Merge branch 'openmrs:master' into FM2-584

api-2.1/src/main/java/org/openmrs/module/fhir2/api/translators/impl/GroupComponentTranslatorImpl.java

@@ -33,7 +33,11 @@ public Group.GroupMemberComponent toFhirResource(@Nonnull GroupMember member) {
 	@Override
 	public GroupMember toOpenmrsType(@Nonnull Group.GroupMemberComponent component) {
 		GroupMember member = new GroupMember();
-		member.setId(component.getId());
+
+		if (component.hasId()) {
+			member.setId(component.getId());
+		}
+
 		member.setEntity(component.getEntity());
 		member.setEntityTarget(component.getEntityTarget());
 		member.setInactive(component.getInactive());

api-2.2/src/main/java/org/openmrs/module/fhir2/api/translators/impl/ConditionTranslatorImpl_2_2.java

@@ -104,7 +104,10 @@ public Condition toOpenmrsType(@Nonnull Condition existingCondition,
 		notNull(existingCondition, "The existing Openmrs Condition object should not be null");
 		notNull(condition, "The Condition object should not be null");
 
-		existingCondition.setUuid(condition.getIdElement().getIdPart());
+		if (condition.hasId()) {
+			existingCondition.setUuid(condition.getIdElement().getIdPart());
+		}
+
 		existingCondition.setPatient(patientReferenceTranslator.toOpenmrsType(condition.getSubject()));
 		existingCondition.setClinicalStatus(clinicalStatusTranslator.toOpenmrsType(condition.getClinicalStatus()));
 		existingCondition

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

@@ -346,4 +346,8 @@ private FhirConstants() {
 	public static final String RX_NORM_SYSTEM_URI = "http://www.nlm.nih.gov/research/umls/rxnorm";
 
 	public static final String UCUM_SYSTEM_URI = "http://unitsofmeasure.org";
+
+	public static final String EXACT_TOTAL_SEARCH_PARAMETER = "_exactTotal";
+
+	public static final String COUNT_QUERY_CACHE = "countQueryCache";
 }

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

@@ -15,6 +15,7 @@
 import java.util.List;
 
 import ca.uhn.fhir.rest.api.PatchTypeEnum;
+import ca.uhn.fhir.rest.api.server.RequestDetails;
 import org.hl7.fhir.instance.model.api.IAnyResource;
 
 public interface FhirService<T extends IAnyResource> {
@@ -27,7 +28,7 @@ public interface FhirService<T extends IAnyResource> {
 
 	T update(@Nonnull String uuid, @Nonnull T updatedResource);
 
-	T patch(@Nonnull String uuid, @Nonnull PatchTypeEnum patchType, @Nonnull String body);
+	T patch(@Nonnull String uuid, @Nonnull PatchTypeEnum patchType, @Nonnull String body, RequestDetails requestDetails);
 
 	void delete(@Nonnull String uuid);
 }

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

@@ -14,6 +14,8 @@
 import static org.hibernate.criterion.Restrictions.in;
 import static org.hibernate.criterion.Restrictions.isNull;
 import static org.hibernate.criterion.Restrictions.or;
+import static org.openmrs.module.fhir2.FhirConstants.COUNT_QUERY_CACHE;
+import static org.openmrs.module.fhir2.FhirConstants.EXACT_TOTAL_SEARCH_PARAMETER;
 
 import javax.annotation.Nonnull;
 
@@ -31,6 +33,7 @@
 import lombok.AccessLevel;
 import lombok.Getter;
 import lombok.Setter;
+import org.hibernate.CacheMode;
 import org.hibernate.Criteria;
 import org.hibernate.Hibernate;
 import org.hibernate.SessionFactory;
@@ -50,6 +53,7 @@
 import org.openmrs.api.handler.VoidHandler;
 import org.openmrs.module.fhir2.FhirConstants;
 import org.openmrs.module.fhir2.api.dao.FhirDao;
+import org.openmrs.module.fhir2.api.search.param.PropParam;
 import org.openmrs.module.fhir2.api.search.param.SearchParameterMap;
 import org.springframework.beans.factory.annotation.Autowired;
 import org.springframework.beans.factory.annotation.Qualifier;
@@ -179,13 +183,30 @@ public boolean hasDistinctResults() {
 	@Override
 	public int getSearchResultsCount(@Nonnull SearchParameterMap theParams) {
 		Criteria criteria = getSearchResultCriteria(theParams);
+
+		applyExactTotal(theParams, criteria);
+
 		if (hasDistinctResults()) {
 			return ((Long) criteria.setProjection(Projections.rowCount()).uniqueResult()).intValue();
 		} else {
 			return ((Long) criteria.setProjection(Projections.countDistinct("id")).uniqueResult()).intValue();
 		}
 	}
 
