Examples with StructureMapUtilities org.hl7.fhir.r4.utils.StructureMapUtilities used on opensource projects

Example 16 with StructureMapUtilities

use of org.hl7.fhir.r4.utils.StructureMapUtilities in project org.hl7.fhir.core by hapifhir.

the class StructureMapTests method testLoadCDA.

@Test
public void testLoadCDA() throws FileNotFoundException, Exception {
    Map<String, StructureMap> maps = new HashMap<String, StructureMap>();
    if (TestingUtilities.context == null)
        TestingUtilities.context = SimpleWorkerContext.fromPack("C:\\work\\org.hl7.fhir\\build\\publish\\validation-min.xml.zip");
    StructureMapUtilities scu = new StructureMapUtilities(TestingUtilities.context, maps, null);
    for (String f : new File("C:\\work\\org.hl7.fhir\\build\\guides\\ccda\\CDA").list()) {
        try {
            StructureDefinition sd = (StructureDefinition) new XmlParser().parse(new FileInputStream("C:\\work\\org.hl7.fhir\\build\\guides\\ccda\\CDA\\" + f));
            ((SimpleWorkerContext) TestingUtilities.context).seeResource(sd.getUrl(), sd);
        } catch (Exception e) {
        }
    }
    for (String f : new File("C:\\work\\org.hl7.fhir\\build\\guides\\ccda\\maps").list()) {
        try {
            StructureMap map = scu.parse(TextFile.fileToString("C:\\work\\org.hl7.fhir\\build\\guides\\ccda\\maps\\" + f));
            maps.put(map.getUrl(), map);
        } catch (Exception e) {
        }
    }
    Element cda = Manager.parse(TestingUtilities.context, new FileInputStream("C:\\work\\org.hl7.fhir\\build\\guides\\ccda\\Example\\ccd.xml"), FhirFormat.XML);
    Manager.compose(TestingUtilities.context, cda, new FileOutputStream("C:\\work\\org.hl7.fhir\\build\\guides\\ccda\\Example\\ccd.out.json"), FhirFormat.JSON, OutputStyle.PRETTY, null);
    Manager.compose(TestingUtilities.context, cda, new FileOutputStream("C:\\work\\org.hl7.fhir\\build\\guides\\ccda\\Example\\ccd.out.xml"), FhirFormat.XML, OutputStyle.PRETTY, null);
    Bundle bundle = new Bundle();
    scu.transform(null, cda, maps.get("http://hl7.org/fhir/StructureMap/cda"), bundle);
    new XmlParser().setOutputStyle(OutputStyle.PRETTY).compose(new FileOutputStream(Utilities.path("[tmp]", "bundle.xml")), bundle);
}

Example 17 with StructureMapUtilities

use of org.hl7.fhir.r4.utils.StructureMapUtilities in project org.hl7.fhir.core by hapifhir.

the class R2R3ConversionManager method prepare.

private void prepare() throws FHIRException {
    if (contextR2 == null)
        throw new FHIRException("No R2 definitions provided");
    if (contextR3 == null)
        throw new FHIRException("No R3 definitions provided");
    if (library == null)
        throw new FHIRException("No R2/R# conversion maps provided");
    if (needPrepare) {
        for (StructureDefinition sd : contextR2.allStructures()) {
            StructureDefinition sdn = sd.copy();
            sdn.getExtension().clear();
            contextR3.seeResource(sdn.getUrl(), sdn);
        }
        for (StructureDefinition sd : contextR3.allStructures()) {
            if (sd.getKind() == StructureDefinitionKind.PRIMITIVETYPE) {
                contextR2.seeResource(sd.getUrl(), sd);
                StructureDefinition sdn = sd.copy();
                sdn.setUrl(sdn.getUrl().replace("http://hl7.org/fhir/", "http://hl7.org/fhir/DSTU2/"));
                sdn.addExtension().setUrl("http://hl7.org/fhir/StructureDefinition/elementdefinition-namespace").setValue(new UriType("http://hl7.org/fhir"));
                contextR2.seeResource(sdn.getUrl(), sdn);
                contextR3.seeResource(sdn.getUrl(), sdn);
            }
        }
        contextR2.setExpansionProfile(new ExpansionProfile().setUrl("urn:uuid:" + UUID.randomUUID().toString().toLowerCase()));
        contextR3.setExpansionProfile(new ExpansionProfile().setUrl("urn:uuid:" + UUID.randomUUID().toString().toLowerCase()));
        smu3 = new StructureMapUtilities(contextR3, library, this);
        smu2 = new StructureMapUtilities(contextR2, library, this);
        needPrepare = false;
    }
}

Example 18 with StructureMapUtilities

use of org.hl7.fhir.r4.utils.StructureMapUtilities in project org.hl7.fhir.core by hapifhir.

the class IgLoader method checkFormat.

private Manager.FhirFormat checkFormat(byte[] cnt, String filename) {
    System.out.println("   ..Detect format for " + filename);
    try {
        JsonTrackingParser.parseJson(cnt);
        return Manager.FhirFormat.JSON;
    } catch (Exception e) {
        log("Not JSON: " + e.getMessage());
    }
    try {
        ValidatorUtils.parseXml(cnt);
        return Manager.FhirFormat.XML;
    } catch (Exception e) {
        log("Not XML: " + e.getMessage());
    }
    try {
        new Turtle().parse(TextFile.bytesToString(cnt));
        return Manager.FhirFormat.TURTLE;
    } catch (Exception e) {
        log("Not Turtle: " + e.getMessage());
    }
    try {
        new StructureMapUtilities(getContext(), null, null).parse(TextFile.bytesToString(cnt), null);
        return Manager.FhirFormat.TEXT;
    } catch (Exception e) {
        log("Not Text: " + e.getMessage());
    }
    log("     .. not a resource: " + filename);
    return null;
}

