Examples with StructureMapUtilities org.hl7.fhir.r4.utils.StructureMapUtilities used on opensource projects

Example 6 with StructureMapUtilities

use of org.hl7.fhir.r4.utils.StructureMapUtilities in project org.hl7.fhir.core by hapifhir.

the class ResourceChecker method checkIsResource.

// protected static Manager.FhirFormat checkIsResource(SimpleWorkerContext context, boolean debug, String path) throws IOException {
// 
// if (Utilities.existsInList(ext, "json"))
// return Manager.FhirFormat.JSON;
// if (Utilities.existsInList(ext, "map"))
// return Manager.FhirFormat.TEXT;
// if (Utilities.existsInList(ext, "txt"))
// return Manager.FhirFormat.TEXT;
// if (Utilities.existsInList(ext, "jwt", "jws"))
// return Manager.FhirFormat.SHC;
// 
// return checkIsResource(context, debug, TextFile.fileToBytes(path), path);
// }
public static Manager.FhirFormat checkIsResource(SimpleWorkerContext context, boolean debug, byte[] cnt, String filename, boolean guessFromExtension) {
    System.out.println("   ..Detect format for " + filename);
    if (cnt.length == 0) {
        System.out.println("   " + filename + " is empty");
        return null;
    }
    if (guessFromExtension) {
        String ext = Utilities.getFileExtension(filename);
        if (Utilities.existsInList(ext, "xml")) {
            return FhirFormat.XML;
        }
        if (Utilities.existsInList(ext, "ttl")) {
            return FhirFormat.TURTLE;
        }
        if (Utilities.existsInList(ext, "map")) {
            return Manager.FhirFormat.TEXT;
        }
        if (Utilities.existsInList(ext, "jwt", "jws")) {
            return Manager.FhirFormat.SHC;
        }
        if (Utilities.existsInList(ext, "json")) {
            // no, we have to look inside, and decide.
            try {
                JsonObject json = JsonTrackingParser.parseJson(cnt);
                if (json.has("verifiableCredential")) {
                    return FhirFormat.SHC;
                }
            } catch (Exception e) {
            }
            return FhirFormat.JSON;
        }
        if (Utilities.existsInList(ext, "txt")) {
            try {
                String src = TextFile.bytesToString(cnt);
                if (src.startsWith("shc:/")) {
                    return FhirFormat.SHC;
                }
            } catch (Exception e) {
            }
            return Manager.FhirFormat.TEXT;
        }
    }
    try {
        Manager.parse(context, new ByteArrayInputStream(cnt), Manager.FhirFormat.JSON);
        return Manager.FhirFormat.JSON;
    } catch (Exception e) {
        if (debug) {
            System.out.println("Not JSON: " + e.getMessage());
        }
    }
    try {
        ValidatorUtils.parseXml(cnt);
        return Manager.FhirFormat.XML;
    } catch (Exception e) {
        if (debug) {
            System.out.println("Not XML: " + e.getMessage());
        }
    }
    try {
        Manager.parse(context, new ByteArrayInputStream(cnt), Manager.FhirFormat.TURTLE);
        return Manager.FhirFormat.TURTLE;
    } catch (Exception e) {
        if (debug) {
            System.out.println("Not Turtle: " + e.getMessage());
        }
    }
    try {
        String s = new String(cnt, StandardCharsets.UTF_8);
        if (s.startsWith("shc:/"))
            s = SHCParser.decodeQRCode(s);
        JWT jwt = new SHCParser(context).decodeJWT(s);
        return Manager.FhirFormat.SHC;
    } catch (Exception e) {
        if (debug) {
            System.out.println("Not a smart health card: " + e.getMessage());
        }
    }
    try {
        new StructureMapUtilities(context, null, null).parse(TextFile.bytesToString(cnt), null);
        return Manager.FhirFormat.TEXT;
    } catch (Exception e) {
        if (debug) {
            System.out.println("Not Text: " + e.getMessage());
        }
    }
    if (debug)
        System.out.println("     .. not a resource: " + filename);
    return null;
}

Example 7 with StructureMapUtilities

use of org.hl7.fhir.r4.utils.StructureMapUtilities in project org.hl7.fhir.core by hapifhir.

the class StructureMapUtilitiesTest method testParseRuleName.

