OmopMeasurement.java

package edu.gatech.i3l.fhir.dstu2.entities;

import java.text.SimpleDateFormat;
import java.util.Date;
import java.util.List;

import javax.persistence.Access;
import javax.persistence.AccessType;
import javax.persistence.CascadeType;
import javax.persistence.Column;
import javax.persistence.Entity;
import javax.persistence.FetchType;
import javax.persistence.GeneratedValue;
import javax.persistence.GenerationType;
import javax.persistence.Id;
import javax.persistence.JoinColumn;
import javax.persistence.ManyToOne;
import javax.persistence.SequenceGenerator;
import javax.persistence.Table;
import javax.persistence.Temporal;
import javax.persistence.TemporalType;
import javax.validation.constraints.NotNull;

import ca.uhn.fhir.context.FhirVersionEnum;
import ca.uhn.fhir.model.api.IDatatype;
import ca.uhn.fhir.model.api.IResource;
import ca.uhn.fhir.model.dstu2.composite.CodeableConceptDt;
import ca.uhn.fhir.model.dstu2.composite.CodingDt;
import ca.uhn.fhir.model.dstu2.composite.PeriodDt;
import ca.uhn.fhir.model.dstu2.composite.QuantityDt;
import ca.uhn.fhir.model.dstu2.composite.ResourceReferenceDt;
import ca.uhn.fhir.model.primitive.DateTimeDt;
import ca.uhn.fhir.model.primitive.InstantDt;
import edu.gatech.i3l.fhir.jpa.entity.BaseResourceEntity;
import edu.gatech.i3l.fhir.jpa.entity.IResourceEntity;
import edu.gatech.i3l.omop.mapping.OmopConceptMapping;

@Entity
@Table(name="measurement")
public class OmopMeasurement extends BaseResourceEntity {

	/**
	 * 
	 */
	private static final String RES_TYPE = "Observation";
	public static final Long SYSTOLIC_CONCEPT_ID = 3004249L;
	public static final Long DIASTOLIC_CONCEPT_ID = 3012888L;		

	@Id
	@GeneratedValue(strategy=GenerationType.SEQUENCE, generator="measurement_occurrence_seq_gen")
	@SequenceGenerator(name="measurement_occurrence_seq_gen", sequenceName="measurement_occurrence_id_seq", allocationSize=1)
	@Column(name = "measurement_id")
	@Access(AccessType.PROPERTY)
	private Long id;

	@ManyToOne(cascade={CascadeType.MERGE})
	@JoinColumn(name="person_id", nullable=false)
	@NotNull
	private PersonComplement person;

	@Column(name="measurement_source_value")
	private String sourceValue; 

	@ManyToOne(cascade={CascadeType.MERGE})
	@JoinColumn(name="measurement_concept_id", nullable=false)
	@NotNull
	private Concept measurementConcept;

	@Column(name = "value_as_number")
	private Double valueAsNumber;

	@ManyToOne(cascade = { CascadeType.MERGE }, fetch = FetchType.LAZY)
	@JoinColumn(name = "value_as_concept_id")
	private Concept valueAsConcept;

	@ManyToOne(cascade = { CascadeType.MERGE }, fetch = FetchType.LAZY)
	@JoinColumn(name = "unit_concept_id")
	private Concept unit;

	@Column(name = "range_low")
	private Double rangeLow;

	@Column(name = "range_high")
	private Double rangeHigh;

	@Column(name = "measurement_date", nullable = false)
	@Temporal(TemporalType.DATE)
	@NotNull
	private Date date;

	@Column(name = "measurement_time")
	// @Temporal(TemporalType.TIME)
	private String time;

	@ManyToOne(fetch = FetchType.LAZY)
	@JoinColumn(name = "visit_occurrence_id")
	private VisitOccurrence visitOccurrence;

	@ManyToOne(cascade = { CascadeType.MERGE }, fetch = FetchType.LAZY)
	@JoinColumn(name = "measurement_type_concept_id")
	private Concept type;

	@Override
	public Long getId() {
		return id;
	}

	public void setId(Long id) {
		this.id = id;
	}
	
	public Person getPerson() {
		return person;
	}
	
	public void setPerson(PersonComplement person) {
		this.person = person;
	}
	
	public String getSourceValue() {
		return sourceValue;
	}
	
	public void setSourceValue(String sourceValue) {
		this.sourceValue = sourceValue;
	}

	public Concept getMeasurementConcept() {
		return measurementConcept;
	}
	
	public void setMeasurementConcept(Concept measurementConcept) {
		this.measurementConcept = measurementConcept;
	}
	
	public Double getValueAsNumber() {
		return valueAsNumber;
	}
	
	public void setValueAsNumber(Double valueAsNumber) {
		this.valueAsNumber = valueAsNumber;
	}
	
	public Concept getValueAsConcept() {
		return valueAsConcept;
	}
	
	public void setValueAsConcept(Concept valueAsConcept) {
		this.valueAsConcept = valueAsConcept;
	}
	
	public Concept getUnit() {
		return unit;
	}
	
	public void setUnit(Concept unit) {
		this.unit = unit;
	}
	
	public Double getRangeLow() {
		return rangeLow;
	}
	
	public void setRangeLow(Double rangeLow) {
		this.rangeLow =rangeLow;
	}
	
	public Double getRangeHigh() {
		return rangeHigh;
	}
	
	public void setRangeHigh(Double rangeHigh) {
		this.rangeHigh = rangeHigh;
	}
	
	public Date getDate() {
		return date;
	}
	
	public void setDate(Date date) {
		this.date = date;
	}
	
	public String getTime() {
		return time;
	}
	
	public void setTime(String time) {
		this.time = time;
	}
	
	public VisitOccurrence getVisitOccurrence() {
		return visitOccurrence;
	}
	
	public void setVisitOccurrence (VisitOccurrence visitOccurrence) {
		this.visitOccurrence = visitOccurrence;
	}
	
	public Concept getType() {
		return type;
	}
	
	public void setType(Concept type) {
		this.type = type;
	}
	
	@Override
	public FhirVersionEnum getFhirVersion() {
		return FhirVersionEnum.DSTU2;
	}

