUpdated, includes));
+		    has, encounterReference, participantReference, occurrence, uuid, lastUpdated, includes));
 	}
 }

api/src/main/java/org/openmrs/module/fhir2/providers/r4/ObservationFhirResourceProvider.java

@@ -46,6 +46,7 @@
 import org.hl7.fhir.r4.model.OperationOutcome;
 import org.hl7.fhir.r4.model.Patient;
 import org.hl7.fhir.r4.model.Resource;
+import org.hl7.fhir.r4.model.ServiceRequest;
 import org.openmrs.module.fhir2.api.FhirObservationService;
 import org.openmrs.module.fhir2.providers.util.FhirProviderUtils;
 import org.springframework.beans.factory.annotation.Autowired;
@@ -108,6 +109,8 @@ public IBundleProvider searchObservations(
 	                Patient.SP_NAME }, targetTypes = Patient.class) ReferenceAndListParam patientReference,
 	        @OptionalParam(name = Observation.SP_HAS_MEMBER, 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,
@@ -136,7 +139,7 @@ public IBundleProvider searchObservations(
 		}
 
 		return observationService.searchForObservations(encounterReference, patientReference, hasMemberReference,
-		    valueConcept, valueDateParam, valueQuantityParam, valueStringParam, date, code, category, id, lastUpdated, sort,
-		    includes, revIncludes);
+		    basedOnReference, valueConcept, valueDateParam, valueQuantityParam, valueStringParam, date, code, category, id,
+		    lastUpdated, sort, includes, revIncludes);
 	}
 }

api/src/main/java/org/openmrs/module/fhir2/providers/r4/ServiceRequestFhirResourceProvider.java

@@ -11,8 +11,12 @@
 
 import javax.annotation.Nonnull;
 
+import java.util.ArrayList;
 import java.util.HashSet;
+import java.util.List;
 
+import ca.uhn.fhir.context.FhirContext;
+import ca.uhn.fhir.model.api.IQueryParameterType;
 import ca.uhn.fhir.model.api.Include;
 import ca.uhn.fhir.rest.annotation.IdParam;
 import ca.uhn.fhir.rest.annotation.IncludeParam;
@@ -21,23 +25,28 @@
 import ca.uhn.fhir.rest.annotation.ResourceParam;
 import ca.uhn.fhir.rest.annotation.Search;
 import ca.uhn.fhir.rest.api.MethodOutcome;
+import ca.uhn.fhir.rest.api.QualifiedParamList;
 import ca.uhn.fhir.rest.api.server.IBundleProvider;
 import ca.uhn.fhir.rest.param.DateRangeParam;
+import ca.uhn.fhir.rest.param.HasParam;
 import ca.uhn.fhir.rest.param.ReferenceAndListParam;
 import ca.uhn.fhir.rest.param.TokenAndListParam;
 import ca.uhn.fhir.rest.server.IResourceProvider;
 import ca.uhn.fhir.rest.server.exceptions.InvalidRequestException;
 import ca.uhn.fhir.rest.server.exceptions.ResourceNotFoundException;
+import com.google.common.collect.Lists;
 import lombok.AccessLevel;
 import lombok.Setter;
 import org.apache.commons.collections.CollectionUtils;
 import org.hl7.fhir.instance.model.api.IBaseResource;
 import org.hl7.fhir.r4.model.Encounter;
 import org.hl7.fhir.r4.model.IdType;
+import org.hl7.fhir.r4.model.Observation;
 import org.hl7.fhir.r4.model.OperationOutcome;
 import org.hl7.fhir.r4.model.Patient;
 import org.hl7.fhir.r4.model.Practitioner;
 import org.hl7.fhir.r4.model.ServiceRequest;
+import org.openmrs.module.fhir2.FhirConstants;
 import org.openmrs.module.fhir2.api.FhirServiceRequestService;
 import org.openmrs.module.fhir2.providers.util.FhirProviderUtils;
 import org.springframework.beans.factory.annotation.Autowired;
@@ -49,6 +58,8 @@
 @Setter(AccessLevel.PACKAGE)
 public class ServiceRequestFhirResourceProvider implements IResourceProvider {
 
