Examples with SampledData org.hl7.fhir.r5.model.SampledData used on opensource projects

Example 11 with SampledData

use of org.hl7.fhir.r5.model.SampledData in project org.hl7.fhir.core by hapifhir.

the class ProfileDrivenRenderer method renderLeaf.

private void renderLeaf(ResourceWrapper res, BaseWrapper ew, ElementDefinition defn, XhtmlNode parent, XhtmlNode x, boolean title, boolean showCodeDetails, Map<String, String> displayHints, String path, int indent) throws FHIRException, UnsupportedEncodingException, IOException, EOperationOutcome {
    if (ew == null)
        return;
    Base e = ew.getBase();
    if (e instanceof StringType)
        x.addText(((StringType) e).getValue());
    else if (e instanceof CodeType)
        x.addText(((CodeType) e).getValue());
    else if (e instanceof IdType)
        x.addText(((IdType) e).getValue());
    else if (e instanceof Extension)
        return;
    else if (e instanceof InstantType)
        x.addText(((InstantType) e).toHumanDisplay());
    else if (e instanceof DateTimeType) {
        renderDateTime(x, e);
    } else if (e instanceof Base64BinaryType)
        x.addText(new Base64().encodeAsString(((Base64BinaryType) e).getValue()));
    else if (e instanceof org.hl7.fhir.r5.model.DateType) {
        org.hl7.fhir.r5.model.DateType dt = ((org.hl7.fhir.r5.model.DateType) e);
        renderDate(x, dt);
    } else if (e instanceof Enumeration) {
        Object ev = ((Enumeration<?>) e).getValue();
        // todo: look up a display name if there is one
        x.addText(ev == null ? "" : ev.toString());
    } else if (e instanceof BooleanType) {
        x.addText(((BooleanType) e).getValue().toString());
    } else if (e instanceof CodeableConcept) {
        renderCodeableConcept(x, (CodeableConcept) e, showCodeDetails);
    } else if (e instanceof Coding) {
        renderCoding(x, (Coding) e, showCodeDetails);
    } else if (e instanceof CodeableReference) {
        renderCodeableReference(x, (CodeableReference) e, showCodeDetails);
    } else if (e instanceof Annotation) {
        renderAnnotation(x, (Annotation) e);
    } else if (e instanceof Identifier) {
        renderIdentifier(x, (Identifier) e);
    } else if (e instanceof org.hl7.fhir.r5.model.IntegerType) {
        if (((org.hl7.fhir.r5.model.IntegerType) e).hasValue()) {
            x.addText(Integer.toString(((org.hl7.fhir.r5.model.IntegerType) e).getValue()));
        } else {
            x.addText("??");
        }
    } else if (e instanceof org.hl7.fhir.r5.model.Integer64Type) {
        if (((org.hl7.fhir.r5.model.Integer64Type) e).hasValue()) {
            x.addText(Long.toString(((org.hl7.fhir.r5.model.Integer64Type) e).getValue()));
        } else {
            x.addText("??");
        }
    } else if (e instanceof org.hl7.fhir.r5.model.DecimalType) {
        x.addText(((org.hl7.fhir.r5.model.DecimalType) e).getValue().toString());
    } else if (e instanceof HumanName) {
        renderHumanName(x, (HumanName) e);
    } else if (e instanceof SampledData) {
        renderSampledData(x, (SampledData) e);
    } else if (e instanceof Address) {
        renderAddress(x, (Address) e);
    } else if (e instanceof ContactPoint) {
        renderContactPoint(x, (ContactPoint) e);
    } else if (e instanceof Expression) {
        renderExpression(x, (Expression) e);
    } else if (e instanceof Money) {
        renderMoney(x, (Money) e);
    } else if (e instanceof ContactDetail) {
        ContactDetail cd = (ContactDetail) e;
        if (cd.hasName()) {
            x.tx(cd.getName() + ": ");
        }
        boolean first = true;
        for (ContactPoint c : cd.getTelecom()) {
            if (first)
                first = false;
            else
                x.tx(",");
            renderContactPoint(x, c);
        }
    } else if (e instanceof UriType) {
        renderUri(x, (UriType) e, defn.getPath(), rcontext != null && rcontext.getResourceResource() != null ? rcontext.getResourceResource().getId() : null);
    } else if (e instanceof Timing) {
        renderTiming(x, (Timing) e);
    } else if (e instanceof Range) {
        renderRange(x, (Range) e);
    } else if (e instanceof Quantity) {
        renderQuantity(x, (Quantity) e, showCodeDetails);
    } else if (e instanceof Ratio) {
        renderQuantity(x, ((Ratio) e).getNumerator(), showCodeDetails);
        x.tx("/");
        renderQuantity(x, ((Ratio) e).getDenominator(), showCodeDetails);
    } else if (e instanceof Period) {
        Period p = (Period) e;
        renderPeriod(x, p);
    } else if (e instanceof Reference) {
        Reference r = (Reference) e;
        if (r.getReference() != null && r.getReference().contains("#")) {
            if (containedIds.contains(r.getReference().substring(1))) {
                x.ah(r.getReference()).tx("See " + r.getReference());
            } else {
                // in this case, we render the resource in line
                ResourceWrapper rw = null;
                for (ResourceWrapper t : res.getContained()) {
                    if (r.getReference().substring(1).equals(t.getId())) {
                        rw = t;
                    }
                }
                if (rw == null) {
                    renderReference(res, x, r);
                } else {
                    x.an(rw.getId());
                    ResourceRenderer rr = RendererFactory.factory(rw, context.copy().setAddGeneratedNarrativeHeader(false));
                    rr.render(parent.blockquote(), rw);
                }
            }
        } else {
            renderReference(res, x, r);
        }
    } else if (e instanceof Resource) {
        return;
    } else if (e instanceof DataRequirement) {
        DataRequirement p = (DataRequirement) e;
        renderDataRequirement(x, p);
    } else if (e instanceof PrimitiveType) {
        x.tx(((PrimitiveType) e).primitiveValue());
    } else if (e instanceof ElementDefinition) {
        x.tx("todo-bundle");
    } else if (e != null && !(e instanceof Attachment) && !(e instanceof Narrative) && !(e instanceof Meta)) {
        throw new NotImplementedException("type " + e.getClass().getName() + " not handled - should not be here");
    }
}

