Examples with IParser org.hl7.fhir.r5.formats.IParser used on opensource projects

Example 51 with IParser

use of org.hl7.fhir.r5.formats.IParser in project syndesis by syndesisio.

the class FhirTransactionCustomizer method beforeProducer.

public void beforeProducer(Exchange exchange) {
    final Message in = exchange.getIn();
    String body = in.getBody(String.class);
    if (body != null) {
        List<IBaseResource> resources = new ArrayList<>();
        DocumentBuilderFactory dbf = DocumentBuilderFactory.newInstance();
        try {
            Document doc = dbf.newDocumentBuilder().parse(new ByteArrayInputStream(body.getBytes("UTF-8")));
            Node transactionElement = doc.getFirstChild();
            NodeList childNodes = transactionElement.getChildNodes();
            IParser parser = fhirContext.newXmlParser();
            for (int i = 0; i < childNodes.getLength(); i++) {
                Node resourceNode = childNodes.item(i);
                Document resourceDocument = toDocument(resourceNode, dbf);
                String resourceXml = toXml(resourceDocument);
                IBaseResource resource = parser.parseResource(resourceXml);
                resources.add(resource);
            }
        } catch (SAXException | IOException | ParserConfigurationException | TransformerException e) {
            throw new RuntimeExchangeException("Cannot convert Transaction to a list of resources", exchange, e);
        }
        in.setHeader("CamelFhir.resources", resources);
    }
}

Example 52 with IParser

use of org.hl7.fhir.r5.formats.IParser in project gpconnect-demonstrator by nhsconnect.

the class ValueSetValidator method findValueSet.

private ValueSet findValueSet(String systemUrl) {
    int valueSetNamePos = systemUrl.lastIndexOf("/") + 1;
    String valueSetFilename = String.format("%s.xml", systemUrl.substring(valueSetNamePos));
    ValueSet valSet = null;
    String xmlContent = null;
    if (fhirValueSetsCheckWebFirst == true) {
        xmlContent = readValueSetFromWeb(valueSetFilename);
    }
    if (xmlContent == null) {
        xmlContent = readValueSetFromDisk(valueSetFilename);
    }
    if (fhirValueSetsCheckWebFirst == false && xmlContent == null) {
        xmlContent = readValueSetFromWeb(valueSetFilename);
    }
    if (xmlContent != null) {
        try {
            FhirContext fhirCtx = FhirContext.forDstu3();
            IParser parser = fhirCtx.newXmlParser();
            valSet = parser.parseResource(ValueSet.class, xmlContent);
        } catch (DataFormatException ex) {
            LOG.error(String.format("Error parsing valueSetFilename: %s", valueSetFilename));
        }
    }
    if (valSet == null) {
        throw OperationOutcomeFactory.buildOperationOutcomeException(new UnprocessableEntityException(String.format("Could not find or parse Value Set [SystemUrl: %s] at: %s. See system log for details.", systemUrl, valueSetFilename)), SystemCode.REFERENCE_NOT_FOUND, IssueType.NOTFOUND);
    }
    return valSet;
}

Example 53 with IParser

use of org.hl7.fhir.r5.formats.IParser in project clinical_quality_language by cqframework.

the class DataRequirementsProcessorTest method TestDataRequirementsFHIRReferences.

@Test
public void TestDataRequirementsFHIRReferences() {
    CqlTranslatorOptions cqlTranslatorOptions = new CqlTranslatorOptions();
    cqlTranslatorOptions.getFormats().add(CqlTranslator.Format.JSON);
    try {
        CqlTranslator translator = createTranslator("FHIRReferencesRevisited.cql", cqlTranslatorOptions);
        translator.toELM();
        assertTrue(translator.getErrors().isEmpty());
        libraryManager.cacheLibrary(translator.getTranslatedLibrary());
        DataRequirementsProcessor dqReqTrans = new DataRequirementsProcessor();
        org.hl7.fhir.r5.model.Library moduleDefinitionLibrary = dqReqTrans.gatherDataRequirements(libraryManager, translator.getTranslatedLibrary(), cqlTranslatorOptions, null, false);
        FhirContext context = getFhirContext();
        IParser parser = context.newJsonParser();
        String moduleDefString = parser.setPrettyPrint(true).encodeResourceToString(moduleDefinitionLibrary);
        logger.debug(moduleDefString);
    // TODO: Validate consolidation of requirements
    } catch (IOException ioException) {
        ioException.printStackTrace();
    }
}

Example 54 with IParser

use of org.hl7.fhir.r5.formats.IParser in project clinical_quality_language by cqframework.

the class DataRequirementsProcessorTest method TestDataRequirementsProcessorWithExpressions.

