org.hl7.fhir.dstu3.model.Condition Java Examples

@Test
public void convertCondition20() throws IOException {
	// condition format of HAPI FHIR 2.0
	String oldContent = AllTests.getResourceAsString("/rsc/json/ConditionFormat20.json");
	assertFalse(FindingsFormatUtil.isCurrentFindingsFormat(oldContent));

	Optional<String> newContent = FindingsFormatUtil.convertToCurrentFindingsFormat(oldContent);
	assertTrue(newContent.isPresent());

	IBaseResource resource = AllTests.getJsonParser().parseResource(newContent.get());
	assertTrue(resource instanceof Condition);
	Condition condition = (Condition) resource;

	// category changed from diagnosis to problem-list-item
	List<CodeableConcept> category = condition.getCategory();
	assertFalse(category.isEmpty());
	CodeableConcept code = category.get(0);
	List<Coding> coding = code.getCoding();
	assertFalse(coding.isEmpty());
	assertTrue(coding.get(0).getCode().equals(ConditionCategory.PROBLEMLISTITEM.getCode()));
	// dateRecorded changed to assertedDate
	Date assertedDate = condition.getAssertedDate();
	assertNotNull(assertedDate);
}
 

/**
 * Helper to get a readable string representation of an Observation's type.
 * 
 * @param observation The observation to get the type from
 * @return A human-readable string representation of the type of observation.value
 */
public static String getObservationType(Observation observation) {
  String type = null;
  
  if (observation.value instanceof Condition) {
    type = "text";
  } else if (observation.value instanceof Code) {
    type = "text";
  } else if (observation.value instanceof String) {
    type = "text";
  } else if (observation.value instanceof Double) {
    type = "numeric";
  } else if (observation.value != null) {
    type = "text";
  }
  
  return type;
}
 

/**
 * Helper to get a readable string representation of an Observation's value.
 * Units are not included.
 * 
 * @param observation The observation to get the value from
 * @return A human-readable string representation of observation.value
 */
public static String getObservationValue(Observation observation) {
  String value = null;
  
  if (observation.value instanceof Condition) {
    Code conditionCode = ((HealthRecord.Entry)observation.value).codes.get(0); 
    value = conditionCode.display;
  } else if (observation.value instanceof Code) {
    value = ((Code)observation.value).display;
  } else if (observation.value instanceof String) {
    value = (String)observation.value;
  } else if (observation.value instanceof Double) {
    // round to 1 decimal place for display
    value = String.format(Locale.US, "%.1f", observation.value);
  } else if (observation.value instanceof SampledData) {
    value = sampledDataToValueString((SampledData) observation.value);
  } else if (observation.value instanceof Attachment) {
    value = attachmentToValueString((Attachment) observation.value);
  } else if (observation.value != null) {
    value = observation.value.toString();
  }

  return value;
}
 

@Create
public MethodOutcome create(HttpServletRequest theRequest, @ResourceParam Condition condition) {

	resourcePermissionProvider.checkPermission("create");
    MethodOutcome method = new MethodOutcome();
    method.setCreated(true);
    OperationOutcome opOutcome = new OperationOutcome();

    method.setOperationOutcome(opOutcome);

    try {
    Condition newCondition = conditionDao.create(ctx,condition, null,null);
    method.setId(newCondition.getIdElement());
    method.setResource(newCondition);
    } catch (BaseServerResponseException srv) {
        // HAPI Exceptions pass through
        throw srv;
    } catch(Exception ex) {
        ProviderResponseLibrary.handleException(method,ex);
    }

    return method;
}
 

@Update
public MethodOutcome update(HttpServletRequest theRequest, @ResourceParam Condition condition, @IdParam IdType theId, @ConditionalUrlParam String theConditional, RequestDetails theRequestDetails) {
	resourcePermissionProvider.checkPermission("update");

    MethodOutcome method = new MethodOutcome();
    method.setCreated(true);
    OperationOutcome opOutcome = new OperationOutcome();

    method.setOperationOutcome(opOutcome);

    try {
        Condition newCondition = conditionDao.create(ctx, condition, theId, theConditional);
        method.setId(newCondition.getIdElement());
        method.setResource(newCondition);
    } catch (BaseServerResponseException srv) {
        // HAPI Exceptions pass through
        throw srv;
    } catch(Exception ex) {
        ProviderResponseLibrary.handleException(method,ex);
    }


    return method;
}
 

@Test
public void getGetConditions() {

  Dataset<Row> conditions = bundles.extractEntry(spark,
      bundlesRdd,
      Condition.class);

