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Example 1 with R4ToR5Loader

use of org.hl7.fhir.convertors.loaders.loaderR5.R4ToR5Loader in project kindling by HL7.

the class PageProcessor method setDefinitions.

public void setDefinitions(Definitions definitions) throws Exception {
    this.definitions = definitions;
    breadCrumbManager.setDefinitions(definitions);
    TerminologyClient client;
    try {
        client = new TerminologyClientR5(tsServer);
        client.setTimeout(60000);
    } catch (Exception e) {
        System.out.println("Warning @ PageProcessor client initialize: " + e.getLocalizedMessage());
        client = null;
    }
    workerContext = new BuildWorkerContext(definitions, client, definitions.getCodeSystems(), definitions.getValuesets(), conceptMaps, profiles, guides, folders.rootDir);
    workerContext.setDefinitions(definitions);
    workerContext.setLogger(this);
    workerContext.setAllowLoadingDuplicates(true);
    log("Load UTG Terminology", LogMessageType.Process);
    NpmPackage utg = new FilesystemPackageCacheManager(true, ToolsVersion.TOOLS_VERSION).loadPackage("hl7.terminology");
    workerContext.loadFromPackage(utg, new R4ToR5Loader(BuildWorkerContext.defaultTypesToLoad(), new UTGLoader(utg.version())));
    log("Load Terminology Cache from " + Utilities.path(folders.rootDir, "vscache"), LogMessageType.Process);
    workerContext.initTS(Utilities.path(folders.rootDir, "vscache"));
    log("  .. loaded", LogMessageType.Process);
    vsValidator = new ValueSetValidator(workerContext, definitions.getVsFixups(), definitions.getStyleExemptions());
    breadCrumbManager.setContext(workerContext);
}
Also used : TerminologyClientR5(org.hl7.fhir.convertors.txClient.TerminologyClientR5) FilesystemPackageCacheManager(org.hl7.fhir.utilities.npm.FilesystemPackageCacheManager) NpmPackage(org.hl7.fhir.utilities.npm.NpmPackage) R4ToR5Loader(org.hl7.fhir.convertors.loaders.R4ToR5Loader) TerminologyClient(org.hl7.fhir.r5.terminologies.TerminologyClient) ValueSetValidator(org.hl7.fhir.definitions.validation.ValueSetValidator) UcumException(org.fhir.ucum.UcumException) TransformerException(javax.xml.transform.TransformerException) TransformerConfigurationException(javax.xml.transform.TransformerConfigurationException) IOException(java.io.IOException) FHIRException(org.hl7.fhir.exceptions.FHIRException) URISyntaxException(java.net.URISyntaxException) PathEngineException(org.hl7.fhir.exceptions.PathEngineException) DefinitionException(org.hl7.fhir.exceptions.DefinitionException) FileNotFoundException(java.io.FileNotFoundException) NotImplementedException(org.apache.commons.lang3.NotImplementedException)

Example 2 with R4ToR5Loader

use of org.hl7.fhir.convertors.loaders.loaderR5.R4ToR5Loader in project org.hl7.fhir.core by hapifhir.

the class ComparisonTests method test.

