minor fixes in object instantiations

gt-health · Sep 1, 2015 · c0b4f4e · c0b4f4e
1 parent 2595bcc
commit c0b4f4e
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Showing 6 changed files with 38 additions and 62 deletions.
diff --git a/gt-fhir-entities/src/main/java/edu/gatech/i3l/fhir/dstu2/entities/ConditionOccurrence.java b/gt-fhir-entities/src/main/java/edu/gatech/i3l/fhir/dstu2/entities/ConditionOccurrence.java
@@ -214,16 +214,14 @@ public IResourceEntity constructEntityFromResource(IResource resource) {
 			Condition condition = (Condition) resource;
 			Long patientRef = condition.getPatient().getReference().getIdPartAsLong();
 			if(patientRef != null){
-				if(this.person == null)
-					this.person =  new Person();
+				this.person =  new Person();
 				this.person.setId(patientRef);
 			}
 
 			OmopConceptMapping ocm = OmopConceptMapping.getInstance();
 			Long conditionConceptRef = ocm.get(condition.getCode().getCodingFirstRep().getCode());
 			if(conditionConceptRef != null){
-				if(this.conditionConcept == null)
-					this.conditionConcept = new Concept();
+				this.conditionConcept = new Concept();
 				this.conditionConcept.setId(conditionConceptRef);
 			}
 			IDatatype onSetDate = condition.getOnset();
@@ -237,15 +235,13 @@ public IResourceEntity constructEntityFromResource(IResource resource) {
 			}
 
 			Long encounterReference = condition.getEncounter().getReference().getIdPartAsLong();
-			if(this.conditionTypeConcept == null)
-				this.conditionTypeConcept = new Concept();
+			this.conditionTypeConcept = new Concept();
 			if (encounterReference == null) {
 				// These concept_id's are defined for Omop 4.0 and have concet_code = "OMOP generated"
 				this.conditionTypeConcept.setId(Omop4ConceptsFixedIds.EHR_PROBLEM_ENTRY.getConceptId());
 			} else {
 				this.conditionTypeConcept.setId(Omop4ConceptsFixedIds.PRIMARY_CONDITION.getConceptId());
-				if(this.encounter == null)
-					this.encounter = new VisitOccurrence();
+				this.encounter = new VisitOccurrence();
 				this.encounter.setId(encounterReference);
 			}
 
@@ -256,8 +252,7 @@ public IResourceEntity constructEntityFromResource(IResource resource) {
 				if (asserterReference.getIdPartAsLong() != null && asserterReference.getResourceType() != null 
 						&& asserterReference.getResourceType().equalsIgnoreCase(Provider.RESOURCE_TYPE)) {
 					long providerId = asserterReference.getIdPartAsLong();
-					if(this.provider ==  null)
-						this.provider = new Provider();
+					this.provider = new Provider();
 					this.provider.setId(providerId);
 				}
 

diff --git a/...s/src/main/java/edu/gatech/i3l/fhir/dstu2/entities/DrugExposurePrescriptionDispensed.java b/...s/src/main/java/edu/gatech/i3l/fhir/dstu2/entities/DrugExposurePrescriptionDispensed.java
@@ -156,8 +156,7 @@ public IResourceEntity constructEntityFromResource(IResource resource) {
 		MedicationDispense md = (MedicationDispense) resource;
 
 		/* Set drup exposure type */
-		if(this.drugExposureType == null)
-			this.drugExposureType = new Concept();
+		this.drugExposureType = new Concept();
 		Long destinationRef = md.getDestination().getReference().getIdPartAsLong();
 		if(destinationRef != null){
 			this.drugExposureType.setId(Omop4ConceptsFixedIds.PRESCRIPTION_DISP_MAIL_ORDER.getConceptId());
@@ -167,15 +166,13 @@ public IResourceEntity constructEntityFromResource(IResource resource) {
 		/* Set drug concept(medication) */
 		Long medicationRef = md.getMedication().getReference().getIdPartAsLong();
 		if(medicationRef != null){
-			if(this.medication == null)
-				this.medication = new Concept();
+			this.medication = new Concept();
 			this.medication.setId(medicationRef);
 		}
 		/* Set patient */
 		Long patientRef = md.getPatient().getReference().getIdPartAsLong();
 		if(patientRef != null){
-			if(this.person == null)
-				this.person = new Person();
+			this.person = new Person();
 			this.person.setId(patientRef);
 		}
 