@Test
public void testParseRuleName() throws IOException, FHIRException {
    StructureMapUtilities scu = new StructureMapUtilities(context, this);
    String fileMap = TestingUtilities.loadTestResource("r5", "structure-mapping", "ActivityDefinition.map");
    StructureMap structureMap = scu.parse(fileMap, "ActivityDefinition3To4");
    // StructureMap/ActivityDefinition3to4: StructureMap.group[3].rule[2].name error id value '"expression"' is not valid
    Assertions.assertEquals("expression", structureMap.getGroup().get(2).getRule().get(1).getName());
}

Example 8 with StructureMapUtilities

use of org.hl7.fhir.r4.utils.StructureMapUtilities in project org.hl7.fhir.core by hapifhir.

the class R3R4ConversionTests method test.

@SuppressWarnings("deprecation")
@ParameterizedTest(name = "{index}: id {0}")
@MethodSource("data")
public void test(String name, byte[] content) throws Exception {
    checkLoad();
    StructureMapUtilities smu4 = new StructureMapUtilities(contextR4, this);
    StructureMapUtilities smu3 = new StructureMapUtilities(contextR3, this);
    String tn = null;
    workingid = null;
    byte[] cnt = content;
    Exception executionError = null;
    List<ValidationMessage> r4validationErrors = new ArrayList<ValidationMessage>();
    String roundTripError = null;
    try {
        extras = new ArrayList<Resource>();
        // load the example (r3)
        org.hl7.fhir.r4.elementmodel.Element r3 = new org.hl7.fhir.r4.elementmodel.XmlParser(contextR3).parse(new ByteArrayInputStream(content));
        tn = r3.fhirType();
        workingid = r3.getChildValue("id");
        if (SAVING) {
            ByteArrayOutputStream bso = new ByteArrayOutputStream();
            new org.hl7.fhir.r4.elementmodel.JsonParser(contextR3).compose(r3, bso, OutputStyle.PRETTY, null);
            cnt = bso.toByteArray();
            Utilities.createDirectory(Utilities.path(TestingUtilities.home(), "implementations", "r3maps", "test-output"));
            TextFile.bytesToFile(cnt, Utilities.path(TestingUtilities.home(), "implementations", "r3maps", "test-output", tn + "-" + workingid + ".input.json"));
        }
        String mapFile = Utilities.path(TestingUtilities.home(), "implementations", "r3maps", "R3toR4", r3.fhirType() + ".map");
        if (new File(mapFile).exists()) {
            StructureMap sm = smu4.parse(TextFile.fileToString(mapFile), mapFile);
            tn = smu4.getTargetType(sm).getType();
            // convert from r3 to r4
            Resource r4 = ResourceFactory.createResource(tn);
            smu4.transform(contextR4, r3, sm, r4);
            ByteArrayOutputStream bs = new ByteArrayOutputStream();
            new org.hl7.fhir.r4.formats.JsonParser().setOutputStyle(OutputStyle.PRETTY).compose(bs, r4);
            if (SAVING) {
                TextFile.bytesToFile(bs.toByteArray(), Utilities.path(TestingUtilities.home(), "implementations", "r3maps", "test-output", tn + "-" + workingid + ".r4.json"));
                for (Resource r : extras) {
                    bs = new ByteArrayOutputStream();
                    new org.hl7.fhir.r4.formats.JsonParser().setOutputStyle(OutputStyle.PRETTY).compose(bs, r);
                    TextFile.bytesToFile(bs.toByteArray(), Utilities.path(TestingUtilities.home(), "implementations", "r3maps", "test-output", r.fhirType() + "-" + r.getId() + ".r4.json"));
                }
            }
            // validate against R4
            IResourceValidator validator = contextR4.newValidator();
            validator.setNoTerminologyChecks(true);
            validator.setFetcher(this);
            validator.validate(null, r4validationErrors, r4);
            // load the R4 to R3 map
            mapFile = Utilities.path(TestingUtilities.home(), "implementations", "r3maps", "R4toR3", getMapFor(r4.fhirType(), r3.fhirType()) + ".map");
            sm = smu3.parse(TextFile.fileToString(mapFile), mapFile);
            // convert to R3
            StructureDefinition sd = smu3.getTargetType(sm);
            org.hl7.fhir.r4.elementmodel.Element ro3 = Manager.build(contextR3, sd);
            smu3.transform(contextR3, r4, sm, ro3);
            // compare the XML
            bs = new ByteArrayOutputStream();
            new org.hl7.fhir.r4.elementmodel.JsonParser(contextR3).compose(ro3, bs, OutputStyle.PRETTY, null);
            if (SAVING)
                TextFile.bytesToFile(bs.toByteArray(), Utilities.path(TestingUtilities.home(), "implementations", "r3maps", "test-output", tn + "-" + workingid + ".output.json"));
            // check(errors, tn, workingid);
            roundTripError = TestingUtilities.checkJsonSrcIsSame(new String(cnt), new String(bs.toByteArray()), filter != null);
            if (roundTripError != null && roundTripError.equals(rules.getStringProperty(tn + "/" + workingid, "roundtrip")))
                roundTripError = null;
        } else {
            if (loadErrors.containsKey(r3.fhirType() + ".map")) {
                executionError = loadErrors.get(r3.fhirType() + ".map");
            }
        }
    } catch (Exception e) {
        executionError = e;
    }
    if (tn != null && workingid != null)
        updateOutcomes(tn, workingid, executionError, r4validationErrors, roundTripError);
    if (executionError != null)
        throw executionError;
}

