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

@Update
public MethodOutcome update(HttpServletRequest theRequest, @ResourceParam DiagnosticReport diagnosticReport, @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 {
    DiagnosticReport newDiagnosticReport = diagnosticReportDao.create(ctx,diagnosticReport, theId, theConditional);
    method.setId(newDiagnosticReport.getIdElement());
    method.setResource(newDiagnosticReport);
    } catch (Exception ex) {

        ProviderResponseLibrary.handleException(method,ex);
    }


    return method;
}
 

@Create
public MethodOutcome create(HttpServletRequest theRequest, @ResourceParam DiagnosticReport diagnosticReport) {

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

    try {
    DiagnosticReport newDiagnosticReport = diagnosticReportDao.create(ctx,diagnosticReport, null,null);
    method.setId(newDiagnosticReport.getIdElement());
    method.setResource(newDiagnosticReport);
    } catch (Exception ex) {

        ProviderResponseLibrary.handleException(method,ex);
    }


    return method;
}
 

@Search
public List<DiagnosticReport> search(HttpServletRequest theRequest,
                              @OptionalParam(name = DiagnosticReport.SP_PATIENT) ReferenceParam patient
        , @OptionalParam(name = DiagnosticReport.SP_IDENTIFIER) TokenParam identifier
        , @OptionalParam(name = DiagnosticReport.SP_RES_ID) StringParam resid
                              ) {
    return diagnosticReportDao.search(ctx,patient,identifier,resid);
}
 

@Read()
public DiagnosticReport get(@IdParam IdType diagnosticReportId) {
	resourcePermissionProvider.checkPermission("read");
    DiagnosticReport diagnosticReport = diagnosticReportDao.read(ctx,diagnosticReportId);

    if ( diagnosticReport == null) {
        throw OperationOutcomeFactory.buildOperationOutcomeException(
                new ResourceNotFoundException("No DiagnosticReport/ " + diagnosticReportId.getIdPart()),
                 OperationOutcome.IssueType.NOTFOUND);
    }

    return diagnosticReport;
}
 

public boolean generate(ResourceContext rcontext, DomainResource r) throws EOperationOutcome, FHIRException, IOException {
  if (rcontext == null)
    rcontext = new ResourceContext(null, r);
  
  if (r instanceof ConceptMap) {
    return generate(rcontext, (ConceptMap) r); // Maintainer = Grahame
  } else if (r instanceof ValueSet) {
    return generate(rcontext, (ValueSet) r, true); // Maintainer = Grahame
  } else if (r instanceof CodeSystem) {
    return generate(rcontext, (CodeSystem) r, true); // Maintainer = Grahame
  } else if (r instanceof OperationOutcome) {
    return generate(rcontext, (OperationOutcome) r); // Maintainer = Grahame
  } else if (r instanceof CapabilityStatement) {
    return generate(rcontext, (CapabilityStatement) r);   // Maintainer = Grahame
  } else if (r instanceof CompartmentDefinition) {
    return generate(rcontext, (CompartmentDefinition) r);   // Maintainer = Grahame
  } else if (r instanceof OperationDefinition) {
    return generate(rcontext, (OperationDefinition) r);   // Maintainer = Grahame
  } else if (r instanceof StructureDefinition) {
    return generate(rcontext, (StructureDefinition) r);   // Maintainer = Grahame
  } else if (r instanceof ImplementationGuide) {
    return generate(rcontext, (ImplementationGuide) r);   // Maintainer = Lloyd (until Grahame wants to take over . . . :))
  } else if (r instanceof DiagnosticReport) {
    inject(r, generateDiagnosticReport(new ResourceWrapperDirect(r)),  NarrativeStatus.GENERATED);   // Maintainer = Grahame
    return true;
  } else {
    StructureDefinition p = null;
    if (r.hasMeta())
      for (UriType pu : r.getMeta().getProfile())
        if (p == null)
          p = context.fetchResource(StructureDefinition.class, pu.getValue());
    if (p == null)
      p = context.fetchResource(StructureDefinition.class, r.getResourceType().toString());
    if (p == null)
      p = context.fetchTypeDefinition(r.getResourceType().toString().toLowerCase());
    if (p != null)
      return generateByProfile(r, p, true);
    else
      return false;
  }
}
 

public DiagnosticReport.DiagnosticReportStatus getStatus() {
    return status;
}
 

public DiagnosticReportEntity setStatus(DiagnosticReport.DiagnosticReportStatus status) {
    this.status = status;
    return this;
}
 

List<DiagnosticReportEntity> searchEntity(FhirContext ctx,
                                     @OptionalParam(name = DiagnosticReport.SP_PATIENT) ReferenceParam patient
        , @OptionalParam(name = DiagnosticReport.SP_IDENTIFIER) TokenParam identifier
        , @OptionalParam(name = DiagnosticReport.SP_RES_ID) StringParam id
);
 

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

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

@Override
public DiagnosticReport transform(final DiagnosticReportEntity diagnosticReportEntity) {
    final DiagnosticReport diagnosticReport = new DiagnosticReport();