Example 19 with StructureMapUtilities

use of org.hl7.fhir.r4.utils.StructureMapUtilities in project org.hl7.fhir.core by hapifhir.

the class IgLoader method loadResourceByVersion.

public Resource loadResourceByVersion(String fhirVersion, byte[] content, String fn) throws IOException, FHIRException {
    Resource r;
    if (fhirVersion.startsWith("3.0")) {
        org.hl7.fhir.dstu3.model.Resource res;
        if (fn.endsWith(".xml") && !fn.endsWith("template.xml"))
            res = new org.hl7.fhir.dstu3.formats.XmlParser().parse(new ByteArrayInputStream(content));
        else if (fn.endsWith(".json") && !fn.endsWith("template.json"))
            res = new org.hl7.fhir.dstu3.formats.JsonParser().parse(new ByteArrayInputStream(content));
        else if (fn.endsWith(".txt") || fn.endsWith(".map"))
            res = new org.hl7.fhir.dstu3.utils.StructureMapUtilities(null).parse(new String(content));
        else
            throw new FHIRException("Unsupported format for " + fn);
        r = VersionConvertorFactory_30_50.convertResource(res);
    } else if (fhirVersion.startsWith("4.0")) {
        org.hl7.fhir.r4.model.Resource res;
        if (fn.endsWith(".xml") && !fn.endsWith("template.xml"))
            res = new org.hl7.fhir.r4.formats.XmlParser().parse(new ByteArrayInputStream(content));
        else if (fn.endsWith(".json") && !fn.endsWith("template.json"))
            res = new org.hl7.fhir.r4.formats.JsonParser().parse(new ByteArrayInputStream(content));
        else if (fn.endsWith(".txt") || fn.endsWith(".map"))
            res = new org.hl7.fhir.r4.utils.StructureMapUtilities(null).parse(new String(content), fn);
        else
            throw new FHIRException("Unsupported format for " + fn);
        r = VersionConvertorFactory_40_50.convertResource(res);
    } else if (fhirVersion.startsWith("1.4")) {
        org.hl7.fhir.dstu2016may.model.Resource res;
        if (fn.endsWith(".xml") && !fn.endsWith("template.xml"))
            res = new org.hl7.fhir.dstu2016may.formats.XmlParser().parse(new ByteArrayInputStream(content));
        else if (fn.endsWith(".json") && !fn.endsWith("template.json"))
            res = new org.hl7.fhir.dstu2016may.formats.JsonParser().parse(new ByteArrayInputStream(content));
        else
            throw new FHIRException("Unsupported format for " + fn);
        r = VersionConvertorFactory_14_50.convertResource(res);
    } else if (fhirVersion.startsWith("1.0")) {
        org.hl7.fhir.dstu2.model.Resource res;
        if (fn.endsWith(".xml") && !fn.endsWith("template.xml"))
            res = new org.hl7.fhir.dstu2.formats.JsonParser().parse(new ByteArrayInputStream(content));
        else if (fn.endsWith(".json") && !fn.endsWith("template.json"))
            res = new org.hl7.fhir.dstu2.formats.JsonParser().parse(new ByteArrayInputStream(content));
        else
            throw new FHIRException("Unsupported format for " + fn);
        r = VersionConvertorFactory_10_50.convertResource(res, new org.hl7.fhir.convertors.misc.IGR2ConvertorAdvisor5());
    } else if (fhirVersion.equals(Constants.VERSION) || "current".equals(fhirVersion)) {
        if (fn.endsWith(".xml") && !fn.endsWith("template.xml"))
            r = new XmlParser().parse(new ByteArrayInputStream(content));
        else if (fn.endsWith(".json") && !fn.endsWith("template.json"))
            r = new JsonParser().parse(new ByteArrayInputStream(content));
        else if (fn.endsWith(".txt"))
            r = new StructureMapUtilities(getContext(), null, null).parse(TextFile.bytesToString(content), fn);
        else if (fn.endsWith(".map"))
            r = new StructureMapUtilities(null).parse(new String(content), fn);
        else
            throw new FHIRException("Unsupported format for " + fn);
    } else
        throw new FHIRException("Unsupported version " + fhirVersion);
    return r;
}

Example 20 with StructureMapUtilities

use of org.hl7.fhir.r4.utils.StructureMapUtilities in project org.hl7.fhir.core by hapifhir.

the class Transformer method process.

public boolean process() {
    try {
        System.out.println("  .. load definitions from " + definitions);
        IWorkerContext context = SimpleWorkerContext.fromPack(definitions);
        scu = new StructureMapUtilities(context, new HashMap<String, StructureMap>(), null);
        for (String folder : folders) {
            System.out.println("  .. load additional definitions from " + folder);
            ((SimpleWorkerContext) context).loadFromFolder(folder);
            loadMaps(folder);
        }
        System.out.println("  .. load source from " + source);
        Element e = Manager.parse(context, new FileInputStream(source), FhirFormat.XML);
        Bundle bundle = new Bundle();
        StructureMap map = scu.getLibrary().get(mapUri);
        if (map == null)
            throw new Error("Unable to find map " + mapUri + " (Known Maps = " + Utilities.listCanonicalUrls(scu.getLibrary().keySet()) + ")");
        scu.transform(null, e, map, bundle);
        new XmlParser().setOutputStyle(OutputStyle.PRETTY).compose(new FileOutputStream(output), bundle);
        return true;
    } catch (Exception e) {
        e.printStackTrace();
        message = e.getMessage();
        return false;
    }
}