Examples with Observation org.mitre.synthea.world.concepts.HealthRecord.Observation used on opensource projects

Example 1 with Observation

use of org.mitre.synthea.world.concepts.HealthRecord.Observation in project synthea by synthetichealth.

the class FhirR4 method convertToFHIR.

/**
 * Convert the given Person into a FHIR Bundle of the Patient and the
 * associated entries from their health record.
 *
 * @param person   Person to generate the FHIR JSON for
 * @param stopTime Time the simulation ended
 * @return FHIR Bundle containing the Person's health record
 */
public static Bundle convertToFHIR(Person person, long stopTime) {
    Bundle bundle = new Bundle();
    if (TRANSACTION_BUNDLE) {
        bundle.setType(BundleType.TRANSACTION);
    } else {
        bundle.setType(BundleType.COLLECTION);
    }
    BundleEntryComponent personEntry = basicInfo(person, bundle, stopTime);
    for (Encounter encounter : person.record.encounters) {
        BundleEntryComponent encounterEntry = encounter(person, personEntry, bundle, encounter);
        for (HealthRecord.Entry condition : encounter.conditions) {
            condition(person, personEntry, bundle, encounterEntry, condition);
        }
        for (HealthRecord.Allergy allergy : encounter.allergies) {
            allergy(person, personEntry, bundle, encounterEntry, allergy);
        }
        for (Observation observation : encounter.observations) {
            // Observation resources in v4 don't support Attachments
            if (observation.value instanceof Attachment) {
                media(person, personEntry, bundle, encounterEntry, observation);
            } else {
                observation(person, personEntry, bundle, encounterEntry, observation);
            }
        }
        for (Procedure procedure : encounter.procedures) {
            procedure(person, personEntry, bundle, encounterEntry, procedure);
        }
        for (HealthRecord.Device device : encounter.devices) {
            device(person, personEntry, bundle, device);
        }
        for (HealthRecord.Supply supply : encounter.supplies) {
            supplyDelivery(person, personEntry, bundle, supply, encounter);
        }
        for (Medication medication : encounter.medications) {
            medicationRequest(person, personEntry, bundle, encounterEntry, medication);
        }
        for (HealthRecord.Entry immunization : encounter.immunizations) {
            immunization(person, personEntry, bundle, encounterEntry, immunization);
        }
        for (Report report : encounter.reports) {
            report(person, personEntry, bundle, encounterEntry, report);
        }
        for (CarePlan careplan : encounter.careplans) {
            BundleEntryComponent careTeamEntry = careTeam(person, personEntry, bundle, encounterEntry, careplan);
            carePlan(person, personEntry, bundle, encounterEntry, encounter.provider, careTeamEntry, careplan);
        }
        for (ImagingStudy imagingStudy : encounter.imagingStudies) {
            imagingStudy(person, personEntry, bundle, encounterEntry, imagingStudy);
        }
        if (USE_US_CORE_IG) {
            String clinicalNoteText = ClinicalNoteExporter.export(person, encounter);
            boolean lastNote = (encounter == person.record.encounters.get(person.record.encounters.size() - 1));
            clinicalNote(person, personEntry, bundle, encounterEntry, clinicalNoteText, lastNote);
        }
        // one claim per encounter
        BundleEntryComponent encounterClaim = encounterClaim(person, personEntry, bundle, encounterEntry, encounter.claim);
        explanationOfBenefit(personEntry, bundle, encounterEntry, person, encounterClaim, encounter);
    }
    if (USE_US_CORE_IG) {
        // Add Provenance to the Bundle
        provenance(bundle, person, stopTime);
    }
    return bundle;
}

Example 2 with Observation

use of org.mitre.synthea.world.concepts.HealthRecord.Observation in project synthea by synthetichealth.

the class FhirR4 method report.

/**
 * Map the given Report to a FHIR DiagnosticReport resource, and add it to the given Bundle.
 *
 * @param rand           Source of randomness to use when generating ids etc
 * @param personEntry    The Entry for the Person
 * @param bundle         Bundle to add the Report to
 * @param encounterEntry Current Encounter entry
 * @param report         The Report
 * @return The added Entry
 */
private static BundleEntryComponent report(RandomNumberGenerator rand, BundleEntryComponent personEntry, Bundle bundle, BundleEntryComponent encounterEntry, Report report) {
    DiagnosticReport reportResource = new DiagnosticReport();
    if (USE_US_CORE_IG) {
        Meta meta = new Meta();
        meta.addProfile("http://hl7.org/fhir/us/core/StructureDefinition/us-core-diagnosticreport-lab");
        reportResource.setMeta(meta);
        org.hl7.fhir.r4.model.Encounter encounterResource = (org.hl7.fhir.r4.model.Encounter) encounterEntry.getResource();
        reportResource.addPerformer(encounterResource.getServiceProvider());
    }
    reportResource.setStatus(DiagnosticReportStatus.FINAL);
    reportResource.addCategory(new CodeableConcept(new Coding("http://terminology.hl7.org/CodeSystem/v2-0074", "LAB", "Laboratory")));
    reportResource.setCode(mapCodeToCodeableConcept(report.codes.get(0), LOINC_URI));
    reportResource.setSubject(new Reference(personEntry.getFullUrl()));
    reportResource.setEncounter(new Reference(encounterEntry.getFullUrl()));
    reportResource.setEffective(convertFhirDateTime(report.start, true));
    reportResource.setIssued(new Date(report.start));
    for (Observation observation : report.observations) {
        Reference reference = new Reference(observation.fullUrl);
        reference.setDisplay(observation.codes.get(0).display);
        reportResource.addResult(reference);
    }
    return newEntry(rand, bundle, reportResource);
}

