Examples with State org.mitre.synthea.engine.State used on opensource projects

Example 6 with State

use of org.mitre.synthea.engine.State 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 7 with State

use of org.mitre.synthea.engine.State in project synthea by synthetichealth.

the class FHIRSTU3ExporterTest method testObservationAttachment.

@Test
public void testObservationAttachment() 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("Pulmonary Resistance", 0.1552);
    person.attributes.put("BMI Multiplier", 0.055);
    person.setVitalSign(VitalSign.BMI, 21.0);
    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 physiology = module.getState("Simulate_CVS");
    assertTrue(physiology.process(person, time));
    person.history.add(physiology);
    State encounter = module.getState("SomeEncounter");
    assertTrue(encounter.process(person, time));
    person.history.add(encounter);
    State chartState = module.getState("ChartObservation");
    assertTrue(chartState.process(person, time));
    person.history.add(chartState);
    State urlState = module.getState("UrlObservation");
    assertTrue(urlState.process(person, time));
    person.history.add(urlState);
    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 Media) {
            Media media = (Media) entry.getResource();
            if (media.getContent().getData() != null) {
                assertEquals(400, media.getWidth());
                assertEquals(200, media.getHeight());
                assertEquals("Invasive arterial pressure", media.getReasonCode().get(0).getText());
                assertTrue(Base64.isBase64(media.getContent().getDataElement().getValueAsString()));
            } else if (media.getContent().getUrl() != null) {
                assertEquals("https://example.com/image/12498596132", media.getContent().getUrl());
                assertEquals("en-US", media.getContent().getLanguage());
                assertTrue(media.getContent().getSize() > 0);
            } else {
                fail("Invalid Media element in output JSON");
            }
        }
    }
}

Example 8 with State

use of org.mitre.synthea.engine.State in project synthea by synthetichealth.

the class ValueSetCodeResolverTest method resolveCodesInImagingStudy.

@Test
public void resolveCodesInImagingStudy() throws Exception {
    // We load the imaging study from a module fixture, as there doesn't seem to be
    // a way to
    // instantiate it programmatically.
    Module module = TestHelper.getFixture("imaging_study_with_valueset.json");
    person.history = new ArrayList<>();
    State encounterState = module.getState("ED_Visit");
    assertTrue(encounterState.process(person, time));
    person.history.add(encounterState);
    State mri = module.getState("Knee_MRI");
    assertTrue(mri.process(person, time));
    ValueSetCodeResolver valueSetCodeResolver = new ValueSetCodeResolver(person);
    Person resolvedPerson = valueSetCodeResolver.resolve();
    // assertEquals(2, resolvedPerson.record.encounters.size());
    Encounter resolvedEncounter = resolvedPerson.record.encounters.get(resolvedPerson.record.encounters.size() - 1);
    assertEquals(1, resolvedEncounter.imagingStudies.size());
    ImagingStudy resolvedImagingStudy = resolvedEncounter.imagingStudies.get(0);
    assertEquals(1, resolvedImagingStudy.series.size());
    Series series = resolvedImagingStudy.series.get(0);
    assertEquals(SNOMED_URI, series.bodySite.system);
    assertEquals("762879008", series.bodySite.code);
    assertEquals("Structure of right common peroneal nerve in popliteal region", series.bodySite.display);
// Modality and SOP class are not really good candidates for ValueSet-based
// selection, so we do
// not currently have a sensible test case for these.
}

Example 9 with State

use of org.mitre.synthea.engine.State in project synthea by synthetichealth.

the class ValueSetCodeResolverTest method handlesNullCodesInImagingStudy.

@Test
public void handlesNullCodesInImagingStudy() throws Exception {
    // We load the imaging study from a module fixture, as there doesn't seem to be
    // a way to
    // instantiate it programmatically.
    Module module = TestHelper.getFixture("imaging_study_with_valueset.json");
    person.history = new ArrayList<>();
    State encounterState = module.getState("ED_Visit");
    assertTrue(encounterState.process(person, time));
    person.history.add(encounterState);
    State mri = module.getState("Knee_MRI");
    assertTrue(mri.process(person, time));
    Encounter imagingEncounter = person.record.encounters.get(person.record.encounters.size() - 1);
    imagingEncounter.imagingStudies.get(0).series.get(0).instances.set(0, null);
    ValueSetCodeResolver valueSetCodeResolver = new ValueSetCodeResolver(person);
    valueSetCodeResolver.resolve();
    imagingEncounter.imagingStudies.get(0).series.set(0, null);
    valueSetCodeResolver = new ValueSetCodeResolver(person);
    valueSetCodeResolver.resolve();
}

Example 10 with State

use of org.mitre.synthea.engine.State in project synthea by synthetichealth.

the class TransitionMetrics method recordStats.

/**
 * Record all appropriate state transition information from the given person.
 *
 * @param person
 *          Person that went through the modules
 * @param simulationEnd
 *          Date the simulation ended
 * @param modules
 *          The collection of modules to record stats for
 */
@SuppressWarnings("unchecked")
public void recordStats(Person person, long simulationEnd, Collection<Module> modules) {
    for (Module m : modules) {
        if (!m.getClass().equals(Module.class)) {
            // java module, not GMF. no states to show
            continue;
        }
        List<State> history = (List<State>) person.attributes.get(m.name);
        if (history == null) {
            continue;
        }
        // count basic "counter" stats for this state
        history.forEach(s -> countStateStats(s, getMetric(m.name, s.name), simulationEnd));
        // count this person only once for each distinct state they hit
        history.stream().map(s -> s.name).distinct().forEach(sName -> getMetric(m.name, sName).population.incrementAndGet());
        getMetric(m.name, history.get(0).name).current.incrementAndGet();
        // and track from->to stats in pair
        if (history.size() >= 2) {
            for (int fromIndex = history.size() - 1; fromIndex > 0; fromIndex--) {
                int toIndex = fromIndex - 1;
                State from = history.get(fromIndex);
                State to = history.get(toIndex);
                getMetric(m.name, from.name).incrementDestination(to.name);
            }
        }
    }
}