    Meta meta = new Meta();
            //.addProfile(CareConnectProfile.Condition_1);

    if (diagnosticReportEntity.getUpdated() != null) {
        meta.setLastUpdated(diagnosticReportEntity.getUpdated());
    }
    else {
        if (diagnosticReportEntity.getCreated() != null) {
            meta.setLastUpdated(diagnosticReportEntity.getCreated());
        }
    }
    diagnosticReport.setMeta(meta);

    diagnosticReport.setId(diagnosticReportEntity.getId().toString());



    if (diagnosticReportEntity.getStatus() != null) {
        diagnosticReport.setStatus(diagnosticReportEntity.getStatus());
    }

    if (diagnosticReportEntity.getPatient() != null) {
        diagnosticReport
                .setSubject(new Reference("Patient/"+diagnosticReportEntity.getPatient().getId())
                .setDisplay(diagnosticReportEntity.getPatient().getNames().get(0).getDisplayName()));
    }



    for (DiagnosticReportIdentifier identifier : diagnosticReportEntity.getIdentifiers()) {
        Identifier ident = diagnosticReport.addIdentifier();
        ident = daoutils.getIdentifier(identifier, ident);
    }

    for (DiagnosticReportResult reportResult : diagnosticReportEntity.getResults()) {
        diagnosticReport.addResult(new Reference("Observation/"+reportResult.getObservation().getId()));
    }

    return diagnosticReport;

}
 

@Test
public void testFHIRDSTU2Export() throws Exception {
  TestHelper.loadTestProperties();
  Generator.DEFAULT_STATE = Config.get("test_state.default", "Massachusetts");
  Config.set("exporter.baseDirectory", tempFolder.newFolder().toString());

  FhirContext ctx = FhirContext.forDstu2();
  IParser parser = ctx.newJsonParser().setPrettyPrint(true);

  FhirValidator validator = ctx.newValidator();
  validator.setValidateAgainstStandardSchema(true);
  validator.setValidateAgainstStandardSchematron(true);

  List<String> validationErrors = new ArrayList<String>();

  int numberOfPeople = 10;
  Generator generator = new Generator(numberOfPeople);
  generator.options.overflow = false;
  for (int i = 0; i < numberOfPeople; i++) {
    int x = validationErrors.size();
    TestHelper.exportOff();
    Person person = generator.generatePerson(i);
    Config.set("exporter.fhir_dstu2.export", "true");
    FhirDstu2.TRANSACTION_BUNDLE = person.random.nextBoolean();
    String fhirJson = FhirDstu2.convertToFHIRJson(person, System.currentTimeMillis());
    // Check that the fhirJSON doesn't contain unresolved SNOMED-CT strings
    // (these should have been converted into URIs)
    if (fhirJson.contains("SNOMED-CT")) {
      validationErrors.add(
          "JSON contains unconverted references to 'SNOMED-CT' (should be URIs)");
    }
    // Now validate the resource...
    IBaseResource resource = ctx.newJsonParser().parseResource(fhirJson);
    ValidationResult result = validator.validateWithResult(resource);
    if (!result.isSuccessful()) {
      // If the validation failed, let's crack open the Bundle and validate
      // each individual entry.resource to get context-sensitive error
      // messages...
      Bundle bundle = parser.parseResource(Bundle.class, fhirJson);
      for (Entry entry : bundle.getEntry()) {
        ValidationResult eresult = validator.validateWithResult(entry.getResource());
        if (!eresult.isSuccessful()) {
          for (SingleValidationMessage emessage : eresult.getMessages()) {
            System.out.println(parser.encodeResourceToString(entry.getResource()));
            System.out.println("ERROR: " + emessage.getMessage());
            validationErrors.add(emessage.getMessage());
          }
        }
        if (entry.getResource() instanceof DiagnosticReport) {
          DiagnosticReport report = (DiagnosticReport) entry.getResource();
          if (report.getPerformer().isEmpty()) {
            validationErrors.add("Performer is a required field on DiagnosticReport!");
          }
        }
      }
    }
    int y = validationErrors.size();
    if (x != y) {
      Exporter.export(person, System.currentTimeMillis());
    }
  }

  assertTrue("Validation of exported FHIR bundle failed: " 
      + String.join("|", validationErrors), validationErrors.size() == 0);
}
 

List<DiagnosticReport> search(FhirContext ctx,

                             @OptionalParam(name = DiagnosticReport.SP_PATIENT) ReferenceParam patient
            , @OptionalParam(name = DiagnosticReport.SP_IDENTIFIER) TokenParam identifier
            , @OptionalParam(name = DiagnosticReport.SP_RES_ID) StringParam id

    );
 

DiagnosticReport read(FhirContext ctx, IdType theId); 

DiagnosticReport create(FhirContext ctx, DiagnosticReport diagnosticReport, @IdParam IdType theId, @ConditionalUrlParam String theConditional) throws OperationOutcomeException;