Merge pull request #218 from ahdis/oliveregger_fml_conformsto
FHIR Mapping Language support for conformsTo function
This commit is contained in:
Grahame Grieve
GitHub
commit
eaab390aa4
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@ -1,149 +0,0 @@
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package org.hl7.fhir.r4.test;
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import org.hl7.fhir.exceptions.FHIRException;
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import org.hl7.fhir.r4.context.SimpleWorkerContext;
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import org.hl7.fhir.r4.elementmodel.Manager;
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import org.hl7.fhir.r4.elementmodel.Manager.FhirFormat;
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import org.hl7.fhir.r4.formats.IParser.OutputStyle;
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import org.hl7.fhir.r4.formats.JsonParser;
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import org.hl7.fhir.r4.model.*;
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import org.hl7.fhir.r4.model.StructureDefinition.StructureDefinitionKind;
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import org.hl7.fhir.r4.terminologies.ConceptMapEngine;
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import org.hl7.fhir.r4.test.utils.TestingUtilities;
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import org.hl7.fhir.r4.utils.StructureMapUtilities;
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import org.hl7.fhir.r4.utils.StructureMapUtilities.ITransformerServices;
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import org.hl7.fhir.utilities.TextFile;
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import org.hl7.fhir.utilities.Utilities;
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import org.hl7.fhir.utilities.cache.FilesystemPackageCacheManager;
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import org.hl7.fhir.utilities.cache.ToolsVersion;
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import org.hl7.fhir.utilities.xml.XMLUtil;
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import org.junit.jupiter.api.BeforeAll;
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import org.junit.jupiter.api.Disabled;
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import org.junit.jupiter.params.ParameterizedTest;
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import org.junit.jupiter.params.provider.Arguments;
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import org.junit.jupiter.params.provider.MethodSource;
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import org.w3c.dom.Document;
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import org.w3c.dom.Element;
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import org.xml.sax.SAXException;
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import javax.xml.parsers.ParserConfigurationException;
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import java.io.ByteArrayInputStream;
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import java.io.ByteArrayOutputStream;
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import java.io.FileNotFoundException;
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import java.io.IOException;
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import java.util.ArrayList;
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import java.util.List;
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import java.util.stream.Stream;
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import static org.junit.Assert.assertTrue;
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@Disabled
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public class FHIRMappingLanguageTests implements ITransformerServices {
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private List<Resource> outputs = new ArrayList<Resource>();
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static private SimpleWorkerContext context;
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static private JsonParser jsonParser;
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public static Stream<Arguments> data()
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throws FileNotFoundException, IOException, ParserConfigurationException, SAXException {
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Document tests = XMLUtil.parseFileToDom(TestingUtilities.resourceNameToFile("fml", "manifest.xml"));
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Element test = XMLUtil.getFirstChild(tests.getDocumentElement());
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List<Arguments> objects = new ArrayList();
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while (test != null && test.getNodeName().equals("test")) {
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objects.add(Arguments.of(test.getAttribute("name"), test.getAttribute("source"), test.getAttribute("map"),
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test.getAttribute("output")));
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test = XMLUtil.getNextSibling(test);
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}
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return objects.stream();
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}
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@BeforeAll
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static public void setUp() throws Exception {
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if (context == null) {
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FilesystemPackageCacheManager pcm = new FilesystemPackageCacheManager(true, ToolsVersion.TOOLS_VERSION);
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context = SimpleWorkerContext.fromPackage(pcm.loadPackage("hl7.fhir.core", "4.0.0"));
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jsonParser = new JsonParser();
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jsonParser.setOutputStyle(OutputStyle.PRETTY);
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}
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}
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@ParameterizedTest(name = "{index}: {0}")
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@MethodSource("data")
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public void test(String name, String source, String map, String output) throws Exception {
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String fileSource = TestingUtilities.resourceNameToFile("fml", source);
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String fileMap = TestingUtilities.resourceNameToFile("fml", map);
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String fileOutput = TestingUtilities.resourceNameToFile("fml", output);
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String fileOutputRes = TestingUtilities.resourceNameToFile("fml", output) + ".out";
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outputs.clear();
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boolean ok = false;
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String msg = null;
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Resource resource = null;
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try {
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StructureMapUtilities scu = new StructureMapUtilities(context, this);