	@Override
	public String getResourceType() {
		return RES_TYPE;
	}

	@Override
	public InstantDt getUpdated() {
		// TODO Auto-generated method stub
		return null;
	}

	@Override
	public String translateSearchParam(String theSearchParam) {
		// TODO Auto-generated method stub
		return null;
	}

	@Override
	public IResource getRelatedResource() {
		// TODO Auto-generated method stub
		return null;
	}

	@Override
	public IResourceEntity constructEntityFromResource(IResource resource) {
		ca.uhn.fhir.model.dstu2.resource.Observation obs = (ca.uhn.fhir.model.dstu2.resource.Observation) resource;
		ResourceReferenceDt subjectReference = obs.getSubject();
		if (subjectReference != null) {
			if ("Patient".equals(subjectReference.getReference().getResourceType())) {
				PersonComplement person = PersonComplement.searchAndUpdate(subjectReference);
				if (person == null) return null; // We must have a patient
				this.setPerson(person);
			} else {
				// Group, Device, and Location are not supported in OMOP v5
				return null;
			}
		} else {
			// We must have subject reference.
			return null;
		}

		// We are writing to the database. Keep the source so we know where it is coming from
		OmopConceptMapping ocm = OmopConceptMapping.getInstance();
		if (obs.getId() != null) {
			// See if we already have this in the source field. If so,
			// then we want update not create
			OmopMeasurement origMeasurement = (OmopMeasurement) ocm.loadEntityBySource(OmopMeasurement.class, "OmopMeasurement", "sourceValue", obs.getId().getIdPart());
			if (origMeasurement == null)
				this.setSourceValue(obs.getId().getIdPart());
			else
				this.setId(origMeasurement.getId());
		}

		String code = obs.getCode().getCodingFirstRep().getCode();
		Long obsConceptRef = ocm.get(code);
		setMeasurementConcept(new Concept());
		if(obsConceptRef != null){
			getMeasurementConcept().setId(obsConceptRef);
		} else {
			getMeasurementConcept().setId(0L);
			System.out.println("Measurement code not recognized: "+code+". System: "+obs.getCode().getCodingFirstRep().getSystem());
		}

		/* Set the value of the observation */
		IDatatype value = obs.getValue();
		if (value instanceof QuantityDt) {
//			Long unitId = ocm.get(((QuantityDt) value).getUnit(), OmopConceptMapping.UCUM_CODE,
//					OmopConceptMapping.UCUM_CODE_STANDARD, OmopConceptMapping.UCUM_CODE_CUSTOM);
			String unitCode = ((QuantityDt) value).getCode();
			if (unitCode == null) {
				unitCode = ((QuantityDt) value).getUnit();
			}
			Long unitId = ocm.get(unitCode);
			this.valueAsNumber = ((QuantityDt) value).getValue().doubleValue();
			if (unitId != null) {
				this.unit = new Concept();
				this.unit.setId(unitId);
			}
			
			if (!obs.getReferenceRangeFirstRep().isEmpty())
				this.rangeHigh = obs.getReferenceRangeFirstRep().getHigh().getValue().doubleValue();
			if (!obs.getReferenceRangeFirstRep().isEmpty())
				this.rangeLow = obs.getReferenceRangeFirstRep().getLow().getValue().doubleValue();
			
		} else if (value instanceof CodeableConceptDt) {
//			Long valueAsConceptId = ocm.get(((CodeableConceptDt) value).getCodingFirstRep().getCode(),
//					OmopConceptMapping.CLINICAL_FINDING);
			Long valueAsConceptId = ocm.get(((CodeableConceptDt) value).getCodingFirstRep().getCode());
			if (valueAsConceptId != null) {
				this.valueAsConcept = new Concept();
				this.valueAsConcept.setId(valueAsConceptId);
			}
		} 
		
		if (obs.getEffective() instanceof DateTimeDt) {
			this.date = ((DateTimeDt) obs.getEffective()).getValue();
			SimpleDateFormat timeFormat = new SimpleDateFormat ("HH:mm:ss");
			this.time = timeFormat.format(((DateTimeDt) obs.getEffective()).getValue());
		} else if (obs.getEffective() instanceof PeriodDt) {
			// TODO: we need to handle period. We can probably use
			// we can use range_low and range_high. These are only available in Measurement
		}

		/* Set visit occurrence */
		Long visitOccurrenceId = obs.getEncounter().getReference().getIdPartAsLong();
		if (visitOccurrenceId != null) {
			this.visitOccurrence = new VisitOccurrence();
			this.visitOccurrence.setId(visitOccurrenceId);
		}

		/* measture type concept id - this is required field in OMOP v5. */
		setType (new Concept());
		CodeableConceptDt obsCategory = obs.getCategory();
		if (obsCategory.isEmpty()) {
			getType().setId(0L);
		} else {
			List<CodingDt> catCodes = obsCategory.getCoding();
			for (CodingDt catCode : catCodes) {
				if (catCode.getCode().equalsIgnoreCase("exam")) {
					getType().setId(44818701L);
				} else if (catCode.getCode().equalsIgnoreCase("laboratory")) {
					getType().setId(44818702L);
				}
			}
		}
		return this;
		
	}


}