  Assert.assertEquals(5, conditions.count());
}
 

static Type mapValueToFHIRType(Object value, String unit) {
  if (value == null) {
    return null;

  } else if (value instanceof Condition) {
    Code conditionCode = ((HealthRecord.Entry) value).codes.get(0);
    return mapCodeToCodeableConcept(conditionCode, SNOMED_URI);

  } else if (value instanceof Code) {
    return mapCodeToCodeableConcept((Code) value, SNOMED_URI);

  } else if (value instanceof String) {
    return new StringType((String) value);

  } else if (value instanceof Number) {
    double dblVal = ((Number) value).doubleValue();
    PlainBigDecimal bigVal = new PlainBigDecimal(dblVal);
    return new Quantity().setValue(bigVal)
        .setCode(unit).setSystem(UNITSOFMEASURE_URI)
        .setUnit(unit);
  } else if (value instanceof Components.SampledData) {
    return mapValueToSampledData((Components.SampledData) value, unit);
  } else {
    throw new IllegalArgumentException("unexpected observation value class: "
        + value.getClass().toString() + "; " + value);
  }
}
 

@Read()
public Condition get(@IdParam IdType conditionId) {

	resourcePermissionProvider.checkPermission("read");
    Condition condition = conditionDao.read(ctx,conditionId);

    if ( condition == null) {
        throw OperationOutcomeFactory.buildOperationOutcomeException(
                new ResourceNotFoundException("No Condition/ " + conditionId.getIdPart()),
                 OperationOutcome.IssueType.NOTFOUND);
    }

    return condition;
}
 

@Search
public List<Condition> search(HttpServletRequest theRequest,
                              @OptionalParam(name = Condition.SP_PATIENT) ReferenceParam patient
        , @OptionalParam(name = Condition.SP_CATEGORY) TokenParam category
        , @OptionalParam(name = Condition.SP_CLINICAL_STATUS) TokenParam clinicalstatus
        , @OptionalParam(name = Condition.SP_ASSERTED_DATE) DateRangeParam asserted
        , @OptionalParam(name = Condition.SP_IDENTIFIER) TokenParam identifier
        , @OptionalParam(name = Condition.SP_RES_ID) StringParam resid
                              ) {
    return conditionDao.search(ctx,patient, category, clinicalstatus, asserted, identifier,resid);
}
 

List<ConditionEntity> searchEntity(FhirContext ctx,
        @OptionalParam(name = Condition.SP_PATIENT) ReferenceParam patient
        , @OptionalParam(name = Condition.SP_CATEGORY) TokenParam category
        , @OptionalParam(name = Condition.SP_CLINICAL_STATUS) TokenParam clinicalstatus
        , @OptionalParam(name = Condition.SP_ASSERTED_DATE) DateRangeParam asserted
        , @OptionalParam(name = Condition.SP_IDENTIFIER) TokenParam identifier
        ,@OptionalParam(name= Condition.SP_RES_ID) StringParam id
);
 

List<Condition> search(FhirContext ctx,

            @OptionalParam(name = Condition.SP_PATIENT) ReferenceParam patient
            , @OptionalParam(name = Condition.SP_CATEGORY) TokenParam category
            , @OptionalParam(name = Condition.SP_CLINICAL_STATUS) TokenParam clinicalstatus
            , @OptionalParam(name = Condition.SP_ASSERTED_DATE) DateRangeParam asserted
            , @OptionalParam(name = Condition.SP_IDENTIFIER) TokenParam identifier
            ,@OptionalParam(name= Condition.SP_RES_ID) StringParam id

    );
 

List<DocumentReferenceEntity> searchEntity(FhirContext ctx,
          @OptionalParam(name = DocumentReference.SP_PATIENT) ReferenceParam patient
        , @OptionalParam(name = Condition.SP_IDENTIFIER) TokenParam identifier
        , @OptionalParam(name = Condition.SP_RES_ID) StringParam id
        , @OptionalParam(name = DocumentReference.SP_TYPE) TokenOrListParam type
        , @OptionalParam(name = DocumentReference.SP_PERIOD)DateRangeParam dateRange
        , @OptionalParam(name = DocumentReference.SP_SETTING) TokenParam setting
);
 

