Examples with BaseWorkerContext org.hl7.fhir.r5.context.BaseWorkerContext used on opensource projects

Example 1 with BaseWorkerContext

use of org.hl7.fhir.r5.context.BaseWorkerContext in project kindling by HL7.

the class TypeParser method parse.

public List<TypeRef> parse(String n, boolean inProfile, String profileExtensionBase, BaseWorkerContext resolver, boolean allowElement, String sheetName) throws Exception {
    ArrayList<TypeRef> a = new ArrayList<TypeRef>();
    String exceptionPrefix = sheetName == null ? "" : "Error parsing sheet " + sheetName + " - ";
    if (n == null || n.equals("") || n.startsWith("!"))
        return a;
    // to allow splitting
    if (n.indexOf("(") != -1 && n.indexOf("|") != -1) {
        String[] typeParts = n.split("[\\(\\)]");
        n = "";
        for (int i = 0; i < typeParts.length; i++) {
            n = n + typeParts[i++];
            if (i < typeParts.length) {
                n = n + "(" + typeParts[i].replace("|", ",") + ")";
            }
        }
    }
    String[] typeList = n.split("[\\|]");
    for (int i = 0; i < typeList.length; i++) {
        TypeRef t = new TypeRef();
        String typeString = typeList[i].trim();
        if (typeString.contains("<")) {
            if (!inProfile) {
                throw new Exception(exceptionPrefix + "Can't specify aggregation mode for types unless defining a profile: " + typeString);
            }
            int startPos = typeString.indexOf("<");
            int endPos = typeString.indexOf(">");
            if (endPos < startPos) {
                throw new Exception(exceptionPrefix + "Missing '>' in data type definition: " + typeList[i]);
            }
            t.getAggregations().addAll(Arrays.asList(typeString.substring(startPos + 1, endPos).trim().split(",")));
            typeString = typeString.substring(0, startPos);
        }
        if (typeString.contains("~")) {
            String v = typeString.substring(typeString.indexOf("~"));
            typeString = typeString.substring(0, typeString.indexOf("~") - 1);
            t.setVersioning(org.hl7.fhir.r5.model.ElementDefinition.ReferenceVersionRules.fromCode(v));
        }
        if (typeString.contains("{")) {
            if (!inProfile) {
                throw new Exception(exceptionPrefix + "Can't specify profile for types unless defining a profile");
            }
            int startPos = typeString.indexOf("{");
            int endPos = typeString.indexOf("}");
            if (endPos < startPos) {
                throw new Exception(exceptionPrefix + "Missing '}' in data type definition: " + typeList[i]);
            }
            String pt = typeString.substring(startPos + 1, endPos).trim();
            typeString = typeString.substring(0, startPos);
            if (pt.startsWith("#")) {
                // what to do here depends on what it refers to
                if (typeString.trim().equals("Extension"))
                    pt = profileExtensionBase + pt.substring(1);
                else if (typeString.trim().startsWith("Reference") || typeString.trim().startsWith("Resource"))
                    pt = pt.substring(1).toLowerCase();
                else
                    throw new Exception(exceptionPrefix + "Unhandled case");
            }
            t.setProfile(pt);
        }
        if (typeString.contains("(")) {
            int startPos = typeString.indexOf("(");
            int endPos = typeString.indexOf(")");
            if (endPos < startPos) {
                throw new Exception(exceptionPrefix + "Missing ')' in data type definition: " + typeList[i]);
            }
            String[] params = typeString.substring(startPos + 1, endPos).split(",");
            for (int j = 0; j < params.length; j++) {
                if (typeString.startsWith("Reference("))
                    if (inProfile && !resolver.getResourceNames().contains(params[j].trim()) && !"Any".equals(params[j].trim()))
                        throw new Exception(exceptionPrefix + "Unknown resource " + params[j].trim());
                t.getParams().add(params[j].trim());
            }
            typeString = typeString.substring(0, startPos);
        }
        t.setName(typeString.trim());
        if (t.getName().equals("Element") && !allowElement)
            throw new Exception(exceptionPrefix + "The type 'Element' is illegal in this context");
        a.add(t);
    }
    return a;
}

Example 2 with BaseWorkerContext

use of org.hl7.fhir.r5.context.BaseWorkerContext 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());
    }
}