diff --git a/...ies/src/main/java/edu/gatech/i3l/fhir/dstu2/entities/DrugExposurePrescriptionWritten.java b/...ies/src/main/java/edu/gatech/i3l/fhir/dstu2/entities/DrugExposurePrescriptionWritten.java
@@ -287,30 +287,26 @@ public IResource getRelatedResource() {
 	public IResourceEntity constructEntityFromResource(IResource resource) {
 		MedicationPrescription mp = (MedicationPrescription) resource;
 		/* Set drup exposure type */
-		if(this.drugExposureType == null)
-			this.drugExposureType = new Concept();
+		this.drugExposureType = new Concept();
 		this.drugExposureType.setId(Omop4ConceptsFixedIds.PRESCRIPTION_WRITTEN.getConceptId());
 		/* Set start date of prescription */
 		this.startDate = mp.getDateWritten();
 		/* Set VisitOccurrence */
 		Long encounterRef = mp.getEncounter().getReference().getIdPartAsLong();
 		if(encounterRef != null){
-			if(this.visitOccurrence == null)
-				this.visitOccurrence = new VisitOccurrenceComplement();
+			this.visitOccurrence = new VisitOccurrenceComplement();
 			this.visitOccurrence.setId(encounterRef);
 		}
 		/* Set Medication */
 		Long medicationRef = mp.getMedication().getReference().getIdPartAsLong();
 		if(medicationRef != null){
-			if(this.medication == null)
-				this.medication = new Concept();
+			this.medication = new Concept();
 			this.medication.setId(medicationRef); 
 		}
 		/* Set patient */
 		Long patientRef = mp.getPatient().getReference().getIdPartAsLong();
 		if(patientRef != null){
-			if(this.person == null)
-				this.person = new Person();
+			this.person = new Person();
 			this.person.setId(patientRef);
 		}
 		return this;

diff --git a/gt-fhir-entities/src/main/java/edu/gatech/i3l/fhir/dstu2/entities/Observation.java b/gt-fhir-entities/src/main/java/edu/gatech/i3l/fhir/dstu2/entities/Observation.java
@@ -297,8 +297,7 @@ public IResourceEntity constructEntityFromResource(IResource resource) {
 		IdDt reference = observation.getSubject().getReference();
 		if(reference.getIdPartAsLong() != null){
 			if("Patient".equals(reference.getResourceType())){
-				if(this.person ==null)
-					this.person = new Person();
+				this.person = new Person();
 				this.person.setId(reference.getIdPartAsLong());
 			} else if("Group".equals(reference.getResourceType())){
 				//
@@ -312,21 +311,18 @@ public IResourceEntity constructEntityFromResource(IResource resource) {
 		/*Set visit occurrence */
 		Long visitOccurrenceId = observation.getEncounter().getReference().getIdPartAsLong();
 		if(visitOccurrenceId != null){
-			if(this.visitOccurrence == null)
-				this.visitOccurrence = new VisitOccurrence();
+			this.visitOccurrence = new VisitOccurrence();
 			this.visitOccurrence.setId(visitOccurrenceId);
 		}
 
 		Long observationConceptId = ocm.get(observation.getCode().getCodingFirstRep().getCode(), OmopConceptMapping.LOINC_CODE);
 		if(observationConceptId != null){
-			if(this.observationConcept == null)
-				this.observationConcept = new Concept();
+			this.observationConcept = new Concept();
 			this.observationConcept.setId(observationConceptId); 
 		}
 
 		/* Set the type of the observation */
-		if(this.type == null)
-			this.type = new Concept();
+		this.type = new Concept();
 		if(observation.getMethod().getCodingFirstRep() != null){
 			this.type.setId(Omop4ConceptsFixedIds.OBSERVATION_FROM_LAB_NUMERIC_RESULT.getConceptId()); //assuming all results on this table are quantitative: http://hl7.org/fhir/2015May/valueset-observation-methods.html
 		} else {
@@ -339,17 +335,15 @@ public IResourceEntity constructEntityFromResource(IResource resource) {
 			Long unitId = ocm.get(((QuantityDt) value).getUnits(), OmopConceptMapping.UCUM_CODE, OmopConceptMapping.UCUM_CODE_STANDARD, OmopConceptMapping.UCUM_CODE_CUSTOM);
 			this.valueAsNumber = ((QuantityDt) value).getValue();
 			if(unitId != null){
-				if(this.unit == null)
-					this.unit = new Concept();
+				this.unit = new Concept();
 				this.unit.setId(unitId); 
 			}
 			this.rangeHigh = observation.getReferenceRangeFirstRep().getHigh().getValue();
 			this.rangeLow = observation.getReferenceRangeFirstRep().getLow().getValue();
 		} else if(value instanceof CodeableConceptDt){
 			Long valueAsConceptId = ocm.get(((CodeableConceptDt) value).getCodingFirstRep().getCode(), OmopConceptMapping.CLINICAL_FINDING);
 			if(valueAsConceptId != null){
-				if(this.valueAsConcept == null)
-					this.valueAsConcept = new Concept();
+				this.valueAsConcept = new Concept();
 				this.valueAsConcept.setId(valueAsConceptId);
 			}
 		} else {