List<DocumentReference> search(FhirContext ctx,

              @OptionalParam(name = Condition.SP_PATIENT) ReferenceParam patient
            , @OptionalParam(name = DocumentReference.SP_IDENTIFIER) TokenParam identifier
            , @OptionalParam(name = DocumentReference.SP_RES_ID) StringParam id
            , @OptionalParam(name = DocumentReference.SP_TYPE) TokenOrListParam type
            , @OptionalParam(name = DocumentReference.SP_PERIOD)DateRangeParam dateRange
            , @OptionalParam(name = DocumentReference.SP_SETTING) TokenParam setting

    );
 

List<CompositionEntity> searchEntity(FhirContext ctx,
          @OptionalParam(name = Composition.SP_PATIENT) ReferenceParam patient
        , @OptionalParam(name = Condition.SP_IDENTIFIER) TokenParam identifier
        , @OptionalParam(name = Condition.SP_RES_ID) StringParam id
        , @OptionalParam(name = Composition.SP_TYPE) TokenParam type
        , @OptionalParam(name = Composition.SP_PERIOD)DateRangeParam dateRange
);
 

List<Composition> search(FhirContext ctx,

              @OptionalParam(name = Condition.SP_PATIENT) ReferenceParam patient
            , @OptionalParam(name = Composition.SP_IDENTIFIER) TokenParam identifier
            , @OptionalParam(name = Composition.SP_RES_ID) StringParam id
            , @OptionalParam(name = Composition.SP_TYPE) TokenParam type
            , @OptionalParam(name = Composition.SP_PERIOD)DateRangeParam dateRange

    );
 

@Test
public void testGetResourcesByClass() {

  Dataset<Row> patients = bundles.extractEntry(spark, bundlesRdd, Patient.class);
  Dataset<Row> conditions = bundles.extractEntry(spark, bundlesRdd, Condition.class);

  checkPatients(patients);
  checkConditions(conditions);
}
 

/**
 * Sets up Spark.
 */
@BeforeClass
public static void setUp() {
  spark = SparkSession.builder()
      .master("local[*]")
      .appName("testing")
      .getOrCreate();

  condition = new Condition();

  condition.setId("Condition/testid");

  conditions = conditionConverter.toDataFrame(spark, ImmutableList.of(condition));
}
 

public ConditionEntity setVerificationStatus(Condition.ConditionVerificationStatus verificationStatus) {
    this.verificationStatus = verificationStatus;
    return this;
}
 

/**
 * Returns a FHIR Condition for testing purposes.
 *
 * @return a FHIR Condition for testing.
 */
public static Condition newCondition() {

  Condition condition = new Condition();

  // Condition based on example from FHIR:
  // https://www.hl7.org/fhir/condition-example.json.html
  condition.setId("Condition/example");

  condition.setLanguage("en_US");

  // Narrative text
  Narrative narrative = new Narrative();
  narrative.setStatusAsString("generated");
  narrative.setDivAsString("This data was generated for test purposes.");
  XhtmlNode node = new XhtmlNode();
  node.setNodeType(NodeType.Text);
  node.setValue("Severe burn of left ear (Date: 24-May 2012)");
  condition.setText(narrative);

  condition.setSubject(new Reference("Patient/12345").setDisplay("Here is a display for you."));

  condition.setVerificationStatus(Condition.ConditionVerificationStatus.CONFIRMED);

  // Condition code
  CodeableConcept code = new CodeableConcept();
  code.addCoding()
      .setSystem("http://snomed.info/sct")
      .setCode("39065001")
      .setDisplay("Severe");
  condition.setSeverity(code);

  // Severity code
  CodeableConcept severity = new CodeableConcept();
  severity.addCoding()
      .setSystem("http://snomed.info/sct")
      .setCode("24484000")
      .setDisplay("Burn of ear")
      .setUserSelected(true);
  condition.setSeverity(severity);

  // Onset date time
  DateTimeType onset = new DateTimeType();
  onset.setValueAsString("2012-05-24");
  condition.setOnset(onset);

  return condition;
}
 

/**
 * Returns a FHIR Condition for testing purposes.
 */
public static Condition newCondition() {

  Condition condition = new Condition();

  // Condition based on example from FHIR:
  // https://www.hl7.org/fhir/condition-example.json.html
  condition.setId("Condition/example");

  condition.setLanguage("en_US");