+	private final FhirContext cntxt = FhirContext.forR4();
+
 	@Autowired
 	private FhirServiceRequestService serviceRequestService;
 
@@ -108,8 +119,9 @@ public IBundleProvider searchForServiceRequests(
 	                Practitioner.SP_GIVEN, Practitioner.SP_FAMILY,
 	                Practitioner.SP_NAME }, targetTypes = Practitioner.class) ReferenceAndListParam participantReference,
 	        @OptionalParam(name = ServiceRequest.SP_OCCURRENCE) DateRangeParam occurrence,
+
 	        @OptionalParam(name = ServiceRequest.SP_RES_ID) TokenAndListParam uuid,
-	        @OptionalParam(name = "_lastUpdated") DateRangeParam lastUpdated,
+	        @OptionalParam(name = "_lastUpdated") DateRangeParam lastUpdated, @OptionalParam(name = "_has") HasParam has,
 	        @IncludeParam(allow = { "ServiceRequest:" + ServiceRequest.SP_PATIENT,
 	                "ServiceRequest:" + ServiceRequest.SP_REQUESTER,
 	                "ServiceRequest:" + ServiceRequest.SP_ENCOUNTER }) HashSet<Include> includes) {
@@ -121,7 +133,45 @@ public IBundleProvider searchForServiceRequests(
 			includes = null;
 		}
 
-		return serviceRequestService.searchForServiceRequests(patientReference, code, encounterReference,
+		hasParameter(has);
+
+		return serviceRequestService.searchForServiceRequests(patientReference, code, has, encounterReference,
 		    participantReference, occurrence, uuid, lastUpdated, includes);
 	}
+
+	private void hasParameter(HasParam has) {
+		List<List<IQueryParameterType>> theHasParameters = Lists.newArrayList();
+		for (List<? extends IQueryParameterType> nextOrList : theHasParameters) {
+			String targetResourceType = null;
+			String paramReference = null;
+			String parameterName = null;
+
+			String paramName = null;
+			List<QualifiedParamList> parameters = new ArrayList<>();
+			for (IQueryParameterType nextParam : nextOrList) {
+				has = (HasParam) nextParam;
+				targetResourceType = has.getTargetResourceType();
+
+				if (targetResourceType.getClass().equals(Observation.class)) {
+					paramReference = has.getReferenceFieldName();
+					parameterName = has.getParameterName();
+					paramName = parameterName.replaceAll("\\..*", "");
+					parameters.add(QualifiedParamList.singleton(null, has.getValueAsQueryToken(cntxt)));
+				} else {
+					return;
+				}
+			}
+			if (paramName == null) {
+				continue;
+			}
+			ArrayList<IQueryParameterType> orValues = Lists.newArrayList();
+			String qualifier = ":not";
+			for (IQueryParameterType next : nextOrList) {
+				has.setValueAsQueryToken(cntxt, FhirConstants.HAS_SEARCH_HANDLER, qualifier,
+				    next.getValueAsQueryToken(cntxt));
+				orValues.add(has);
+			}
+
+		}
+	}
 }

api/src/test/java/org/openmrs/module/fhir2/api/impl/FhirObservationServiceImplTest.java

@@ -126,7 +126,7 @@ public void searchForObservations_shouldReturnObservationsByParameters() {
 		when(translator.toFhirResource(obs)).thenReturn(observation);
 
 		IBundleProvider results = fhirObservationService.searchForObservations(null, patientReference, null, null, null,
-		    null, null, null, null, null, null, null, null, null, null);
+		    null, null, null, null, null, null, null, null, null, null, null);
 
 		assertThat(results, notNullValue());
 		assertThat(results.size(), equalTo(1));