+	protected void applyExactTotal(SearchParameterMap theParams, Criteria criteria) {
+
+		List<PropParam<?>> exactTotal = theParams.getParameters(EXACT_TOTAL_SEARCH_PARAMETER);
+		if (!exactTotal.isEmpty()) {
+			PropParam<Boolean> propParam = (PropParam<Boolean>) exactTotal.get(0);
+			if (propParam.getParam()) {
+				criteria.setCacheMode(CacheMode.REFRESH);
+			}
+		} else {
+			criteria.setCacheable(true);
+			criteria.setCacheRegion(COUNT_QUERY_CACHE);
+		}
+	}
+
 	@Override
 	public List<T> getSearchResults(@Nonnull SearchParameterMap theParams) {
 		Criteria criteria = getSearchResultCriteria(theParams);

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

@@ -91,7 +91,7 @@ public List<Obs> getSearchResults(@Nonnull SearchParameterMap theParams) {
 						results.add(obs);
 						groupCount--;
 					}
-
+					
 					if (results.size() >= theParams.getToIndex()) {
 						//Load only as many results as requested per page
 						break;
@@ -121,6 +121,7 @@ public int getSearchResultsCount(@Nonnull SearchParameterMap theParams) {
 			criteria.addOrder(Order.asc("concept")).addOrder(Order.desc("obsDatetime"));
 			criteria.setProjection(Projections.projectionList().add(Projections.groupProperty("concept.id"))
 			        .add(Projections.groupProperty("obsDatetime")).add(Projections.rowCount()));
+			applyExactTotal(theParams, criteria);
 			List<Object[]> rows = criteria.list();
 			final int maxGroupCount = getMaxParameter(theParams);
 			int groupCount = maxGroupCount;

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

@@ -16,7 +16,9 @@
 import java.util.stream.Collectors;
 
 import ca.uhn.fhir.context.FhirContext;
+import ca.uhn.fhir.rest.api.Constants;
 import ca.uhn.fhir.rest.api.PatchTypeEnum;
+import ca.uhn.fhir.rest.api.server.RequestDetails;
 import ca.uhn.fhir.rest.server.exceptions.InvalidRequestException;
 import ca.uhn.fhir.rest.server.exceptions.ResourceGoneException;
 import ca.uhn.fhir.rest.server.exceptions.ResourceNotFoundException;
@@ -126,7 +128,8 @@ public T update(@Nonnull String uuid, @Nonnull T updatedResource) {
 	}
 
 	@Override
-	public T patch(@Nonnull String uuid, @Nonnull PatchTypeEnum patchType, @Nonnull String body) {
+	public T patch(@Nonnull String uuid, @Nonnull PatchTypeEnum patchType, @Nonnull String body,
+	        RequestDetails requestDetails) {
 		if (uuid == null) {
 			throw new InvalidRequestException("id cannot be null");
 		}
@@ -144,12 +147,15 @@ public T patch(@Nonnull String uuid, @Nonnull PatchTypeEnum patchType, @Nonnull
 
 		switch (patchType) {
 			case JSON_PATCH:
-				// note that we are actually doing a JSON Merge Patch, not a JSON Patch, but FHIR doesn't seem to support this type
-				// see https://erosb.github.io/post/json-patch-vs-merge-patch/ for an example of the difference
-				updatedFhirObject = JsonPatchUtils.apply(fhirContext, existingFhirObject, body);
+				if (isJsonMergePatch(requestDetails)) {
+					updatedFhirObject = JsonPatchUtils.applyJsonMergePatch(fhirContext, existingFhirObject, body);
+				} else {
+					updatedFhirObject = JsonPatchUtils.applyJsonPatch(fhirContext, existingFhirObject, body);
+				}
 				break;
 			default:
-				throw new InvalidRequestException("only JSON patches currently supported");
+				throw new InvalidRequestException("only JSON-formatted patches are currently supported");
+
 		}
 		return applyUpdate(existingObject, updatedFhirObject);
 	}
@@ -236,6 +242,15 @@ protected void validateObject(U object) {
 		}
 	}
 
+	/**
+	 * checks the Content-Type header of the request to determine if it corresponds to a merge json
+	 * patch
+	 */
+	private Boolean isJsonMergePatch(RequestDetails requestDetails) {
+		String contentType = requestDetails.getHeader(Constants.HEADER_CONTENT_TYPE);
+		return contentType != null && contentType.equalsIgnoreCase("application/merge-patch+json");
+	}
+
 	protected ResourceNotFoundException resourceNotFound(String uuid) {
 		return new ResourceNotFoundException(
 		        "Resource of type " + resourceClass.getSimpleName() + " with ID " + uuid + " is not known");

