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

Example 11 with Turtle

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

the class NativeHostServices method unConvertResource.

/**
 * Convert a resource from R4 to the specified version
 *
 * @param r - the source of the resource to convert from
 * @param fmt  - the format of the content. one of XML, JSON, TURTLE
 * @param version - the version to convert to. one of r2, r3
 * @return - the converted resource (or an exception if can't be converted)
 * @throws FHIRException
 * @throws IOException
 */
public byte[] unConvertResource(byte[] r, String fmt, String version) throws FHIRException, IOException {
    try {
        if ("3.0".equals(version) || "3.0.1".equals(version) || "r3".equals(version)) {
            org.hl7.fhir.r5.formats.ParserBase p4 = org.hl7.fhir.r5.formats.FormatUtilities.makeParser(fmt);
            org.hl7.fhir.r5.model.Resource res4 = p4.parse(r);
            org.hl7.fhir.dstu3.model.Resource res3 = VersionConvertorFactory_30_50.convertResource(res4);
            org.hl7.fhir.dstu3.formats.ParserBase p3 = org.hl7.fhir.dstu3.formats.FormatUtilities.makeParser(fmt);
            unConvertCount++;
            return p3.composeBytes(res3);
        } else if ("1.0".equals(version) || "1.0.2".equals(version) || "r2".equals(version)) {
            org.hl7.fhir.r5.formats.ParserBase p4 = org.hl7.fhir.r5.formats.FormatUtilities.makeParser(fmt);
            org.hl7.fhir.r5.model.Resource res4 = p4.parse(r);
            org.hl7.fhir.dstu2.model.Resource res2 = VersionConvertorFactory_10_50.convertResource(res4, conv_10_50_advisor);
            org.hl7.fhir.dstu2.formats.ParserBase p2 = org.hl7.fhir.dstu2.formats.FormatUtilities.makeParser(fmt);
            unConvertCount++;
            return p2.composeBytes(res2);
        } else if ("1.4".equals(version) || "1.4.0".equals(version)) {
            org.hl7.fhir.r5.formats.ParserBase p4 = org.hl7.fhir.r5.formats.FormatUtilities.makeParser(fmt);
            org.hl7.fhir.r5.model.Resource res4 = p4.parse(r);
            org.hl7.fhir.dstu2016may.model.Resource res2 = VersionConvertorFactory_14_50.convertResource(res4);
            org.hl7.fhir.dstu2016may.formats.ParserBase p2 = org.hl7.fhir.dstu2016may.formats.FormatUtilities.makeParser(fmt);
            unConvertCount++;
            return p2.composeBytes(res2);
        } else
            throw new FHIRException("Unsupported version " + version);
    } catch (Exception e) {
        exceptionCount++;
        synchronized (lock) {
            lastException = e.getMessage();
        }
        throw e;
    }
}

Example 12 with Turtle

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

the class NativeHostServices method validateResource.