Example 3 with Observation

use of org.mitre.synthea.world.concepts.HealthRecord.Observation in project synthea by synthetichealth.

the class FhirR4 method observation.

/**
 * Map the given Observation into a FHIR Observation resource, and add it to the given Bundle.
 *
 * @param rand           Source of randomness to use when generating ids etc
 * @param personEntry    The Person Entry
 * @param bundle         The Bundle to add to
 * @param encounterEntry The current Encounter entry
 * @param observation    The Observation
 * @return The added Entry
 */
private static BundleEntryComponent observation(RandomNumberGenerator rand, BundleEntryComponent personEntry, Bundle bundle, BundleEntryComponent encounterEntry, Observation observation) {
    org.hl7.fhir.r4.model.Observation observationResource = new org.hl7.fhir.r4.model.Observation();
    observationResource.setSubject(new Reference(personEntry.getFullUrl()));
    observationResource.setEncounter(new Reference(encounterEntry.getFullUrl()));
    observationResource.setStatus(ObservationStatus.FINAL);
    Code code = observation.codes.get(0);
    observationResource.setCode(mapCodeToCodeableConcept(code, LOINC_URI));
    // add extra codes, if there are any...
    if (observation.codes.size() > 1) {
        for (int i = 1; i < observation.codes.size(); i++) {
            code = observation.codes.get(i);
            Coding coding = new Coding();
            coding.setCode(code.code);
            coding.setDisplay(code.display);
            coding.setSystem(LOINC_URI);
            observationResource.getCode().addCoding(coding);
        }
    }
    observationResource.addCategory().addCoding().setCode(observation.category).setSystem("http://terminology.hl7.org/CodeSystem/observation-category").setDisplay(observation.category);
    if (observation.value != null) {
        Type value = mapValueToFHIRType(observation.value, observation.unit);
        observationResource.setValue(value);
    } else if (observation.observations != null && !observation.observations.isEmpty()) {
        // multi-observation (ex blood pressure)
        for (Observation subObs : observation.observations) {
            ObservationComponentComponent comp = new ObservationComponentComponent();
            comp.setCode(mapCodeToCodeableConcept(subObs.codes.get(0), LOINC_URI));
            Type value = mapValueToFHIRType(subObs.value, subObs.unit);
            comp.setValue(value);
            observationResource.addComponent(comp);
        }
    }
    observationResource.setEffective(convertFhirDateTime(observation.start, true));
    observationResource.setIssued(new Date(observation.start));
    if (USE_US_CORE_IG) {
        Meta meta = new Meta();
        // add the specific profile based on code
        String codeMappingUri = US_CORE_MAPPING.get(LOINC_URI, code.code);
        if (codeMappingUri != null) {
            meta.addProfile(codeMappingUri);
            if (!codeMappingUri.contains("/us/core/") && observation.category.equals("vital-signs")) {
                meta.addProfile("http://hl7.org/fhir/StructureDefinition/vitalsigns");
            }
        } else if (observation.report != null && observation.category.equals("laboratory")) {
            meta.addProfile("http://hl7.org/fhir/us/core/StructureDefinition/us-core-observation-lab");
        }
        if (meta.hasProfile()) {
            observationResource.setMeta(meta);
        }
    } else if (USE_SHR_EXTENSIONS) {
        Meta meta = new Meta();
        // all Observations are Observations
        meta.addProfile(SHR_EXT + "shr-finding-Observation");
        if ("vital-signs".equals(observation.category)) {
            meta.addProfile(SHR_EXT + "shr-vital-VitalSign");
        }
        // add the specific profile based on code
        String codeMappingUri = SHR_MAPPING.get(LOINC_URI, code.code);
        if (codeMappingUri != null) {
            meta.addProfile(codeMappingUri);
        }
        observationResource.setMeta(meta);
    }
    BundleEntryComponent entry = newEntry(rand, bundle, observationResource);
    observation.fullUrl = entry.getFullUrl();
    return entry;
}

Example 4 with Observation

use of org.mitre.synthea.world.concepts.HealthRecord.Observation in project synthea by synthetichealth.

the class FhirDstu2 method convertToFHIR.