  // Narrative text
  Narrative narrative = new Narrative();
  narrative.setStatusAsString("generated");
  narrative.setDivAsString("This data was generated for test purposes.");
  XhtmlNode node = new XhtmlNode();
  node.setNodeType(NodeType.Text);
  node.setValue("Severe burn of left ear (Date: 24-May 2012)");
  condition.setText(narrative);

  condition.setSubject(new Reference("Patient/example").setDisplay("Here is a display for you."));

  condition.setVerificationStatus(Condition.ConditionVerificationStatus.CONFIRMED);

  // Condition code
  CodeableConcept code = new CodeableConcept();
  code.addCoding()
      .setSystem("http://snomed.info/sct")
      .setCode("39065001")
      .setDisplay("Severe");
  condition.setSeverity(code);

  // Severity code
  CodeableConcept severity = new CodeableConcept();
  severity.addCoding()
      .setSystem("http://snomed.info/sct")
      .setCode("24484000")
      .setDisplay("Burn of ear")
      .setUserSelected(true);
  condition.setSeverity(severity);

  // Onset date time
  DateTimeType onset = new DateTimeType();
  onset.setValueAsString("2012-05-24");
  condition.setOnset(onset);

  return condition;
}
 

/**
 * Map the given CarePlan to a FHIR CarePlan resource, and add it to the given Bundle.
 *
 * @param personEntry The Entry for the Person
 * @param bundle Bundle to add the CarePlan to
 * @param encounterEntry Current Encounter entry
 * @param carePlan The CarePlan to map to FHIR and add to the bundle
 * @return The added Entry
 */
private static BundleEntryComponent careplan(BundleEntryComponent personEntry, Bundle bundle,
    BundleEntryComponent encounterEntry, CarePlan carePlan) {
  org.hl7.fhir.dstu3.model.CarePlan careplanResource = new org.hl7.fhir.dstu3.model.CarePlan();
  careplanResource.setIntent(CarePlanIntent.ORDER);
  careplanResource.setSubject(new Reference(personEntry.getFullUrl()));
  careplanResource.setContext(new Reference(encounterEntry.getFullUrl()));

  Code code = carePlan.codes.get(0);
  careplanResource.addCategory(mapCodeToCodeableConcept(code, SNOMED_URI));

  CarePlanActivityStatus activityStatus;
  GoalStatus goalStatus;

  Period period = new Period().setStart(new Date(carePlan.start));
  careplanResource.setPeriod(period);
  if (carePlan.stop != 0L) {
    period.setEnd(new Date(carePlan.stop));
    careplanResource.setStatus(CarePlanStatus.COMPLETED);
    activityStatus = CarePlanActivityStatus.COMPLETED;
    goalStatus = GoalStatus.ACHIEVED;
  } else {
    careplanResource.setStatus(CarePlanStatus.ACTIVE);
    activityStatus = CarePlanActivityStatus.INPROGRESS;
    goalStatus = GoalStatus.INPROGRESS;
  }

  if (!carePlan.activities.isEmpty()) {
    for (Code activity : carePlan.activities) {
      CarePlanActivityComponent activityComponent = new CarePlanActivityComponent();
      CarePlanActivityDetailComponent activityDetailComponent =
          new CarePlanActivityDetailComponent();

      activityDetailComponent.setStatus(activityStatus);

      activityDetailComponent.setCode(mapCodeToCodeableConcept(activity, SNOMED_URI));
      activityComponent.setDetail(activityDetailComponent);

      careplanResource.addActivity(activityComponent);
    }
  }

  if (!carePlan.reasons.isEmpty()) {
    // Only one element in list
    Code reason = carePlan.reasons.get(0);
    for (BundleEntryComponent entry : bundle.getEntry()) {
      if (entry.getResource().fhirType().equals("Condition")) {
        Condition condition = (Condition) entry.getResource();
        // Only one element in list
        Coding coding = condition.getCode().getCoding().get(0);
        if (reason.code.equals(coding.getCode())) {
          careplanResource.addAddresses().setReference(entry.getFullUrl());
        }
      }
    }
  }

  for (JsonObject goal : carePlan.goals) {
    BundleEntryComponent goalEntry = caregoal(bundle, goalStatus, goal);
    careplanResource.addGoal().setReference(goalEntry.getFullUrl());
  }

  return newEntry(bundle, careplanResource);
}
 

/**
 * Add a MedicationAdministration if needed for the given medication.
 * 
 * @param personEntry       The Entry for the Person
 * @param bundle            Bundle to add the MedicationAdministration to
 * @param encounterEntry    Current Encounter entry
 * @param medication        The Medication
 * @param medicationRequest The related medicationRequest
 * @return The added Entry
 */
private static BundleEntryComponent medicationAdministration(
    BundleEntryComponent personEntry, Bundle bundle, BundleEntryComponent encounterEntry,
    Medication medication, MedicationRequest medicationRequest) {