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org.hl7.fhir.r4.elementmodel.Element src = Manager.parse(context,
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new ByteArrayInputStream(TextFile.fileToBytes(fileSource)), FhirFormat.JSON);
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StructureMap structureMap = scu.parse(TextFile.fileToString(fileMap), name);
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String typeName = scu.getTargetType(structureMap).getType();
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resource = ResourceFactory.createResource(typeName);
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scu.transform(null, src, structureMap, resource);
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ok = true;
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} catch (Exception e) {
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ok = false;
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msg = e.getMessage();
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}
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if (ok) {
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ByteArrayOutputStream boas = new ByteArrayOutputStream();
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jsonParser.compose(boas, resource);
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log(boas.toString());
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TextFile.bytesToFile(boas.toByteArray(), fileOutputRes);
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msg = TestingUtilities.checkJsonIsSame(fileOutputRes, fileOutput);
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assertTrue(msg, Utilities.noString(msg));
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} else
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assertTrue("Error, but proper output was expected (" + msg + ")", output.equals("$error"));
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}
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@Override
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public void log(String message) {
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System.out.println(message);
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}
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@Override
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public Base createType(Object appInfo, String name) throws FHIRException {
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StructureDefinition sd = context.fetchResource(StructureDefinition.class, name);
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if (sd != null && sd.getKind() == StructureDefinitionKind.LOGICAL) {
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return Manager.build(context, sd);
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} else {
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if (name.startsWith("http://hl7.org/fhir/StructureDefinition/"))
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name = name.substring("http://hl7.org/fhir/StructureDefinition/".length());
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return ResourceFactory.createResourceOrType(name);
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}
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}
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@Override
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public Base createResource(Object appInfo, Base res, boolean atRootofTransform) {
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if (atRootofTransform)
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outputs.add((Resource) res);
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return res;
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}
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@Override
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public Coding translate(Object appInfo, Coding source, String conceptMapUrl) throws FHIRException {
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ConceptMapEngine cme = new ConceptMapEngine(context);
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return cme.translate(source, conceptMapUrl);
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}
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@Override
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public Base resolveReference(Object appContext, String url) throws FHIRException {
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throw new FHIRException("resolveReference is not supported yet");
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}
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@Override
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public List<Base> performSearch(Object appContext, String url) throws FHIRException {
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throw new FHIRException("performSearch is not supported yet");
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}
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}
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@ -1 +0,0 @@
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*.out
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@ -1,6 +0,0 @@
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<fml-tests>
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<test name="http://github.com/hapifhir/org.hl7.fhir.core/org.hl7.fhir.r4.tests/qr2patassignment" source="qr.json" map="qr2pat-assignment.map" output="qr2pat-assignment-res.json" />
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<test name="http://github.com/hapifhir/org.hl7.fhir.core/org.hl7.fhir.r4.tests/qr2patgender" source="qr.json" map="qr2pat-gender.map" output="qr2pat-gender-res.json" />
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<test name="http://github.com/hapifhir/org.hl7.fhir.core/org.hl7.fhir.r4.tests/qr2pathumannametwice" source="qr.json" map="qr2pat-humannametwice.map" output="qr2pat-humannametwice-res.json" />
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<test name="http://github.com/hapifhir/org.hl7.fhir.core/org.hl7.fhir.r4.tests/qr2pathumannameshared" source="qr.json" map="qr2pat-humannameshared.map" output="qr2pat-humannameshared-res.json" />
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</fml-tests>
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{
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"resourceType": "QuestionnaireResponse",
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"status": "in-progress",
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"item": [
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{
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"linkId": "patient",
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"text": "Patient",
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"item": [
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{
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"linkId": "patient.lastname",
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"text": "Name",
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"answer": [
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{
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"valueString": "Brönnimann-Bertholet"
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}
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]