@Test
public void TestDataRequirementsProcessorWithExpressions() {
    CqlTranslatorOptions cqlTranslatorOptions = new CqlTranslatorOptions();
    cqlTranslatorOptions.getFormats().add(CqlTranslator.Format.JSON);
    try {
        Set<String> expressions = new HashSet<>();
        // TODO - add expressions to expressions
        // Active Ambulatory Opioid Rx");
        expressions.add("Conditions Indicating End of Life or With Limited Life Expectancy");
        CqlTranslator translator = createTranslator("OpioidCDS/cql/OpioidCDSCommon.cql", cqlTranslatorOptions);
        translator.toELM();
        assertTrue(translator.getErrors().isEmpty());
        libraryManager.cacheLibrary(translator.getTranslatedLibrary());
        DataRequirementsProcessor dqReqTrans = new DataRequirementsProcessor();
        org.hl7.fhir.r5.model.Library moduleDefinitionLibrary = dqReqTrans.gatherDataRequirements(libraryManager, translator.getTranslatedLibrary(), cqlTranslatorOptions, expressions, false);
        assertTrue(moduleDefinitionLibrary.getType().getCode("http://terminology.hl7.org/CodeSystem/library-type").equalsIgnoreCase("module-definition"));
        List<Extension> directReferenceCodes = moduleDefinitionLibrary.getExtensionsByUrl("http://hl7.org/fhir/us/cqfmeasures/StructureDefinition/cqfm-directReferenceCode");
        assertTrue(directReferenceCodes.size() == 4);
        Extension directReferenceCode = directReferenceCodes.get(0);
        Coding coding = directReferenceCode.getValueCoding();
        assertEquals("http://hl7.org/fhir/condition-category", coding.getSystem());
        assertEquals("encounter-diagnosis", coding.getCode());
        assertEquals("Encounter Diagnosis", coding.getDisplay());
        assertTrue(moduleDefinitionLibrary.getRelatedArtifact().size() == 6);
        RelatedArtifact conditionCategoryCodes = null;
        for (RelatedArtifact relatedArtifact : moduleDefinitionLibrary.getRelatedArtifact()) {
            if (relatedArtifact.getType() == RelatedArtifact.RelatedArtifactType.DEPENDSON && relatedArtifact.getResource() != null && relatedArtifact.getResource().equals("http://hl7.org/fhir/condition-category")) {
                conditionCategoryCodes = relatedArtifact;
                break;
            }
        }
        assertTrue(conditionCategoryCodes != null);
        assertTrue(moduleDefinitionLibrary.getParameter().size() == 1);
        ParameterDefinition conditionsIndicatingEndOfLife = null;
        for (ParameterDefinition parameter : moduleDefinitionLibrary.getParameter()) {
            if (parameter.getName().equals("Conditions Indicating End of Life or With Limited Life Expectancy")) {
                conditionsIndicatingEndOfLife = parameter;
                break;
            }
        }
        assertTrue(conditionsIndicatingEndOfLife != null);
        assertTrue(moduleDefinitionLibrary.getDataRequirement().size() == 3);
        DataRequirement diagnosisRequirement = null;
        for (DataRequirement requirement : moduleDefinitionLibrary.getDataRequirement()) {
            if (requirement.getType() == Enumerations.FHIRAllTypes.CONDITION && requirement.getCodeFilter().size() == 1) {
                DataRequirement.DataRequirementCodeFilterComponent cfc = requirement.getCodeFilterFirstRep();
                if (cfc.hasPath() && cfc.getPath().equals("category") && cfc.getCode().size() == 1 && cfc.getCodeFirstRep().hasCode() && cfc.getCodeFirstRep().getCode().equals("encounter-diagnosis")) {
                    diagnosisRequirement = requirement;
                    break;
                }
            }
        }
        assertTrue(diagnosisRequirement != null);
        FhirContext context = getFhirContext();
        IParser parser = context.newJsonParser();
        String moduleDefString = parser.setPrettyPrint(true).encodeResourceToString(moduleDefinitionLibrary);
        logger.debug(moduleDefString);
    } catch (IOException ioException) {
        ioException.printStackTrace();
    }
}

Example 55 with IParser

use of org.hl7.fhir.r5.formats.IParser in project clinical_quality_language by cqframework.

the class DataRequirementsProcessorTest method TestLibraryDataRequirements.

