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

Example 81 with IParser

use of org.hl7.fhir.r5.formats.IParser in project synthea by synthetichealth.

the class ValidationSupportR4 method loadFromDirectory.

/**
 * Loads the structure definitions from the given directory.
 * @param rootDir the directory to load structure definitions from
 * @return a list of structure definitions
 * @throws Throwable when there is an error reading the structure definitions.
 */
private void loadFromDirectory(String rootDir) throws Throwable {
    IParser jsonParser = FhirR4.getContext().newJsonParser();
    jsonParser.setParserErrorHandler(new StrictErrorHandler());
    URL profilesFolder = ClassLoader.getSystemClassLoader().getResource(rootDir);
    Path path = Paths.get(profilesFolder.toURI());
    Files.walk(path, Integer.MAX_VALUE).filter(Files::isReadable).filter(Files::isRegularFile).filter(p -> p.toString().endsWith(".json")).forEach(f -> {
        try {
            IBaseResource resource = jsonParser.parseResource(new FileReader(f.toFile()));
            handleResource(resource);
        } catch (FileNotFoundException e) {
            throw new RuntimeException(e);
        }
    });
}

Example 82 with IParser

use of org.hl7.fhir.r5.formats.IParser in project synthea by synthetichealth.

the class ValidationSupportSTU3 method loadFromDirectory.

/**
 * Loads the structure definitions from the given directory.
 * @param rootDir the directory to load structure definitions from
 * @return a list of structure definitions
 * @throws Throwable when there is an error reading the structure definitions.
 */
private void loadFromDirectory(String rootDir) throws Throwable {
    IParser jsonParser = FhirStu3.getContext().newJsonParser();
    jsonParser.setParserErrorHandler(new StrictErrorHandler());
    URL profilesFolder = ClassLoader.getSystemClassLoader().getResource(rootDir);
    Path path = Paths.get(profilesFolder.toURI());
    Files.walk(path, Integer.MAX_VALUE).filter(Files::isReadable).filter(Files::isRegularFile).filter(p -> p.toString().endsWith(".json")).forEach(f -> {
        try {
            IBaseResource resource = jsonParser.parseResource(new FileReader(f.toFile()));
            if (resource instanceof CodeSystem) {
                this.addCodeSystem(resource);
            } else if (resource instanceof ValueSet) {
            // The PrePopulatedValidationSupport base class only supports
            // R4 ValueSets so we don't validate these here
            // ValueSet vs = (ValueSet) resource;
            // this.addValueSet(vs);
            } else if (resource instanceof StructureDefinition) {
                this.addStructureDefinition(resource);
            }
        } catch (FileNotFoundException e) {
            throw new RuntimeException(e);
        }
    });
}

Example 83 with IParser

use of org.hl7.fhir.r5.formats.IParser in project synthea by synthetichealth.

the class FhirGroupExporterR4 method exportAndSave.

/**
 * Export the current patient list as a FHIR Group resource and save it as a JSON file.
 * @param stop The stop time.
 */
public static void exportAndSave(RandomNumberGenerator rand, long stop) {
    if (Config.getAsBoolean("exporter.groups.fhir.export")) {
        Group group = export(rand, stop);
        // get output folder
        List<String> folders = new ArrayList<>();
        folders.add("fhir");
        String baseDirectory = Config.get("exporter.baseDirectory");
        File f = Paths.get(baseDirectory, folders.toArray(new String[0])).toFile();
        f.mkdirs();
        Path outFilePath = null;
        String groupJson = null;
        if (Config.getAsBoolean("exporter.fhir.bulk_data")) {
            IParser parser = FhirR4.getContext().newJsonParser().setPrettyPrint(false);
            groupJson = parser.encodeResourceToString(group);
            String filename = group.getResourceType().toString() + ".ndjson";
            outFilePath = f.toPath().resolve(filename);
        } else {
            IParser parser = FhirR4.getContext().newJsonParser().setPrettyPrint(true);
            groupJson = parser.encodeResourceToString(group);
            outFilePath = f.toPath().resolve("groupInformation" + stop + ".json");
        }
        try {
            Files.write(outFilePath, Collections.singleton(groupJson), StandardOpenOption.CREATE_NEW);
        } catch (IOException e) {
            e.printStackTrace();
        }
    }
}

Example 84 with IParser

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

the class DataRequirementsProcessorTest method TestDataRequirementsProcessor.

@Test
public void TestDataRequirementsProcessor() {
    CqlTranslatorOptions cqlTranslatorOptions = new CqlTranslatorOptions();
    cqlTranslatorOptions.getFormats().add(CqlTranslator.Format.JSON);
    cqlTranslatorOptions.getOptions().add(CqlTranslatorOptions.Options.EnableAnnotations);
    try {
        /*
                OpioidCDSCommon.cql
                DataRequirements.cql
                AdultOutpatientEncountersFHIR4.xml
                AdvancedIllnessandFrailtyExclusionECQMFHIR4.xml
                BCSComponent.xml
                CCSComponent.xml
                FHIRHelpers.xml
                HBPComponent.xml
                HospiceFHIR4.xml
                MATGlobalCommonFunctionsFHIR4.xml
                PVSComponent.xml
                SupplementalDataElementsFHIR4.xml
                TSCComponent.xml
                BCSComponent-v0-0-001-FHIR-4-0-1.xml
                CCSComponent-v0-0-001-FHIR-4-0-1.xml
                HBPComponent-v0-0-001-FHIR-4-0-1.xml
                PVSComponent-v0-0-001-FHIR-4-0-1.xml
                TSCComponent-v0-0-001-FHIR-4-0-1.xml
                PreventiveCareandWellness-v0-0-001-FHIR-4-0-1.xml
             */
        // "OpioidCDS/cql/OpioidCDSCommon.cql", cqlTranslatorOptions);
        CqlTranslator translator = createTranslator("CompositeMeasures/cql/EXM124-9.0.000.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"));
        FhirContext context = getFhirContext();
        IParser parser = context.newJsonParser();
        String moduleDefString = parser.setPrettyPrint(true).encodeResourceToString(moduleDefinitionLibrary);
        logger.debug(moduleDefString);
    } catch (IOException ioException) {
        ioException.printStackTrace();
    }
}

Example 85 with IParser

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

the class DataRequirementsProcessorTest method assertEqualToExpectedModuleDefinitionLibrary.

private void assertEqualToExpectedModuleDefinitionLibrary(org.hl7.fhir.r5.model.Library actualModuleDefinitionLibrary, String pathToExpectedModuleDefinitionLibrary) {
    FhirContext context = getFhirContext();
    IParser parser = context.newJsonParser();
    org.hl7.fhir.r5.model.Library expectedModuleDefinitionLibrary = (org.hl7.fhir.r5.model.Library) parser.parseResource(DataRequirementsProcessorTest.class.getResourceAsStream(pathToExpectedModuleDefinitionLibrary));
    assertNotNull(expectedModuleDefinitionLibrary);
    actualModuleDefinitionLibrary.setDate(null);
    expectedModuleDefinitionLibrary.setDate(null);
    assertTrue(actualModuleDefinitionLibrary.equalsDeep(expectedModuleDefinitionLibrary));
}