/**
 * Convert the given Person into a FHIR Bundle with the Patient and the
 * associated entries from their health record.
 *
 * @param person Person to generate the FHIR Bundle
 * @param stopTime Time the simulation ended
 * @return String containing a FHIR Bundle containing the Person's health record
 */
public static Bundle convertToFHIR(Person person, long stopTime) {
    Bundle bundle = new Bundle();
    if (TRANSACTION_BUNDLE) {
        bundle.setType(BundleTypeEnum.TRANSACTION);
    } else {
        bundle.setType(BundleTypeEnum.COLLECTION);
    }
    Entry personEntry = basicInfo(person, bundle, stopTime);
    for (Encounter encounter : person.record.encounters) {
        Entry encounterEntry = encounter(person, personEntry, bundle, encounter);
        for (HealthRecord.Entry condition : encounter.conditions) {
            condition(person, personEntry, bundle, encounterEntry, condition);
        }
        for (HealthRecord.Entry allergy : encounter.allergies) {
            allergy(person, personEntry, bundle, encounterEntry, allergy);
        }
        for (Observation observation : encounter.observations) {
            // Observation resources in stu3 don't support Attachments
            if (observation.value instanceof Attachment) {
                media(person, personEntry, bundle, encounterEntry, observation);
            } else {
                observation(person, personEntry, bundle, encounterEntry, observation);
            }
        }
        for (Procedure procedure : encounter.procedures) {
            procedure(person, personEntry, bundle, encounterEntry, procedure);
        }
        for (Medication medication : encounter.medications) {
            medication(person, personEntry, bundle, encounterEntry, medication);
        }
        for (HealthRecord.Entry immunization : encounter.immunizations) {
            immunization(person, personEntry, bundle, encounterEntry, immunization);
        }
        for (Report report : encounter.reports) {
            report(person, personEntry, bundle, encounterEntry, report);
        }
        for (CarePlan careplan : encounter.careplans) {
            careplan(person, personEntry, bundle, encounterEntry, careplan);
        }
        for (ImagingStudy imagingStudy : encounter.imagingStudies) {
            imagingStudy(person, personEntry, bundle, encounterEntry, imagingStudy);
        }
        for (HealthRecord.Device device : encounter.devices) {
            device(person, personEntry, bundle, device);
        }
        for (HealthRecord.Supply supply : encounter.supplies) {
            supplyDelivery(person, personEntry, bundle, supply, encounter);
        }
        // one claim per encounter
        encounterClaim(person, personEntry, bundle, encounterEntry, encounter.claim);
    }
    return bundle;
}

Example 5 with Observation

use of org.mitre.synthea.world.concepts.HealthRecord.Observation in project synthea by synthetichealth.

the class FhirDstu2 method report.

/**
 * Map the given Report to a FHIR DiagnosticReport resource, and add it to the given Bundle.
 *
 * @param rand
 *          Source of randomness to use when generating ids etc
 * @param personEntry
 *          The Entry for the Person
 * @param bundle
 *          Bundle to add the Report to
 * @param encounterEntry
 *          Current Encounter entry
 * @param report
 *          The Report
 * @return The added Entry
 */
private static Entry report(RandomNumberGenerator rand, Entry personEntry, Bundle bundle, Entry encounterEntry, Report report) {
    DiagnosticReport reportResource = new DiagnosticReport();
    reportResource.setStatus(DiagnosticReportStatusEnum.FINAL);
    /*
     * Technically, the CodeableConcept system should be "http://hl7.org/fhir/v2/0074"
     * But the official Argonauts profiles incorrectly list the category pattern as
     * the ValueSet (which contains the above system) as
     * "http://hl7.org/fhir/ValueSet/diagnostic-service-sections", so we repeat the
     * error here.
     */
    CodeableConceptDt category = new CodeableConceptDt("http://hl7.org/fhir/ValueSet/diagnostic-service-sections", "LAB");
    reportResource.setCategory(category);
    reportResource.setCode(mapCodeToCodeableConcept(report.codes.get(0), LOINC_URI));
    reportResource.setSubject(new ResourceReferenceDt(personEntry.getFullUrl()));
    reportResource.setEncounter(new ResourceReferenceDt(encounterEntry.getFullUrl()));
    reportResource.setEffective(convertFhirDateTime(report.start, true));
    reportResource.setIssued(new InstantDt(new Date(report.start)));
    ca.uhn.fhir.model.dstu2.resource.Encounter encounter = (ca.uhn.fhir.model.dstu2.resource.Encounter) encounterEntry.getResource();
    reportResource.setPerformer(encounter.getServiceProvider());
    for (Observation observation : report.observations) {
        ResourceReferenceDt reference = new ResourceReferenceDt(observation.fullUrl);
        reference.setDisplay(observation.codes.get(0).display);
        List<ResourceReferenceDt> result = new ArrayList<ResourceReferenceDt>();
        result.add(reference);
        reportResource.setResult(result);
    }
    return newEntry(rand, bundle, reportResource);
}