Example 12 with SampledData

use of org.hl7.fhir.r5.model.SampledData in project synthea by synthetichealth.

the class FHIRR4ExporterTest method testSampledDataExport.

@Test
public void testSampledDataExport() throws Exception {
    Person person = new Person(0L);
    person.attributes.put(Person.GENDER, "F");
    person.attributes.put(Person.FIRST_LANGUAGE, "spanish");
    person.attributes.put(Person.RACE, "other");
    person.attributes.put(Person.ETHNICITY, "hispanic");
    person.attributes.put(Person.INCOME, Integer.parseInt(Config.get("generate.demographics.socioeconomic.income.poverty")) * 2);
    person.attributes.put(Person.OCCUPATION_LEVEL, 1.0);
    person.attributes.put(Person.CONTACT_EMAIL, "test@test.test");
    person.attributes.put(Person.CONTACT_GIVEN_NAME, "John");
    person.attributes.put(Person.CONTACT_FAMILY_NAME, "Appleseed");
    person.history = new LinkedList<>();
    Provider mock = Mockito.mock(Provider.class);
    Mockito.when(mock.getResourceID()).thenReturn("Mock-UUID");
    person.setProvider(EncounterType.AMBULATORY, mock);
    person.setProvider(EncounterType.WELLNESS, mock);
    person.setProvider(EncounterType.EMERGENCY, mock);
    person.setProvider(EncounterType.INPATIENT, mock);
    Long time = System.currentTimeMillis();
    int age = 35;
    long birthTime = time - Utilities.convertTime("years", age);
    person.attributes.put(Person.BIRTHDATE, birthTime);
    Payer.loadNoInsurance();
    for (int i = 0; i < age; i++) {
        long yearTime = time - Utilities.convertTime("years", i);
        person.coverage.setPayerAtTime(yearTime, Payer.noInsurance);
    }
    Module module = TestHelper.getFixture("observation.json");
    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 sampleObs = module.getState("SampledDataObservation");
    assertTrue(sampleObs.process(person, time));
    person.history.add(sampleObs);
    FhirContext ctx = FhirR4.getContext();
    IParser parser = ctx.newJsonParser().setPrettyPrint(true);
    String fhirJson = FhirR4.convertToFHIRJson(person, System.currentTimeMillis());
    Bundle bundle = parser.parseResource(Bundle.class, fhirJson);
    for (BundleEntryComponent entry : bundle.getEntry()) {
        if (entry.getResource() instanceof Observation) {
            Observation obs = (Observation) entry.getResource();
            assertTrue(obs.getValue() instanceof SampledData);
            SampledData data = (SampledData) obs.getValue();
            // 0.01s == 10ms
            assertEquals(10, data.getPeriod().doubleValue(), 0.001);
            assertEquals(3, (int) data.getDimensions());
        }
    }
}

Example 13 with SampledData

use of org.hl7.fhir.r5.model.SampledData in project synthea by synthetichealth.

the class FHIRSTU3ExporterTest method testSampledDataExport.

