Examples with Source org.hl7.fhir.utilities.validation.ValidationMessage.Source used on opensource projects

Example 16 with Source

use of org.hl7.fhir.utilities.validation.ValidationMessage.Source in project kindling by HL7.

the class BindingsParser method loadValueSet.

private ValueSet loadValueSet(String ref, String committee) throws Exception {
    String folder = new File(filename).getParent();
    String srcName;
    IParser p;
    if (new File(Utilities.path(folder, ref + ".xml")).exists()) {
        p = new XmlParser();
        srcName = Utilities.path(folder, ref + ".xml");
    } else if (new File(Utilities.path(folder, ref + ".json")).exists()) {
        p = new JsonParser();
        srcName = Utilities.path(folder, ref + ".json");
    } else
        throw new Exception("Unable to find source for " + ref + " in " + filename + " (" + Utilities.path(folder, ref + ".xml/json)"));
    FileInputStream input = new FileInputStream(srcName);
    try {
        ValueSet result = ValueSetUtilities.makeShareable((ValueSet) p.parse(input));
        result.setId(ref.substring(9));
        if (!result.hasExperimental())
            result.setExperimental(false);
        // if (!result.hasUrl())
        result.setUrl("http://hl7.org/fhir/ValueSet/" + ref.substring(9));
        if (!result.hasVersion() || result.getUrl().startsWith("http://hl7.org/fhir"))
            result.setVersion(version);
        if (!Utilities.noString(committee)) {
            if (!result.hasExtension(ToolingExtensions.EXT_WORKGROUP)) {
                result.addExtension().setUrl(ToolingExtensions.EXT_WORKGROUP).setValue(new CodeType(committee));
            } else {
                String ec = ToolingExtensions.readStringExtension(result, ToolingExtensions.EXT_WORKGROUP);
                if (!ec.equals(committee))
                    System.out.println("ValueSet " + result.getUrl() + " WG mismatch 1: is " + ec + ", want to set to " + committee);
            }
        }
        result.setUserData("filename", "valueset-" + ref.substring(9));
        result.setUserData("path", "valueset-" + ref.substring(9) + ".html");
        new CodeSystemConvertor(codeSystems).convert(p, result, srcName, packageInfo);
        return result;
    } finally {
        IOUtils.closeQuietly(input);
    }
}

Example 17 with Source

use of org.hl7.fhir.utilities.validation.ValidationMessage.Source in project kindling by HL7.

the class OldSpreadsheetParser method findContext.

private ElementDefn findContext(ElementDefn root, String pathname, String source) throws Exception {
    String[] path = pathname.split("\\.");
    if (!path[0].equals(root.getName()))
        throw new Exception("Element Path '" + pathname + "' is not legal found at " + source);
    ElementDefn res = root;
    for (int i = 1; i < path.length; i++) {
        String en = path[i];
        if (en.length() == 0)
            throw new Exception("Improper path " + pathname + " found at " + source);
        if (en.charAt(en.length() - 1) == '*')
            throw new Exception("no-list wrapper found at " + source);
        ElementDefn t = res.getElementByName(en, true, definitions, "find context", false);
        if (t == null) {
            throw new Exception("Reference to undefined Element " + pathname + " found at " + source);
        }
        res = t;
    }
    return res;
}

Example 18 with Source

use of org.hl7.fhir.utilities.validation.ValidationMessage.Source in project kindling by HL7.

the class SourceParser method loadIgs.

private void loadIgs() throws Exception {
    DocumentBuilderFactory factory = DocumentBuilderFactory.newInstance();
    factory.setNamespaceAware(true);
    DocumentBuilder builder = factory.newDocumentBuilder();
    Document xdoc = builder.parse(new CSFileInputStream(srcDir + "igs.xml"));
    Element root = xdoc.getDocumentElement();
    if (root.getNodeName().equals("igs")) {
        Element ig = XMLUtil.getFirstChild(root);
        while (ig != null) {
            if (ig.getNodeName().equals("ig") && (!ig.hasAttribute("local") || isOkLocally(ig.getAttribute("code"))) && !isRuledOutLocally(ig.getAttribute("code"))) {
                ImplementationGuideDefn igg = new ImplementationGuideDefn(ig.getAttribute("committee"), ig.getAttribute("code"), ig.getAttribute("name"), ig.getAttribute("brief"), ig.getAttribute("source").replace('\\', File.separatorChar), "1".equals(ig.getAttribute("review")), ig.getAttribute("ballot"), ig.getAttribute("fmm"), ig.getAttribute("section"), "yes".equals(ig.getAttribute("core")), page.getValidationErrors());
                definitions.getIgs().put(igg.getCode(), igg);
                definitions.getSortedIgs().add(igg);
            }
            ig = XMLUtil.getNextSibling(ig);
        }
    }
}

Example 19 with Source

use of org.hl7.fhir.utilities.validation.ValidationMessage.Source in project kindling by HL7.