@ParameterizedTest(name = "{index}: id {0}")
@MethodSource("data")
public void test(String name, JsonObject content) throws Exception {
    this.content = content;
    if (content.has("use-test") && !content.get("use-test").getAsBoolean())
        return;
    if (context == null) {
        System.out.println("---- Load R5 ----------------------------------------------------------------");
        context = TestingUtilities.getSharedWorkerContext();
        FilesystemPackageCacheManager pcm = new FilesystemPackageCacheManager(true, ToolsVersion.TOOLS_VERSION);
        NpmPackage npm = pcm.loadPackage("hl7.fhir.us.core#3.1.0");
        BaseWorkerContext bc = (BaseWorkerContext) context;
        boolean dupl = bc.isAllowLoadingDuplicates();
        bc.setAllowLoadingDuplicates(true);
        context.loadFromPackage(npm, new R4ToR5Loader(new String[] { "CapabilityStatement", "StructureDefinition", "ValueSet", "CodeSystem", "SearchParameter", "OperationDefinition", "Questionnaire", "ConceptMap", "StructureMap", "NamingSystem" }, new NullLoaderKnowledgeProviderR5(), context.getVersion()));
        bc.setAllowLoadingDuplicates(dupl);
    }
    if (!new File(Utilities.path("[tmp]", "comparison")).exists()) {
        System.out.println("---- Set up Output ----------------------------------------------------------");
        Utilities.createDirectory(Utilities.path("[tmp]", "comparison"));
        FilesystemPackageCacheManager pcm = new FilesystemPackageCacheManager(true, ToolsVersion.TOOLS_VERSION);
        NpmPackage npm = pcm.loadPackage(CommonPackages.ID_PUBPACK, CommonPackages.VER_PUBPACK);
        for (String f : npm.list("other")) {
            TextFile.streamToFile(npm.load("other", f), Utilities.path("[tmp]", "comparison", f));
        }
    }
    System.out.println("---- " + name + " ----------------------------------------------------------------");
    CanonicalResource left = load("left");
    CanonicalResource right = load("right");
    ComparisonSession session = new ComparisonSession(context, context, "Comparison Tests", null);
    if (left instanceof CodeSystem && right instanceof CodeSystem) {
        CodeSystemComparer cs = new CodeSystemComparer(session);
        CodeSystemComparison csc = cs.compare((CodeSystem) left, (CodeSystem) right);
        Assertions.assertTrue(csc.getUnion().getConcept().size() > csc.getIntersection().getConcept().size());
        new org.hl7.fhir.r5.formats.JsonParser().setOutputStyle(OutputStyle.PRETTY).compose(new FileOutputStream(Utilities.path("[tmp]", "comparison", name + "-union.json")), csc.getUnion());
        new org.hl7.fhir.r5.formats.JsonParser().setOutputStyle(OutputStyle.PRETTY).compose(new FileOutputStream(Utilities.path("[tmp]", "comparison", name + "-intersection.json")), csc.getIntersection());
        String xmle = new XhtmlComposer(true).compose(cs.renderErrors(csc));
        String xml1 = new XhtmlComposer(true).compose(cs.renderMetadata(csc, "", ""));
        String xml2 = new XhtmlComposer(true).compose(cs.renderConcepts(csc, "", ""));
        TextFile.stringToFile(HEADER + hd("Messages") + xmle + BREAK + hd("Metadata") + xml1 + BREAK + hd("Concepts") + xml2 + FOOTER, Utilities.path("[tmp]", "comparison", name + ".html"));
        checkOutcomes(csc.getMessages(), content);
    } else if (left instanceof ValueSet && right instanceof ValueSet) {
        ValueSetComparer cs = new ValueSetComparer(session);
        ValueSetComparison csc = cs.compare((ValueSet) left, (ValueSet) right);
        new org.hl7.fhir.r5.formats.JsonParser().setOutputStyle(OutputStyle.PRETTY).compose(new FileOutputStream(Utilities.path("[tmp]", "comparison", name + "-union.json")), csc.getUnion());
        new org.hl7.fhir.r5.formats.JsonParser().setOutputStyle(OutputStyle.PRETTY).compose(new FileOutputStream(Utilities.path("[tmp]", "comparison", name + "-intersection.json")), csc.getIntersection());
        String xmle = new XhtmlComposer(true).compose(cs.renderErrors(csc));
        String xml1 = new XhtmlComposer(true).compose(cs.renderMetadata(csc, "", ""));
        String xml2 = new XhtmlComposer(true).compose(cs.renderCompose(csc, "", ""));
        String xml3 = new XhtmlComposer(true).compose(cs.renderExpansion(csc, "", ""));
        TextFile.stringToFile(HEADER + hd("Messages") + xmle + BREAK + hd("Metadata") + xml1 + BREAK + hd("Definition") + xml2 + BREAK + hd("Expansion") + xml3 + FOOTER, Utilities.path("[tmp]", "comparison", name + ".html"));
        checkOutcomes(csc.getMessages(), content);
    } else if (left instanceof StructureDefinition && right instanceof StructureDefinition) {
