// Load MDHT CDA packages. Otherwise ContinuityOfCareDocument and similar documents will not be recognised.
// This has to be called before loading the document; otherwise will have no effect.
CDAUtil.loadPackages();

// Read a Continuity of Care Document (CCD) instance, which is the official sample CCD instance
// distributed with C-CDA 2.1 specs, with a few extensions for having a more complete document
FileInputStream fis = new FileInputStream("src/test/resources/C-CDA_R2-1_CCD.xml");
ClinicalDocument cda = CDAUtil.load(fis);

// Init an object of CCDTransformerImpl class, which implements the generic ICDATransformer interface.
// FHIR resource id generator can be either an incremental counter, or a UUID generator.
// The default is UUID; here it is set as COUNTER.
ICDATransformer ccdTransformer = new CCDTransformerImpl(IdGeneratorEnum.COUNTER);

// By default, FHIR DSTU2 resources are generated by setting the appropriate DAF profile URLs
// in meta.profile attribute of resources. This is configurable through the statically (i.e. globally)
// managed Config class, and can be turned on or off.
Config.setGenerateDafProfileMetadata(true);

// By default, html formatted narratives are generated in text.div attributes of FHIR DSTU2 resources,
// thanks to the automated narrative generation capability of HAPI that is enabled via thymeleaf library.
// This is configurable through the statically managed Config class, and can be turned on or off.
Config.setGenerateNarrative(true);

// Finally, the CCD document instance is transformed to a FHIR Bundle, where the first entry is
// the Composition corresponding to the ClinicalDocument, and further entries are the ones referenced
// from the Composition.
Bundle bundle = ccdTransformer.transformDocument(cda);

// Through HAPI library, the Bundle can easily be printed in JSON or XML format.
FHIRUtil.printJSON(bundle, "src/test/resources/output/C-CDA_R2-1_CCD-w-daf.json");

// Init an object of ResourceTransformerImpl class, which implements the IResourceTransformer
// interface. When instantiated separately from the CDATransformer context, FHIR resources are
// generated with UUID ids, and a default patient reference is added as "Patient/0"
IResourceTransformer resTransformer = new ResourceTransformerImpl();

// Configuration of DAF profile URL creation in meta.profile and narrative generation in text.div is
// again configurable through the statically managed Config class.
Config.setGenerateDafProfileMetadata(true);
Config.setGenerateNarrative(false);

// Assume we already have a CCD instance in the ccd object below (skipping CDA artifact creation from scratch)
// Traverse all the sections of the CCD instance
for(Section cdaSec: ccd.getSections()) {
    // Transform a CDA section to a FHIR Composition.Section backbone resource
    Composition.Section fhirSec = resTransformer.tSection2Section(cdaSec);

    // if a CDA section is instance of a Family History Section (as identified through its templateId)
    if(cdaSec instanceof FamilyHistorySection) {
        // cast the section to FamilyHistorySection
        FamilyHistorySection famSec = (FamilyHistorySection) cdaSec;
        // traverse the Family History Organizers within the Family History Section
        for(FamilyHistoryOrganizer fhOrganizer : famSec.getFamilyHistories()) {
            // Transform each C-CDA FamilyHistoryOrganizer instance to FHIR (DAF) FamilyMemberHistory instance
            FamilyMemberHistory fmh = resTransformer.tFamilyHistoryOrganizer2FamilyMemberHistory(fhOrganizer);
        }
    }
}

// Again, any FHIR resource can be printed through FHIRUtil methods.
FHIRUtil.printXML(fmh, "src/test/resources/output/family-member-history.xml");

// Init an object of ValidatorImpl class, which implements the IValidator interface.
IValidator validator = new ValidatorImpl();

// Assume we already have a Bundle object to be validated at hand. Call the validateBundle method
// of the validator and get the validation outcome as HTML in a ByteArrayOutputStream.
ByteArrayOutputStream valOutcomeOs = (ByteArrayOutputStream) validator.validateBundle(bundle);

// The HTML can be printed to a file.
FileOutputStream fos = new FileOutputStream(new File("src/test/resources/output/validation-result-w-profile-for-C-CDA_R2-1_CCD.html"));
valOutcomeOs.writeTo(fos);

// Close the streams
valOutcomeOs.close();
fos.close();