/**
 * Validate a resource.
 *
 * Possible options:
 *   - id-optional : no resource id is required (default)
 *   - id-required : a resource id is required
 *   - id-prohibited : no resource id is allowed
 *   - any-extensions : allow extensions other than those defined by the encountered structure definitions
 *   - bp-ignore : ignore best practice recommendations (default)
 *   - bp-hint : treat best practice recommendations as a hint
 *   - bp-warning : treat best practice recommendations as a warning
 *   - bp-error : treat best practice recommendations as an error
 *   - display-ignore : ignore Coding.display and do not validate it (default)
 *   - display-check : check Coding.display - must be correct
 *   - display-case-space : check Coding.display but allow case and whitespace variation
 *   - display-case : check Coding.display but allow case variation
 *   - display-space : check Coding.display but allow whitespace variation
 *
 * @param location - a text description of the context of validation (for human consumers to help locate the problem - echoed into error messages)
 * @param source - the bytes to validate
 * @param cntType - the format of the content. one of XML, JSON, TURTLE
 * @param options - a list of space separated options
 * @return
 * @throws Exception
 */
public byte[] validateResource(String location, byte[] source, String cntType, String options) throws Exception {
    try {
        IdStatus resourceIdRule = IdStatus.OPTIONAL;
        boolean anyExtensionsAllowed = true;
        BestPracticeWarningLevel bpWarnings = BestPracticeWarningLevel.Ignore;
        CheckDisplayOption displayOption = CheckDisplayOption.Ignore;
        for (String s : options.split(" ")) {
            if ("id-optional".equalsIgnoreCase(s))
                resourceIdRule = IdStatus.OPTIONAL;
            else if ("id-required".equalsIgnoreCase(s))
                resourceIdRule = IdStatus.REQUIRED;
            else if ("id-prohibited".equalsIgnoreCase(s))
                resourceIdRule = IdStatus.PROHIBITED;
            else if ("any-extensions".equalsIgnoreCase(s))
                // This is already the default
                anyExtensionsAllowed = true;
            else if ("strict-extensions".equalsIgnoreCase(s))
                anyExtensionsAllowed = false;
            else if ("bp-ignore".equalsIgnoreCase(s))
                bpWarnings = BestPracticeWarningLevel.Ignore;
            else if ("bp-hint".equalsIgnoreCase(s))
                bpWarnings = BestPracticeWarningLevel.Hint;
            else if ("bp-warning".equalsIgnoreCase(s))
                bpWarnings = BestPracticeWarningLevel.Warning;
            else if ("bp-error".equalsIgnoreCase(s))
                bpWarnings = BestPracticeWarningLevel.Error;
            else if ("display-ignore".equalsIgnoreCase(s))
                displayOption = CheckDisplayOption.Ignore;
            else if ("display-check".equalsIgnoreCase(s))
                displayOption = CheckDisplayOption.Check;
            else if ("display-case-space".equalsIgnoreCase(s))
                displayOption = CheckDisplayOption.CheckCaseAndSpace;
            else if ("display-case".equalsIgnoreCase(s))
                displayOption = CheckDisplayOption.CheckCase;
            else if ("display-space".equalsIgnoreCase(s))
                displayOption = CheckDisplayOption.CheckSpace;
            else if (!Utilities.noString(s))
                throw new Exception("Unknown option " + s);
        }
        OperationOutcome oo = validator.validate(location, source, FhirFormat.valueOf(cntType), null, resourceIdRule, anyExtensionsAllowed, bpWarnings, displayOption);
        ByteArrayOutputStream bs = new ByteArrayOutputStream();
        new XmlParser().compose(bs, oo);
        validationCount++;
        return bs.toByteArray();
    } catch (Exception e) {
        exceptionCount++;
        synchronized (lock) {
            lastException = e.getMessage();
        }
        throw e;
    }
}

Example 13 with Turtle

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

the class ResourceChecker method checkIsResource.