        ProfileUtilities utils = new ProfileUtilities(context, null, null);
        genSnapshot(utils, (StructureDefinition) left);
        genSnapshot(utils, (StructureDefinition) right);
        ProfileComparer pc = new ProfileComparer(session, utils, utils);
        ProfileComparison csc = pc.compare((StructureDefinition) left, (StructureDefinition) right);
        new org.hl7.fhir.r5.formats.JsonParser().setOutputStyle(OutputStyle.PRETTY).compose(new FileOutputStream(Utilities.path("[tmp]", "comparison", name + "-union.json")), csc.getUnion());
        new org.hl7.fhir.r5.formats.JsonParser().setOutputStyle(OutputStyle.PRETTY).compose(new FileOutputStream(Utilities.path("[tmp]", "comparison", name + "-intersection.json")), csc.getIntersection());
        String xmle = new XhtmlComposer(true).compose(pc.renderErrors(csc));
        String xml1 = new XhtmlComposer(true).compose(pc.renderMetadata(csc, "", ""));
        String xml2 = new XhtmlComposer(true).compose(pc.renderStructure(csc, "", "", "http://hl7.org/fhir"));
        // String xml3 = new XhtmlComposer(true).compose(cs.renderExpansion(csc, "", ""));
        TextFile.stringToFile(HEADER + hd("Messages") + xmle + BREAK + hd("Metadata") + xml1 + BREAK + hd("Structure") + xml2 + FOOTER, Utilities.path("[tmp]", "comparison", name + ".html"));
        checkOutcomes(csc.getMessages(), content);
    } else if (left instanceof CapabilityStatement && right instanceof CapabilityStatement) {
        CapabilityStatementComparer pc = new CapabilityStatementComparer(session);
        CapabilityStatementComparison csc = pc.compare((CapabilityStatement) left, (CapabilityStatement) right);
        new org.hl7.fhir.r5.formats.JsonParser().setOutputStyle(OutputStyle.PRETTY).compose(new FileOutputStream(Utilities.path("[tmp]", "comparison", name + "-union.json")), csc.getUnion());
        new org.hl7.fhir.r5.formats.JsonParser().setOutputStyle(OutputStyle.PRETTY).compose(new FileOutputStream(Utilities.path("[tmp]", "comparison", name + "-intersection.json")), csc.getIntersection());
        String xmle = new XhtmlComposer(true).compose(pc.renderErrors(csc));
        String xml1 = new XhtmlComposer(true).compose(pc.renderMetadata(csc, "", ""));
        String xml2 = new XhtmlComposer(true).compose(pc.renderStatements(csc, "", ""));
        // String xml3 = new XhtmlComposer(true).compose(cs.renderExpansion(csc, "", ""));
        TextFile.stringToFile(HEADER + hd("Messages") + xmle + BREAK + hd("Metadata") + xml1 + BREAK + hd("Structure") + xml2 + FOOTER, Utilities.path("[tmp]", "comparison", name + ".html"));
        checkOutcomes(csc.getMessages(), content);
    } else {
        throw new FHIRException("Can't compare " + left.fhirType() + " to " + right.fhirType());
    }
}
Also used : ProfileComparison(org.hl7.fhir.r5.comparison.ProfileComparer.ProfileComparison) ComparisonSession(org.hl7.fhir.r5.comparison.ComparisonSession) ProfileComparer(org.hl7.fhir.r5.comparison.ProfileComparer) BaseWorkerContext(org.hl7.fhir.r5.context.BaseWorkerContext) StructureDefinition(org.hl7.fhir.r5.model.StructureDefinition) CapabilityStatementComparison(org.hl7.fhir.r5.comparison.CapabilityStatementComparer.CapabilityStatementComparison) XhtmlComposer(org.hl7.fhir.utilities.xhtml.XhtmlComposer) CapabilityStatement(org.hl7.fhir.r5.model.CapabilityStatement) CapabilityStatementComparer(org.hl7.fhir.r5.comparison.CapabilityStatementComparer) ValueSet(org.hl7.fhir.r5.model.ValueSet) JsonParser(org.hl7.fhir.r5.formats.JsonParser) FilesystemPackageCacheManager(org.hl7.fhir.utilities.npm.FilesystemPackageCacheManager) ValueSetComparison(org.hl7.fhir.r5.comparison.ValueSetComparer.ValueSetComparison) CodeSystem(org.hl7.fhir.r5.model.CodeSystem) JsonParser(org.hl7.fhir.r5.formats.JsonParser) FHIRException(org.hl7.fhir.exceptions.FHIRException) CodeSystemComparer(org.hl7.fhir.r5.comparison.CodeSystemComparer) NpmPackage(org.hl7.fhir.utilities.npm.NpmPackage) CodeSystemComparison(org.hl7.fhir.r5.comparison.CodeSystemComparer.CodeSystemComparison) ProfileUtilities(org.hl7.fhir.r5.conformance.ProfileUtilities) R4ToR5Loader(org.hl7.fhir.convertors.loaders.loaderR5.R4ToR5Loader) FileOutputStream(java.io.FileOutputStream) ValueSetComparer(org.hl7.fhir.r5.comparison.ValueSetComparer) File(java.io.File) TextFile(org.hl7.fhir.utilities.TextFile) CanonicalResource(org.hl7.fhir.r5.model.CanonicalResource) NullLoaderKnowledgeProviderR5(org.hl7.fhir.convertors.loaders.loaderR5.NullLoaderKnowledgeProviderR5) ParameterizedTest(org.junit.jupiter.params.ParameterizedTest) MethodSource(org.junit.jupiter.params.provider.MethodSource)