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

@@ -16,6 +16,7 @@
 
 import ca.uhn.fhir.rest.api.PatchTypeEnum;
 import ca.uhn.fhir.rest.api.server.IBundleProvider;
+import ca.uhn.fhir.rest.api.server.RequestDetails;
 import ca.uhn.fhir.rest.server.SimpleBundleProvider;
 import ca.uhn.fhir.rest.server.exceptions.ResourceNotFoundException;
 import lombok.AccessLevel;
@@ -56,7 +57,8 @@ public MedicationDispense update(@Nonnull String uuid, @Nonnull MedicationDispen
 	}
 
 	@Override
-	public MedicationDispense patch(@Nonnull String uuid, @Nonnull PatchTypeEnum patchType, @Nonnull String body) {
+	public MedicationDispense patch(@Nonnull String uuid, @Nonnull PatchTypeEnum patchType, @Nonnull String body,
+	        RequestDetails requestDetails) {
 		throw new UnsupportedOperationException("MedicationDispense is not available in OpenMRS versions < 2.6.0");
 	}
 

api/src/main/java/org/openmrs/module/fhir2/api/search/param/BaseResourceSearchParams.java

@@ -44,7 +44,8 @@ protected final SearchParameterMap baseSearchParameterMap() {
 		return new SearchParameterMap().addParameter(FhirConstants.COMMON_SEARCH_HANDLER, FhirConstants.ID_PROPERTY, getId())
 		        .addParameter(FhirConstants.COMMON_SEARCH_HANDLER, FhirConstants.LAST_UPDATED_PROPERTY, getLastUpdated())
 		        .addParameter(FhirConstants.INCLUDE_SEARCH_HANDLER, getIncludes())
-		        .addParameter(FhirConstants.REVERSE_INCLUDE_SEARCH_HANDLER, getRevIncludes()).setSortSpec(getSort());
+		        .addParameter(FhirConstants.REVERSE_INCLUDE_SEARCH_HANDLER, getRevIncludes()).setSortSpec(getSort())
+		        .addParameter(FhirConstants.EXACT_TOTAL_SEARCH_PARAMETER, Boolean.FALSE);
 	}
 
 	public abstract SearchParameterMap toSearchParameterMap();

api/src/main/java/org/openmrs/module/fhir2/api/translators/impl/AllergyIntoleranceTranslatorImpl.java

@@ -99,8 +99,8 @@ public Allergy toOpenmrsType(@Nonnull Allergy allergy, @Nonnull AllergyIntoleran
 		notNull(allergy, "The existing Allergy should not be null");
 		notNull(fhirAllergy, "The AllergyIntolerance object should not be null");
 
-		if (fhirAllergy.getId() != null) {
-			allergy.setUuid(fhirAllergy.getId());
+		if (fhirAllergy.hasId()) {
+			allergy.setUuid(fhirAllergy.getIdElement().getIdPart());
 		}
 
 		if (fhirAllergy.hasCode()) {

api/src/main/java/org/openmrs/module/fhir2/api/translators/impl/BaseGroupTranslator.java

@@ -59,7 +59,7 @@ public Cohort toOpenmrsType(@Nonnull Cohort existingCohort, @Nonnull Group group
 		notNull(existingCohort, "ExistingCohort object should not be null");
 
 		if (group.hasId()) {
-			existingCohort.setUuid(group.getId());
+			existingCohort.setUuid(group.getIdElement().getIdPart());
 		}
 
 		if (group.hasName()) {

api/src/main/java/org/openmrs/module/fhir2/api/translators/impl/ConditionTranslatorImpl.java

@@ -96,7 +96,11 @@ public Obs toOpenmrsType(@Nonnull org.hl7.fhir.r4.model.Condition condition) {
 	public Obs toOpenmrsType(@Nonnull Obs existingObsCondition, @Nonnull org.hl7.fhir.r4.model.Condition condition) {
 		notNull(existingObsCondition, "The existing Openmrs Obs Condition object should not be null");
 		notNull(condition, "The Condition object should not be null");
-		existingObsCondition.setUuid(condition.getIdElement().getIdPart());
+
+		if (condition.hasId()) {
+			existingObsCondition.setUuid(condition.getIdElement().getIdPart());
+		}
+
 		CodeableConcept codeableConcept = condition.getCode();
 		existingObsCondition.setValueCoded(conceptTranslator.toOpenmrsType(codeableConcept));
 		existingObsCondition.setPerson(patientReferenceTranslator.toOpenmrsType(condition.getSubject()));

api/src/main/java/org/openmrs/module/fhir2/api/translators/impl/EncounterTranslatorImpl.java

@@ -99,7 +99,9 @@ public org.openmrs.Encounter toOpenmrsType(@Nonnull org.openmrs.Encounter existi
 		notNull(existingEncounter, "The existing Openmrs Encounter object should not be null");
 		notNull(encounter, "The Encounter object should not be null");
 