// protected static Manager.FhirFormat checkIsResource(SimpleWorkerContext context, boolean debug, String path) throws IOException {
// 
// if (Utilities.existsInList(ext, "json"))
// return Manager.FhirFormat.JSON;
// if (Utilities.existsInList(ext, "map"))
// return Manager.FhirFormat.TEXT;
// if (Utilities.existsInList(ext, "txt"))
// return Manager.FhirFormat.TEXT;
// if (Utilities.existsInList(ext, "jwt", "jws"))
// return Manager.FhirFormat.SHC;
// 
// return checkIsResource(context, debug, TextFile.fileToBytes(path), path);
// }
public static Manager.FhirFormat checkIsResource(SimpleWorkerContext context, boolean debug, byte[] cnt, String filename, boolean guessFromExtension) {
    System.out.println("   ..Detect format for " + filename);
    if (cnt.length == 0) {
        System.out.println("   " + filename + " is empty");
        return null;
    }
    if (guessFromExtension) {
        String ext = Utilities.getFileExtension(filename);
        if (Utilities.existsInList(ext, "xml")) {
            return FhirFormat.XML;
        }
        if (Utilities.existsInList(ext, "ttl")) {
            return FhirFormat.TURTLE;
        }
        if (Utilities.existsInList(ext, "map")) {
            return Manager.FhirFormat.TEXT;
        }
        if (Utilities.existsInList(ext, "jwt", "jws")) {
            return Manager.FhirFormat.SHC;
        }
        if (Utilities.existsInList(ext, "json")) {
            // no, we have to look inside, and decide.
            try {
                JsonObject json = JsonTrackingParser.parseJson(cnt);
                if (json.has("verifiableCredential")) {
                    return FhirFormat.SHC;
                }
            } catch (Exception e) {
            }
            return FhirFormat.JSON;
        }
        if (Utilities.existsInList(ext, "txt")) {
            try {
                String src = TextFile.bytesToString(cnt);
                if (src.startsWith("shc:/")) {
                    return FhirFormat.SHC;
                }
            } catch (Exception e) {
            }
            return Manager.FhirFormat.TEXT;
        }
    }
    try {
        Manager.parse(context, new ByteArrayInputStream(cnt), Manager.FhirFormat.JSON);
        return Manager.FhirFormat.JSON;
    } catch (Exception e) {
        if (debug) {
            System.out.println("Not JSON: " + e.getMessage());
        }
    }
    try {
        ValidatorUtils.parseXml(cnt);
        return Manager.FhirFormat.XML;
    } catch (Exception e) {
        if (debug) {
            System.out.println("Not XML: " + e.getMessage());
        }
    }
    try {
        Manager.parse(context, new ByteArrayInputStream(cnt), Manager.FhirFormat.TURTLE);
        return Manager.FhirFormat.TURTLE;
    } catch (Exception e) {
        if (debug) {
            System.out.println("Not Turtle: " + e.getMessage());
        }
    }
    try {
        String s = new String(cnt, StandardCharsets.UTF_8);
        if (s.startsWith("shc:/"))
            s = SHCParser.decodeQRCode(s);
        JWT jwt = new SHCParser(context).decodeJWT(s);
        return Manager.FhirFormat.SHC;
    } catch (Exception e) {
        if (debug) {
            System.out.println("Not a smart health card: " + e.getMessage());
        }
    }
    try {
        new StructureMapUtilities(context, null, null).parse(TextFile.bytesToString(cnt), null);
        return Manager.FhirFormat.TEXT;
    } catch (Exception e) {
        if (debug) {
            System.out.println("Not Text: " + e.getMessage());
        }
    }
    if (debug)
        System.out.println("     .. not a resource: " + filename);
    return null;
}

Example 14 with Turtle

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

the class RdfParserBase method compose.

@Override
public void compose(OutputStream stream, Resource resource) throws IOException {
    Turtle ttl = new Turtle();
    // ttl.setFormat(FFormat);
    ttl.prefix("fhir", "http://hl7.org/fhir/");
    ttl.prefix("rdfs", "http://www.w3.org/2000/01/rdf-schema#");
    Section section = ttl.section("resource");
    Subject subject;
    if (url != null)
        subject = section.triple("<" + url + ">", "a", "fhir:" + resource.getResourceType().toString());
    else
        subject = section.triple("[]", "a", "fhir:" + resource.getResourceType().toString());
    composeResource(subject, resource);
    try {
        ttl.commit(stream, false);
    } catch (Exception e) {
        throw new IOException(e);
    }
}

Example 15 with Turtle

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

the class BinaryRenderer method ttl.

private void ttl(XhtmlNode x, Binary bin) {
    String content = "\r\n" + getBinContentAsString(bin);
    XhtmlNode pre = x.pre("rdf language-turtle");
    pre.code(content);
}