Examples with Attachment org.mitre.synthea.engine.Components.Attachment used on opensource projects

Example 1 with Attachment

use of org.mitre.synthea.engine.Components.Attachment 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 Attachment

use of org.mitre.synthea.engine.Components.Attachment 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 3 with Attachment

use of org.mitre.synthea.engine.Components.Attachment in project synthea by synthetichealth.

the class FhirDstu2 method media.

/**
 * Map the given Media element to a FHIR Media 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 Media to
 * @param encounterEntry Current Encounter entry
 * @param obs   The Observation to map to FHIR and add to the bundle
 * @return The added Entry
 */
private static Entry media(RandomNumberGenerator rand, Entry personEntry, Bundle bundle, Entry encounterEntry, Observation obs) {
    ca.uhn.fhir.model.dstu2.resource.Media mediaResource = new ca.uhn.fhir.model.dstu2.resource.Media();
    // Hard code as a photo
    mediaResource.setType(DigitalMediaTypeEnum.PHOTO);
    mediaResource.setSubject(new ResourceReferenceDt(personEntry.getFullUrl()));
    Attachment content = (Attachment) obs.value;
    ca.uhn.fhir.model.dstu2.composite.AttachmentDt contentResource = new ca.uhn.fhir.model.dstu2.composite.AttachmentDt();
    contentResource.setContentType(content.contentType);
    contentResource.setLanguage(content.language);
    if (content.data != null) {
        ca.uhn.fhir.model.primitive.Base64BinaryDt data = new ca.uhn.fhir.model.primitive.Base64BinaryDt();
        data.setValueAsString(content.data);
        contentResource.setData(data);
    }
    contentResource.setUrl(content.url);
    contentResource.setSize(content.size);
    contentResource.setTitle(content.title);
    if (content.hash != null) {
        ca.uhn.fhir.model.primitive.Base64BinaryDt hash = new ca.uhn.fhir.model.primitive.Base64BinaryDt();
        hash.setValueAsString(content.hash);
        contentResource.setHash(hash);
    }
    mediaResource.setWidth(content.width);
    mediaResource.setHeight(content.height);
    mediaResource.setContent(contentResource);
    return newEntry(rand, bundle, mediaResource);
}

Example 4 with Attachment

use of org.mitre.synthea.engine.Components.Attachment in project synthea by synthetichealth.

the class StateTest method observation.