Example 9 with StructureMapUtilities

use of org.hl7.fhir.r4.utils.StructureMapUtilities in project org.hl7.fhir.core by hapifhir.

the class R3R4ConversionTests method loadLib.

private void loadLib(String dir) throws FileNotFoundException, IOException {
    StructureMapUtilities smu = new StructureMapUtilities(contextR4);
    for (String s : new File(dir).list()) {
        String map = TextFile.fileToString(Utilities.path(dir, s));
        try {
            StructureMap sm = smu.parse(map, s);
            contextR3.cacheResource(sm);
            contextR4.cacheResource(sm);
            for (Resource r : sm.getContained()) {
                if (r instanceof MetadataResource) {
                    MetadataResource mr = (MetadataResource) r.copy();
                    mr.setUrl(sm.getUrl() + "#" + r.getId());
                    contextR3.cacheResource(mr);
                    contextR4.cacheResource(mr);
                }
            }
        } catch (FHIRException e) {
            System.out.println("Unable to load " + Utilities.path(dir, s) + ": " + e.getMessage());
            loadErrors.put(s, e);
        // e.printStackTrace();
        }
    }
}

Example 10 with StructureMapUtilities

use of org.hl7.fhir.r4.utils.StructureMapUtilities in project kindling by HL7.

the class PageProcessor method dtR3R4Transform.

private String dtR3R4Transform(String name) throws Exception {
    File f = new File(Utilities.path(folders.rootDir, "implementations", "r3maps", "R4toR3", name + ".map"));
    if (!f.exists()) {
        return "No R3/R4 map exists for " + name;
    }
    String n = name.toLowerCase();
    String status = r3r4StatusForResource(name);
    String fwds = TextFile.fileToString(Utilities.path(folders.rootDir, "implementations", "r3maps", "R3toR4", r3nameForResource(name) + ".map"));
    String bcks = TextFile.fileToString(Utilities.path(folders.rootDir, "implementations", "r3maps", "R4toR3", name + ".map"));
    String fwdsStatus = "";
    String bcksStatus = "";
    try {
        new StructureMapUtilities(workerContext).parse(fwds, r3nameForResource(name) + ".map");
    } catch (FHIRException e) {
        fwdsStatus = "<p style=\"background-color: #ffb3b3; border:1px solid maroon; padding: 5px;\">This script does not compile: " + e.getMessage() + "</p>\r\n";
    }
    try {
        new StructureMapUtilities(workerContext).parse(bcks, name + ".map");
    } catch (FHIRException e) {
        bcksStatus = "<p style=\"background-color: #ffb3b3; border:1px solid maroon; padding: 5px;\">This script does not compile: " + e.getMessage() + "</p>\r\n";
    }
    return "<p>Functional status for this map: " + status + " (based on R2 -> R3 -> R2 round tripping)</p>\r\n" + "\r\n" + "<h4>R3 to R4</h4>\r\n" + "\r\n" + "<div class=\"mapping\">\r\n" + "<pre>\r\n" + Utilities.escapeXml(fwds) + "\r\n" + "</pre>\r\n" + "</div>\r\n" + "\r\n" + fwdsStatus + "\r\n" + "\r\n" + "<h4>R4 to R3</h4>\r\n" + "\r\n" + "<div class=\"mapping\">\r\n" + "<pre>\r\n" + Utilities.escapeXml(bcks) + "\r\n" + "</pre>\r\n" + "</div>\r\n" + "\r\n" + bcksStatus + "\r\n";
}