diff --git a/gt-fhir-entities/src/main/java/edu/gatech/i3l/fhir/dstu2/entities/Person.java b/gt-fhir-entities/src/main/java/edu/gatech/i3l/fhir/dstu2/entities/Person.java
@@ -313,8 +313,7 @@ public IResourceEntity constructEntityFromResource(IResource resource) {
 			this.dayOfBirth = c.get(Calendar.DAY_OF_MONTH);
 			//TODO set deceased value in Person; Set gender concept (source value is set); list of addresses (?)
 //			this.death = patient.getDeceased(); 
-			if(this.genderConcept == null)
-				this.genderConcept = new Concept();
+			this.genderConcept = new Concept();
 			this.genderConcept.setId(OmopConceptMapping.getInstance().get(patient.getGender(), OmopConceptMapping.GENDER));
 
 			LocationComplement location;

diff --git a/gt-fhir-webapp/src/main/java/edu/gatech/i3l/fhir/jpa/providers/JpaResourceProviderDstu2.java b/gt-fhir-webapp/src/main/java/edu/gatech/i3l/fhir/jpa/providers/JpaResourceProviderDstu2.java
@@ -1,8 +1,6 @@
 package edu.gatech.i3l.fhir.jpa.providers;
 
 
-import java.util.Date;
-
 import javax.servlet.http.HttpServletRequest;
 
 import org.springframework.beans.factory.annotation.Required;
@@ -13,17 +11,14 @@
 import ca.uhn.fhir.rest.annotation.ConditionalUrlParam;
 import ca.uhn.fhir.rest.annotation.Create;
 import ca.uhn.fhir.rest.annotation.Delete;
-import ca.uhn.fhir.rest.annotation.History;
 import ca.uhn.fhir.rest.annotation.IdParam;
 import ca.uhn.fhir.rest.annotation.Read;
 import ca.uhn.fhir.rest.annotation.ResourceParam;
-import ca.uhn.fhir.rest.annotation.Since;
 import ca.uhn.fhir.rest.annotation.Update;
 import ca.uhn.fhir.rest.annotation.Validate;
 import ca.uhn.fhir.rest.api.MethodOutcome;
 import ca.uhn.fhir.rest.api.ValidationModeEnum;
 import ca.uhn.fhir.rest.server.EncodingEnum;
-import ca.uhn.fhir.rest.server.IBundleProvider;
 import ca.uhn.fhir.rest.server.IResourceProvider;
 import ca.uhn.fhir.rest.server.exceptions.ResourceNotFoundException;
 import edu.gatech.i3l.fhir.jpa.dao.IFhirResourceDao;
@@ -49,25 +44,25 @@ public IFhirResourceDao<T> getDao() {
 		return myDao;
 	}
 
-	@History
-	public IBundleProvider getHistoryForResourceInstance(HttpServletRequest theRequest, @IdParam IdDt theId, @Since Date theDate) {
-		startRequest(theRequest);
-		try {
-			return myDao.history(theId, theDate);
-		} finally {
-			endRequest(theRequest);
-		}
-	}
-
-	@History
-	public IBundleProvider getHistoryForResourceType(HttpServletRequest theRequest, @Since Date theDate) {
-		startRequest(theRequest);
-		try {
-			return myDao.history(theDate);
-		} finally {
-			endRequest(theRequest);
-		}
-	}
+//	@History
+//	public IBundleProvider getHistoryForResourceInstance(HttpServletRequest theRequest, @IdParam IdDt theId, @Since Date theDate) {
+//		startRequest(theRequest);
+//		try {
+//			return myDao.history(theId, theDate);
+//		} finally {
+//			endRequest(theRequest);
+//		}
+//	}
+//
+//	@History
+//	public IBundleProvider getHistoryForResourceType(HttpServletRequest theRequest, @Since Date theDate) {
+//		startRequest(theRequest);
+//		try {
+//			return myDao.history(theDate);
+//		} finally {
+//			endRequest(theRequest);
+//		}
+//	}
 
 	@Override
 	public Class<? extends IResource> getResourceType() {