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

Example 96 with Source

use of org.hl7.fhir.utilities.validation.ValidationMessage.Source in project org.hl7.fhir.core by hapifhir.

the class StructureMapUtilities method executeDependency.

private void executeDependency(String indent, TransformContext context, StructureMap map, Variables vin, StructureMapGroupComponent group, StructureMapGroupRuleDependentComponent dependent) throws FHIRException {
    ResolvedGroup rg = resolveGroupReference(map, group, dependent.getName());
    if (rg.target.getInput().size() != dependent.getVariable().size()) {
        throw new FHIRException("Rule '" + dependent.getName() + "' has " + Integer.toString(rg.target.getInput().size()) + " but the invocation has " + Integer.toString(dependent.getVariable().size()) + " variables");
    }
    Variables v = new Variables();
    for (int i = 0; i < rg.target.getInput().size(); i++) {
        StructureMapGroupInputComponent input = rg.target.getInput().get(i);
        StringType rdp = dependent.getVariable().get(i);
        String var = rdp.asStringValue();
        VariableMode mode = input.getMode() == StructureMapInputMode.SOURCE ? VariableMode.INPUT : VariableMode.OUTPUT;
        Base vv = vin.get(mode, var);
        if (// * once source, always source. but target can be treated as source at user convenient
        vv == null && mode == VariableMode.INPUT)
            vv = vin.get(VariableMode.OUTPUT, var);
        if (vv == null)
            throw new FHIRException("Rule '" + dependent.getName() + "' " + mode.toString() + " variable '" + input.getName() + "' named as '" + var + "' has no value");
        v.add(mode, input.getName(), vv);
    }
    executeGroup(indent + "  ", context, rg.targetMap, v, rg.target);
}

Example 97 with Source

use of org.hl7.fhir.utilities.validation.ValidationMessage.Source in project org.hl7.fhir.core by hapifhir.

the class StructureMapUtilities method parseConceptMap.

private void parseConceptMap(StructureMap result, FHIRLexer lexer) throws FHIRLexerException {
    lexer.token("conceptmap");
    ConceptMap map = new ConceptMap();
    String id = lexer.readConstant("map id");
    if (!id.startsWith("#"))
        lexer.error("Concept Map identifier must start with #");
    map.setId(id);
    // todo: how to add this to the text format
    map.setStatus(PublicationStatus.DRAFT);
    result.getContained().add(map);
    lexer.token("{");
    lexer.skipComments();
    // lexer.token("source");
    // map.setSource(new UriType(lexer.readConstant("source")));
    // lexer.token("target");
    // map.setSource(new UriType(lexer.readConstant("target")));
    Map<String, String> prefixes = new HashMap<String, String>();
    while (lexer.hasToken("prefix")) {
        lexer.token("prefix");
        String n = lexer.take();
        lexer.token("=");
        String v = lexer.readConstant("prefix url");
        prefixes.put(n, v);
    }
    while (lexer.hasToken("unmapped")) {
        lexer.token("unmapped");
        lexer.token("for");
        String n = readPrefix(prefixes, lexer);
        ConceptMapGroupComponent g = getGroup(map, n, null);
        lexer.token("=");
        String v = lexer.take();
        if (v.equals("provided")) {
            g.getUnmapped().setMode(ConceptMapGroupUnmappedMode.PROVIDED);
        } else
            lexer.error("Only unmapped mode PROVIDED is supported at this time");
    }
    while (!lexer.hasToken("}")) {
        String srcs = readPrefix(prefixes, lexer);
        lexer.token(":");
        String sc = lexer.getCurrent().startsWith("\"") ? lexer.readConstant("code") : lexer.take();
        ConceptMapEquivalence eq = readEquivalence(lexer);
        String tgts = (eq != ConceptMapEquivalence.UNMATCHED) ? readPrefix(prefixes, lexer) : "";
        ConceptMapGroupComponent g = getGroup(map, srcs, tgts);
        SourceElementComponent e = g.addElement();
        e.setCode(sc);
        if (e.getCode().startsWith("\""))
            e.setCode(lexer.processConstant(e.getCode()));
        TargetElementComponent tgt = e.addTarget();
        if (eq != ConceptMapEquivalence.EQUIVALENT)
            tgt.setEquivalence(eq);
        if (tgt.getEquivalence() != ConceptMapEquivalence.UNMATCHED) {
            lexer.token(":");
            tgt.setCode(lexer.take());
            if (tgt.getCode().startsWith("\""))
                tgt.setCode(lexer.processConstant(tgt.getCode()));
        }
        if (lexer.hasComment())
            tgt.setComment(lexer.take().substring(2).trim());
    }
    lexer.token("}");
}