-		existingEncounter.setUuid(encounter.getId());
+		if (encounter.hasId()) {
+			existingEncounter.setUuid(encounter.getIdElement().getIdPart());
+		}
 
 		EncounterType encounterType = encounterTypeTranslator.toOpenmrsType(encounter.getType());
 		if (encounterType != null) {

api/src/main/java/org/openmrs/module/fhir2/api/translators/impl/LocationTranslatorImpl.java

@@ -148,7 +148,10 @@ public org.openmrs.Location toOpenmrsType(@Nonnull org.openmrs.Location openmrsL
 		notNull(openmrsLocation, "The existing Openmrs location should not be null");
 		notNull(fhirLocation, "The Location object should not be null");
 
-		openmrsLocation.setUuid(fhirLocation.getIdElement().getIdPart());
+		if (fhirLocation.hasId()) {
+			openmrsLocation.setUuid(fhirLocation.getIdElement().getIdPart());
+		}
+
 		openmrsLocation.setName(fhirLocation.getName());
 		openmrsLocation.setDescription(fhirLocation.getDescription());
 

api/src/main/java/org/openmrs/module/fhir2/api/translators/impl/MedicationTranslatorImpl.java

@@ -94,8 +94,8 @@ public Drug toOpenmrsType(@Nonnull Drug existingDrug, @Nonnull Medication medica
 			return null;
 		}
 
-		if (medication.getId() != null) {
-			existingDrug.setUuid(medication.getId());
+		if (medication.hasId()) {
+			existingDrug.setUuid(medication.getIdElement().getIdPart());
 		}
 
 		if (medication.hasCode()) {

api/src/main/java/org/openmrs/module/fhir2/api/translators/impl/PatientTranslatorImpl.java

@@ -134,7 +134,9 @@ public org.openmrs.Patient toOpenmrsType(@Nonnull org.openmrs.Patient currentPat
 		notNull(currentPatient, "The existing Openmrs Patient object should not be null");
 		notNull(patient, "The Patient object should not be null");
 
-		currentPatient.setUuid(patient.getId());
+		if (patient.hasId()) {
+			currentPatient.setUuid(patient.getIdElement().getIdPart());
+		}
 
 		for (Identifier identifier : patient.getIdentifier()) {
 			PatientIdentifier omrsIdentifier = identifierTranslator.toOpenmrsType(identifier);

api/src/main/java/org/openmrs/module/fhir2/api/translators/impl/PersonTranslatorImpl.java

@@ -106,7 +106,9 @@ public Person toOpenmrsType(@Nonnull Person openmrsPerson, @Nonnull org.hl7.fhir
 		notNull(openmrsPerson, "The existing Openmrs Person object should not be null");
 		notNull(person, "The Person object should not be null");
 
-		openmrsPerson.setUuid(person.getId());
+		if (person.hasId()) {
+			openmrsPerson.setUuid(person.getIdElement().getIdPart());
+		}
 
 		for (HumanName name : person.getName()) {
 			openmrsPerson.addName(nameTranslator.toOpenmrsType(name));

api/src/main/java/org/openmrs/module/fhir2/api/translators/impl/PractitionerTranslatorProviderImpl.java

@@ -77,7 +77,9 @@ public Provider toOpenmrsType(@Nonnull Provider existingProvider, @Nonnull Pract
 			return null;
 		}
 
-		existingProvider.setUuid(practitioner.getId());
+		if (practitioner.hasId()) {
+			existingProvider.setUuid(practitioner.getIdElement().getIdPart());
+		}
 
 		existingProvider.setIdentifier(practitioner.getIdentifierFirstRep().getValue());
 

api/src/main/java/org/openmrs/module/fhir2/api/translators/impl/PractitionerTranslatorUserImpl.java

@@ -85,7 +85,10 @@ public User toOpenmrsType(@Nonnull User user, @Nonnull Practitioner practitioner
 			return null;
 		}
 
-		user.setUuid(practitioner.getId());
+		if (practitioner.hasId()) {
+			user.setUuid(practitioner.getIdElement().getIdPart());
+		}
+
 		setSystemId(practitioner, user);
 
 		if (practitioner.hasBirthDateElement()) {

api/src/main/java/org/openmrs/module/fhir2/api/translators/impl/VisitTranslatorImpl.java

@@ -79,7 +79,9 @@ public Visit toOpenmrsType(@Nonnull Visit existingVisit, @Nonnull Encounter enco
 		notNull(existingVisit, "The existingVisit object should not be null");
 		notNull(encounter, "The Encounter object should not be null");
 
-		existingVisit.setUuid(encounter.getId());
+		if (encounter.hasId()) {
+			existingVisit.setUuid(encounter.getIdElement().getIdPart());
+		}
 
 		VisitType visitType = visitTypeTranslator.toOpenmrsType(encounter.getType());
 		if (visitType != null) {