  MedicationAdministration medicationResource = new MedicationAdministration();

  medicationResource.setSubject(new Reference(personEntry.getFullUrl()));
  medicationResource.setContext(new Reference(encounterEntry.getFullUrl()));

  Code code = medication.codes.get(0);
  String system = code.system.equals("SNOMED-CT") ? SNOMED_URI : RXNORM_URI;

  medicationResource.setMedication(mapCodeToCodeableConcept(code, system));
  medicationResource.setEffective(new DateTimeType(new Date(medication.start)));

  medicationResource.setStatus(MedicationAdministrationStatus.fromCode("completed"));

  if (medication.prescriptionDetails != null) {
    JsonObject rxInfo = medication.prescriptionDetails;
    MedicationAdministrationDosageComponent dosage =
        new MedicationAdministrationDosageComponent();

    // as_needed is true if present
    if ((rxInfo.has("dosage")) && (!rxInfo.has("as_needed"))) {
      Quantity dose = new SimpleQuantity().setValue(
          rxInfo.get("dosage").getAsJsonObject().get("amount").getAsDouble());
      dosage.setDose((SimpleQuantity) dose);

      if (rxInfo.has("instructions")) {
        for (JsonElement instructionElement : rxInfo.get("instructions").getAsJsonArray()) {
          JsonObject instruction = instructionElement.getAsJsonObject();

          dosage.setText(instruction.get("display").getAsString());
        }
      }
    }
    medicationResource.setDosage(dosage);
  }

  if (!medication.reasons.isEmpty()) {
    // Only one element in list
    Code reason = medication.reasons.get(0);
    for (BundleEntryComponent entry : bundle.getEntry()) {
      if (entry.getResource().fhirType().equals("Condition")) {
        Condition condition = (Condition) entry.getResource();
        // Only one element in list
        Coding coding = condition.getCode().getCoding().get(0);
        if (reason.code.equals(coding.getCode())) {
          medicationResource.addReasonReference().setReference(entry.getFullUrl());
        }
      }
    }
  }

  BundleEntryComponent medicationAdminEntry = newEntry(bundle, medicationResource);
  return medicationAdminEntry;
}
 

@Validate
public MethodOutcome testResource(@ResourceParam Condition resource,
                              @Validate.Mode ValidationModeEnum theMode,
                              @Validate.Profile String theProfile) {
    return resourceTestProvider.testResource(resource,theMode,theProfile);
}
 

@Validate
public MethodOutcome testResource(@ResourceParam Condition resource,
                              @Validate.Mode ValidationModeEnum theMode,
                              @Validate.Profile String theProfile) {
    return resourceTestProvider.testResource(resource,theMode,theProfile);
}
 

@Override
public Class<? extends IBaseResource> getResourceType() {
    return Condition.class;
}
 

public Condition.ConditionClinicalStatus getClinicalStatus() {
    return clinicalStatus;
}
 

public ConditionEntity setClinicalStatus(Condition.ConditionClinicalStatus clinicalStatus) {
    this.clinicalStatus = clinicalStatus;
    return this;
}
 

public Condition.ConditionVerificationStatus getVerificationStatus() {
    return verificationStatus;
}
 

@Test
public void bundleToJson() {

  String jsonBundle = Functions.toJsonBundle(conditions, "Condition");

  Bundle bundle = (Bundle) CONTEXT.newJsonParser().parseResource(jsonBundle);

  Condition parsedCondition = (Condition) bundle.getEntryFirstRep().getResource();

  Assert.assertEquals(condition.getId(), parsedCondition.getId());
}
 

@Test
public void resourceToJson() {

  Dataset<String> jsonDs = Functions.toJson(conditions, "Condition");

  String conditionJson = jsonDs.first();

  Condition parsedCondition = (Condition) CONTEXT.newJsonParser()
      .parseResource(conditionJson);

  Assert.assertEquals(condition.getId(), parsedCondition.getId());
}