Example 98 with Source

use of org.hl7.fhir.utilities.validation.ValidationMessage.Source in project org.hl7.fhir.core by hapifhir.

the class ToolsHelper method executeRoundTrip.

public void executeRoundTrip(String[] args) throws IOException, FHIRException {
    FileInputStream in;
    File source = new CSFile(args[1]);
    File dest = new CSFile(args[2]);
    if (args.length >= 4) {
        Utilities.copyFile(args[1], args[3]);
    }
    if (!source.exists())
        throw new FHIRException("Source File \"" + source.getAbsolutePath() + "\" not found");
    in = new CSFileInputStream(source);
    XmlParser p = new XmlParser();
    JsonParser parser = new JsonParser();
    JsonParser pj = parser;
    Resource rf = p.parse(in);
    ByteArrayOutputStream json = new ByteArrayOutputStream();
    parser.setOutputStyle(OutputStyle.PRETTY);
    parser.compose(json, rf);
    json.close();
    TextFile.stringToFile(new String(json.toByteArray()), Utilities.changeFileExt(dest.getAbsolutePath(), ".json"));
    rf = pj.parse(new ByteArrayInputStream(json.toByteArray()));
    FileOutputStream s = new FileOutputStream(dest);
    new XmlParser().compose(s, rf, true);
    s.close();
}

Example 99 with Source

use of org.hl7.fhir.utilities.validation.ValidationMessage.Source in project org.hl7.fhir.core by hapifhir.

the class ToolsHelper method testRoundTrip.

public void testRoundTrip(String rootDir, String tmpDir, Collection<String> names) throws Throwable {
    try {
        System.err.println("Round trip from " + rootDir + " to " + tmpDir + ":" + Integer.toString(names.size()) + " files");
        for (String n : names) {
            System.err.print("  " + n);
            String source = rootDir + n + ".xml";
            // String tmpJson = tmpDir + n + ".json";
            String tmp = tmpDir + n.replace(File.separator, "-") + ".tmp";
            String dest = tmpDir + n.replace(File.separator, "-") + ".java.xml";
            FileInputStream in = new FileInputStream(source);
            XmlParser xp = new XmlParser();
            Resource r = xp.parse(in);
            System.err.print(".");
            JsonParser jp = new JsonParser();
            FileOutputStream out = new FileOutputStream(tmp);
            jp.setOutputStyle(OutputStyle.PRETTY);
            jp.compose(out, r);
            out.close();
            r = null;
            System.err.print(".");
            in = new FileInputStream(tmp);
            System.err.print(",");
            r = jp.parse(in);
            System.err.print(".");
            out = new FileOutputStream(dest);
            new XmlParser().compose(out, r, true);
            System.err.println("!");
            out.close();
            r = null;
            System.gc();
        }
    } catch (Throwable e) {
        System.err.println("Error: " + e.getMessage());
        throw e;
    }
}

Example 100 with Source

use of org.hl7.fhir.utilities.validation.ValidationMessage.Source in project org.hl7.fhir.core by hapifhir.

the class ToolsHelper method executeJson.

public String executeJson(String[] args) throws IOException, FHIRException {
    FileInputStream in;
    File source = new CSFile(args[1]);
    File dest = new CSFile(args[2]);
    File destc = new CSFile(Utilities.changeFileExt(args[2], ".canonical.json"));
    File destt = new CSFile(args[2] + ".tmp");
    File destr = new CSFile(Utilities.changeFileExt(args[2], ".ttl"));
    if (!source.exists())
        throw new FHIRException("Source File \"" + source.getAbsolutePath() + "\" not found");
    in = new CSFileInputStream(source);
    XmlParser p = new XmlParser();
    Resource rf = p.parse(in);
    JsonParser json = new JsonParser();
    json.setOutputStyle(OutputStyle.PRETTY);
    FileOutputStream s = new FileOutputStream(dest);
    json.compose(s, rf);
    s.close();
    json.setOutputStyle(OutputStyle.CANONICAL);
    s = new FileOutputStream(destc);
    json.compose(s, rf);
    s.close();
    json.setSuppressXhtml("Snipped for Brevity");
    json.setOutputStyle(OutputStyle.PRETTY);
    s = new FileOutputStream(destt);
    json.compose(s, rf);
    s.close();
    RdfParserBase rdf = new RdfParser();
    s = new FileOutputStream(destr);
    rdf.compose(s, rf);
    s.close();
    return TextFile.fileToString(destt.getAbsolutePath());
}