@Test
public void observation() throws Exception {
    Module module = TestHelper.getFixture("observation.json");
    State vitalsign = module.getState("VitalSign");
    assertTrue(vitalsign.process(person, time));
    person.history.add(vitalsign);
    State encounter = module.getState("SomeEncounter");
    assertTrue(encounter.process(person, time));
    person.history.add(encounter);
    State physiology = module.getState("Simulate_CVS");
    assertTrue(physiology.process(person, time));
    person.history.add(physiology);
    State vitalObs = module.getState("VitalSignObservation");
    assertTrue(vitalObs.process(person, time));
    State codeObs = module.getState("CodeObservation");
    assertTrue(codeObs.process(person, time));
    State sampleObs = module.getState("SampledDataObservation");
    assertTrue(sampleObs.process(person, time));
    State chartObs = module.getState("ChartObservation");
    assertTrue(chartObs.process(person, time));
    State urlObs = module.getState("UrlObservation");
    assertTrue(urlObs.process(person, time));
    HealthRecord.Observation vitalObservation = person.record.encounters.get(0).observations.get(0);
    assertEquals(120.0, vitalObservation.value);
    assertEquals("vital-signs", vitalObservation.category);
    assertEquals("mm[Hg]", vitalObservation.unit);
    Code vitalObsCode = vitalObservation.codes.get(0);
    assertEquals("8480-6", vitalObsCode.code);
    assertEquals("Systolic Blood Pressure", vitalObsCode.display);
    HealthRecord.Observation codeObservation = person.record.encounters.get(0).observations.get(1);
    assertEquals("procedure", codeObservation.category);
    // assertEquals("LOINC", codeObservation.value.system);
    // assertEquals("25428-4", codeObservation.value.code);
    // assertEquals("Glucose [Presence] in Urine by Test strip", codeObservation.value.system);
    Code testCode = new Code("LOINC", "25428-4", "Glucose [Presence] in Urine by Test strip");
    assertEquals(testCode.toString(), codeObservation.value.toString());
    Code codeObsCode = codeObservation.codes.get(0);
    assertEquals("24356-8", codeObsCode.code);
    assertEquals("Urinalysis complete panel - Urine", codeObsCode.display);
    HealthRecord.Observation sampleObservation = person.record.encounters.get(0).observations.get(2);
    assertEquals("procedure", sampleObservation.category);
    assertEquals("mmHg", sampleObservation.unit);
    assertTrue(sampleObservation.value instanceof SampledData);
    SampledData sampledData = (SampledData) sampleObservation.value;
    assertEquals("P_ao", sampledData.attributes.get(0));
    assertEquals("P_lv", sampledData.attributes.get(1));
    assertEquals("P_rv", sampledData.attributes.get(2));
    assertEquals(3, sampledData.series.size());
    HealthRecord.Observation chartObservation = person.record.encounters.get(0).observations.get(3);
    assertTrue(chartObservation.value instanceof Attachment);
    Attachment obsAttachment = (Attachment) chartObservation.value;
    assertEquals("Media Test", obsAttachment.title);
    assertEquals(400, obsAttachment.width);
    assertEquals(200, obsAttachment.height);
    assertEquals("image/png", obsAttachment.contentType);
    assertTrue(Base64.isBase64(obsAttachment.data));
    HealthRecord.Observation urlObservation = person.record.encounters.get(0).observations.get(4);
    assertTrue(urlObservation.value instanceof Attachment);
    Attachment urlAttachment = (Attachment) urlObservation.value;
    assertEquals("Test Image URL", urlAttachment.title);
    assertEquals("66bb1cb31c9b502daa7081ae36631f9df9c6d16a", urlAttachment.hash);
    assertEquals("en-US", urlAttachment.language);
    assertEquals("https://example.com/image/12498596132", urlAttachment.url);
}

Example 5 with Attachment

use of org.mitre.synthea.engine.Components.Attachment in project synthea by synthetichealth.

the class FhirR4 method media.

/**
 * Map the given Observation with attachment element to a FHIR Media 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 Media to
 * @param encounterEntry Current Encounter entry
 * @param obs   The Observation to map to FHIR and add to the bundle
 * @return The added Entry
 */
private static BundleEntryComponent media(RandomNumberGenerator rand, BundleEntryComponent personEntry, Bundle bundle, BundleEntryComponent encounterEntry, Observation obs) {
    org.hl7.fhir.r4.model.Media mediaResource = new org.hl7.fhir.r4.model.Media();
    // Hard code as Image since we don't anticipate using video or audio any time soon
    Code mediaType = new Code("http://terminology.hl7.org/CodeSystem/media-type", "image", "Image");
    if (obs.codes != null && obs.codes.size() > 0) {
        List<CodeableConcept> reasonList = obs.codes.stream().map(code -> mapCodeToCodeableConcept(code, SNOMED_URI)).collect(Collectors.toList());
        mediaResource.setReasonCode(reasonList);
    }
    mediaResource.setType(mapCodeToCodeableConcept(mediaType, MEDIA_TYPE_URI));
    mediaResource.setStatus(MediaStatus.COMPLETED);
    mediaResource.setSubject(new Reference(personEntry.getFullUrl()));
    mediaResource.setEncounter(new Reference(encounterEntry.getFullUrl()));
    Attachment content = (Attachment) obs.value;
    org.hl7.fhir.r4.model.Attachment contentResource = new org.hl7.fhir.r4.model.Attachment();
    contentResource.setContentType(content.contentType);
    contentResource.setLanguage(content.language);
    if (content.data != null) {
        contentResource.setDataElement(new org.hl7.fhir.r4.model.Base64BinaryType(content.data));
    } else {
        contentResource.setSize(content.size);
    }
    contentResource.setUrl(content.url);
    contentResource.setTitle(content.title);
    if (content.hash != null) {
        contentResource.setHashElement(new org.hl7.fhir.r4.model.Base64BinaryType(content.hash));
    }
    mediaResource.setWidth(content.width);
    mediaResource.setHeight(content.height);
    mediaResource.setContent(contentResource);
    return newEntry(rand, bundle, mediaResource);
}