@Test
public void testSampledDataExport() throws Exception {
    Person person = new Person(0L);
    person.attributes.put(Person.GENDER, "F");
    person.attributes.put(Person.FIRST_LANGUAGE, "spanish");
    person.attributes.put(Person.RACE, "other");
    person.attributes.put(Person.ETHNICITY, "hispanic");
    person.attributes.put(Person.INCOME, Integer.parseInt(Config.get("generate.demographics.socioeconomic.income.poverty")) * 2);
    person.attributes.put(Person.OCCUPATION_LEVEL, 1.0);
    person.attributes.put(Person.CONTACT_EMAIL, "test@test.test");
    person.attributes.put(Person.CONTACT_GIVEN_NAME, "John");
    person.attributes.put(Person.CONTACT_FAMILY_NAME, "Appleseed");
    person.history = new LinkedList<>();
    Provider mock = Mockito.mock(Provider.class);
    Mockito.when(mock.getResourceID()).thenReturn("Mock-UUID");
    person.setProvider(EncounterType.AMBULATORY, mock);
    person.setProvider(EncounterType.WELLNESS, mock);
    person.setProvider(EncounterType.EMERGENCY, mock);
    person.setProvider(EncounterType.INPATIENT, mock);
    Long time = System.currentTimeMillis();
    int age = 35;
    long birthTime = time - Utilities.convertTime("years", age);
    person.attributes.put(Person.BIRTHDATE, birthTime);
    Payer.loadNoInsurance();
    for (int i = 0; i < age; i++) {
        long yearTime = time - Utilities.convertTime("years", i);
        person.coverage.setPayerAtTime(yearTime, Payer.noInsurance);
    }
    Module module = TestHelper.getFixture("observation.json");
    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 sampleObs = module.getState("SampledDataObservation");
    assertTrue(sampleObs.process(person, time));
    person.history.add(sampleObs);
    FhirContext ctx = FhirStu3.getContext();
    IParser parser = ctx.newJsonParser().setPrettyPrint(true);
    String fhirJson = FhirStu3.convertToFHIRJson(person, System.currentTimeMillis());
    Bundle bundle = parser.parseResource(Bundle.class, fhirJson);
    for (BundleEntryComponent entry : bundle.getEntry()) {
        if (entry.getResource() instanceof Observation) {
            Observation obs = (Observation) entry.getResource();
            assertTrue(obs.getValue() instanceof SampledData);
            SampledData data = (SampledData) obs.getValue();
            // 0.01s == 10ms
            assertEquals(10, data.getPeriod().doubleValue(), 0.001);
            assertEquals(3, (int) data.getDimensions());
        }
    }
}

Example 14 with SampledData

use of org.hl7.fhir.r5.model.SampledData in project synthea by synthetichealth.

the class FhirR4 method mapValueToSampledData.

/**
 * Maps a Synthea internal SampledData object to the FHIR standard SampledData
 * representation.
 *
 * @param value Synthea internal SampledData instance
 * @param unit Observation unit value
 * @return
 */
static org.hl7.fhir.r4.model.SampledData mapValueToSampledData(Components.SampledData value, String unit) {
    org.hl7.fhir.r4.model.SampledData recordData = new org.hl7.fhir.r4.model.SampledData();
    recordData.setOrigin(new Quantity().setValue(value.originValue).setCode(unit).setSystem(UNITSOFMEASURE_URI).setUnit(unit));
    // Use the period from the first series. They should all be the same.
    // FHIR output is milliseconds so we need to convert from TimeSeriesData seconds.
    recordData.setPeriod(value.series.get(0).getPeriod() * 1000);
    // Set optional fields if they were provided
    if (value.factor != null) {
        recordData.setFactor(value.factor);
    }
    if (value.lowerLimit != null) {
        recordData.setLowerLimit(value.lowerLimit);
    }
    if (value.upperLimit != null) {
        recordData.setUpperLimit(value.upperLimit);
    }
    recordData.setDimensions(value.series.size());
    recordData.setData(ExportHelper.sampledDataToValueString(value));
    return recordData;
}

Example 15 with SampledData

use of org.hl7.fhir.r5.model.SampledData in project synthea by synthetichealth.

the class FhirStu3 method mapValueToSampledData.

/**
 * Maps a Synthea internal SampledData object to the FHIR standard SampledData
 * representation.
 *
 * @param value Synthea internal SampledData instance
 * @param unit Observation unit value
 * @return
 */
static org.hl7.fhir.dstu3.model.SampledData mapValueToSampledData(Components.SampledData value, String unit) {
    org.hl7.fhir.dstu3.model.SampledData recordData = new org.hl7.fhir.dstu3.model.SampledData();
    SimpleQuantity origin = new SimpleQuantity();
    origin.setValue(new BigDecimal(value.originValue)).setCode(unit).setSystem(UNITSOFMEASURE_URI).setUnit(unit);
    recordData.setOrigin(origin);
    // Use the period from the first series. They should all be the same.
    // FHIR output is milliseconds so we need to convert from TimeSeriesData seconds.
    recordData.setPeriod(value.series.get(0).getPeriod() * 1000);
    // Set optional fields if they were provided
    if (value.factor != null) {
        recordData.setFactor(value.factor);
    }
    if (value.lowerLimit != null) {
        recordData.setLowerLimit(value.lowerLimit);
    }
    if (value.upperLimit != null) {
        recordData.setUpperLimit(value.upperLimit);
    }
    recordData.setDimensions(value.series.size());
    recordData.setData(ExportHelper.sampledDataToValueString(value));
    return recordData;
}