@Test
public void TestLibraryDataRequirements() {
    CqlTranslatorOptions cqlTranslatorOptions = new CqlTranslatorOptions();
    cqlTranslatorOptions.getFormats().add(CqlTranslator.Format.JSON);
    try {
        // CqlTranslator translator = createTranslator("/ecqm/resources/library-EXM506-2.2.000.json", cqlTranslatorOptions);
        CqlTranslator translator = createTranslator("CompositeMeasures/cql/BCSComponent.cql", cqlTranslatorOptions);
        translator.toELM();
        assertTrue(translator.getErrors().isEmpty());
        libraryManager.cacheLibrary(translator.getTranslatedLibrary());
        DataRequirementsProcessor dqReqTrans = new DataRequirementsProcessor();
        org.hl7.fhir.r5.model.Library moduleDefinitionLibrary = dqReqTrans.gatherDataRequirements(libraryManager, translator.getTranslatedLibrary(), cqlTranslatorOptions, null, false);
        assertTrue(moduleDefinitionLibrary.getType().getCode("http://terminology.hl7.org/CodeSystem/library-type").equalsIgnoreCase("module-definition"));
        List<Extension> directReferenceCodes = moduleDefinitionLibrary.getExtensionsByUrl("http://hl7.org/fhir/us/cqfmeasures/StructureDefinition/cqfm-directReferenceCode");
        assertTrue(directReferenceCodes.size() == 5);
        Extension directReferenceCode = directReferenceCodes.get(0);
        Coding coding = directReferenceCode.getValueCoding();
        assertEquals("http://loinc.org", coding.getSystem());
        assertEquals("21112-8", coding.getCode());
        assertEquals("Birth date", coding.getDisplay());
        assertTrue(moduleDefinitionLibrary.getRelatedArtifact().size() >= 45);
        RelatedArtifact loincCodeSystem = null;
        for (RelatedArtifact relatedArtifact : moduleDefinitionLibrary.getRelatedArtifact()) {
            if (relatedArtifact.getType() == RelatedArtifact.RelatedArtifactType.DEPENDSON && relatedArtifact.getResource() != null && relatedArtifact.getResource().equals("http://loinc.org")) {
                loincCodeSystem = relatedArtifact;
                break;
            }
        }
        assertTrue(loincCodeSystem != null);
        assertTrue(moduleDefinitionLibrary.getParameter().size() >= 16);
        ParameterDefinition measurementPeriod = null;
        for (ParameterDefinition parameter : moduleDefinitionLibrary.getParameter()) {
            if (parameter.getName().equals("Measurement Period")) {
                measurementPeriod = parameter;
                break;
            }
        }
        assertTrue(measurementPeriod != null);
        assertTrue(moduleDefinitionLibrary.getDataRequirement().size() >= 15);
        DataRequirement diagnosisRequirement = null;
        for (DataRequirement requirement : moduleDefinitionLibrary.getDataRequirement()) {
            if (requirement.getType() == Enumerations.FHIRAllTypes.CONDITION && requirement.getCodeFilter().size() == 1) {
                DataRequirement.DataRequirementCodeFilterComponent cfc = requirement.getCodeFilterFirstRep();
                if (cfc.hasPath() && cfc.getPath().equals("code") && cfc.hasValueSet() && cfc.getValueSet().equals("http://cts.nlm.nih.gov/fhir/ValueSet/2.16.840.1.113883.3.464.1003.198.12.1071")) {
                    diagnosisRequirement = requirement;
                    break;
                }
            }
        }
        assertTrue(diagnosisRequirement != null);
        FhirContext context = getFhirContext();
        IParser parser = context.newJsonParser();
        String moduleDefString = parser.setPrettyPrint(true).encodeResourceToString(moduleDefinitionLibrary);
        logger.debug(moduleDefString);
    } catch (IOException ioException) {
        ioException.printStackTrace();
    }
}