Aggregations

FHIRException (org.hl7.fhir.exceptions.FHIRException)2 FilesystemPackageCacheManager (org.hl7.fhir.utilities.npm.FilesystemPackageCacheManager)2 NpmPackage (org.hl7.fhir.utilities.npm.NpmPackage)2 File (java.io.File)1 FileNotFoundException (java.io.FileNotFoundException)1 FileOutputStream (java.io.FileOutputStream)1 IOException (java.io.IOException)1 URISyntaxException (java.net.URISyntaxException)1 TransformerConfigurationException (javax.xml.transform.TransformerConfigurationException)1 TransformerException (javax.xml.transform.TransformerException)1 NotImplementedException (org.apache.commons.lang3.NotImplementedException)1 UcumException (org.fhir.ucum.UcumException)1 R4ToR5Loader (org.hl7.fhir.convertors.loaders.R4ToR5Loader)1 NullLoaderKnowledgeProviderR5 (org.hl7.fhir.convertors.loaders.loaderR5.NullLoaderKnowledgeProviderR5)1 R4ToR5Loader (org.hl7.fhir.convertors.loaders.loaderR5.R4ToR5Loader)1 TerminologyClientR5 (org.hl7.fhir.convertors.txClient.TerminologyClientR5)1 ValueSetValidator (org.hl7.fhir.definitions.validation.ValueSetValidator)1 DefinitionException (org.hl7.fhir.exceptions.DefinitionException)1 PathEngineException (org.hl7.fhir.exceptions.PathEngineException)1 CapabilityStatementComparer (org.hl7.fhir.r5.comparison.CapabilityStatementComparer)1