the class SourceParser method checkConditions.

public void checkConditions(List<String> errors, Map<String, Long> dates) throws Exception {
    Utilities.checkFolder(srcDir, errors);
    Utilities.checkFolder(termDir, errors);
    Utilities.checkFolder(imgDir, errors);
    this.dates = dates;
    checkFile("required", termDir, "bindings.xml", errors, "all");
    checkFile("required", dtDir, "primitives.xml", errors, "all");
    for (String n : ini.getPropertyNames("types")) if (ini.getStringProperty("types", n).equals("")) {
        TypeRef t = new TypeParser(version.toString()).parse(n, false, null, context, true).get(0);
        checkFile("type definition", dtDir, t.getName().toLowerCase() + ".xml", errors, "all");
    }
    String[] shared = ini.getPropertyNames("shared");
    if (shared != null)
        for (String n : shared) checkFile("shared structure definition", dtDir, n.toLowerCase() + ".xml", errors, "all");
    for (String n : ini.getPropertyNames("infrastructure")) checkFile("infrastructure definition", dtDir, n.toLowerCase() + ".xml", errors, "all");
    for (String n : ini.getPropertyNames("resources")) {
        if (!new File(srcDir + n).exists())
            errors.add("unable to find folder for resource " + n);
        else {
            for (String fn : new File(srcDir + n + File.separatorChar).list()) checkFile("source", srcDir + n + File.separatorChar, fn, errors, n);
        }
    }
    for (String n : ini.getPropertyNames("special-resources")) {
        // now iterate all the files in the directory checking data
        for (String fn : new File(srcDir + n + File.separatorChar).list()) checkFile("source", srcDir + n + File.separatorChar, fn, errors, n);
    }
}

Example 20 with Source

use of org.hl7.fhir.utilities.validation.ValidationMessage.Source in project kindling by HL7.

the class ADLImporter method execute.

private void execute() throws Exception {
    // load config
    DocumentBuilderFactory factory = DocumentBuilderFactory.newInstance();
    factory.setNamespaceAware(true);
    DocumentBuilder builder = factory.newDocumentBuilder();
    adlConfig = builder.parse(new FileInputStream(config)).getDocumentElement();
    // load ADL
    builder = factory.newDocumentBuilder();
    adl = builder.parse(new FileInputStream(source)).getDocumentElement();
    check("root", adl.getNamespaceURI(), "http://schemas.openehr.org/v1", "Wrong namespace for ADL XML");
    check("root", adl.getNodeName(), "archetype", "Wrong XML for ADL XML");
    check("root", XMLUtil.getNamedChild(adl, "adl_version").getTextContent(), "1.4", "unsupported ADL version");
    String id = XMLUtil.getFirstChild(XMLUtil.getNamedChild(adl, "archetype_id")).getTextContent().split("\\.")[1];
    String baseType = XMLUtil.getNamedChild(XMLUtil.getNamedChild(adl, "definition"), "rm_type_name").getTextContent();
    if (!baseType.equals("OBSERVATION"))
        return;
    // load texts from ontology
    List<Element> set = new ArrayList<Element>();
    Element ontology = XMLUtil.getNamedChild(adl, "ontology");
    Element term_definitions = XMLUtil.getNamedChild(ontology, "term_definitions");
    set.clear();
    XMLUtil.getNamedChildren(term_definitions, "items", set);
    for (Element item : set) {
        processTextItem(item);
    }
    // create structure definition
    StructureDefinition sd = new StructureDefinition();
    sd.setId("netha-" + id);
    sd.setUrl("http://hl7.org/fhir/StructureDefinition/" + sd.getId());
    sd.setKind(StructureDefinitionKind.LOGICAL);
    populateMetadata(set, sd);
    // load data and protocol
    Element definition = XMLUtil.getNamedChild(adl, "definition");
    NodeTreeEntry root = new NodeTreeEntry();
    root.typeName = XMLUtil.getNamedChild(definition, "rm_type_name").getTextContent();
    root.atCode = XMLUtil.getNamedChild(definition, "node_id").getTextContent();
    root.name = generateToken(root.atCode, true);
    sd.setName(root.name);
    root.cardinality = readCardinality("root", XMLUtil.getNamedChild(definition, "occurrences"));
    set.clear();
    XMLUtil.getNamedChildren(definition, "attributes", set);
    for (Element item : set) {
        // we're actually skipping this level - we don't care about data protocol etc.
        // XMLUtil.getNamedChild(XMLUtil.getNamedChild(item, "children"), "attributes");
        Element attributes = item;
        loadChildren(root.atCode, root, attributes);
    }
    dumpChildren("", root);
    genElements(sd, root.name, root);
    // save
    new XmlParser().setOutputStyle(OutputStyle.PRETTY).compose(new FileOutputStream(dest), sd);
    System.out.println("done. saved as " + dest);
}