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},
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{
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"linkId": "patient.firstname",
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"text": "Vorname",
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"answer": [
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{
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"valueString": "Elisabeth"
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}
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]
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},
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{
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"linkId": "patient.sex",
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"text": "Geschlecht",
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"answer": [
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{
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"valueString": "female"
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}
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]
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}
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]
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}
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]
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}
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{
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"resourceType" : "Patient",
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"gender" : "female"
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}
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map "http://github.com/hapifhir/org.hl7.fhir.core/org.hl7.fhir.r4.tests/qr2patassignment" = "qr2patassignment"
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uses "http://hl7.org/fhir/StructureDefinition/QuestionnaireResponse" alias QuestionnaireResponse as source
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uses "http://hl7.org/fhir/StructureDefinition/Patient" alias Patient as target
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group QuestionnaireResponse(source src : QuestionnaireResponse, target tgt : Patient) {
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src -> tgt.gender = 'female' "Simple Assignment";
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}
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{
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"resourceType" : "Patient",
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"gender" : "female"
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}
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map "http://github.com/hapifhir/org.hl7.fhir.core/org.hl7.fhir.r4.tests/qr2patgender" = "qr2patgender"
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uses "http://hl7.org/fhir/StructureDefinition/QuestionnaireResponse" alias QuestionnaireResponse as source
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uses "http://hl7.org/fhir/StructureDefinition/Patient" alias Patient as target
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group QuestionnaireResponse(source src : QuestionnaireResponse, target tgt : Patient) {
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src.item as item -> tgt as patient then item(item, patient);
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}
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group item(source src, target tgt: Patient) {
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src.item as item where linkId.value in ('patient.sex') -> tgt.gender = (item.answer.valueString);
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}
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{
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"resourceType" : "Patient",
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"name" : [{
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"family" : "Brönnimann-Bertholet",
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"given" : ["Elisabeth"]
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}],
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"gender" : "female"
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}
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@ -1,26 +0,0 @@
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map "http://github.com/hapifhir/org.hl7.fhir.core/org.hl7.fhir.r4.tests/qr2pathumannameshared" = "qr2pathumannametwice"
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uses "http://hl7.org/fhir/StructureDefinition/QuestionnaireResponse" alias QuestionnaireResponse as source
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uses "http://hl7.org/fhir/StructureDefinition/Patient" alias Patient as target
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group entry(source src : QuestionnaireResponse, target tgt : Patient) {
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src.item as item then item(item, tgt);
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}
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group item(source src, target tgt) {
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src.item as item then item(item, tgt);
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src.item as item where linkId.value = 'patient.lastname' -> tgt.name as name share patientName then humanNameFamily(item, name);
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src.item as item where linkId.value = 'patient.firstname' -> tgt.name as name share patientName then humanNameGiven(item, name);
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src.item as item where linkId.value = 'patient.sex' -> tgt.gender = (item.answer.valueString);
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}
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group humanNameFamily(source src, target tgt: HumanName) {
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src.answer as answer -> tgt.family = (answer.valueString);
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}
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group humanNameGiven(source src, target tgt: HumanName) {
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src.answer as answer -> tgt.given = (answer.valueString);
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}
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group administrativeGender(source src, target tgt: code) {
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src.answer as answer -> tgt = (answer.valueString);
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}
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{
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"resourceType" : "Patient",
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"name" : [{
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"family" : "Brönnimann-Bertholet"
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},
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{
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"given" : ["Elisabeth"]
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}],
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"gender" : "female"
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}
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@ -1,26 +0,0 @@
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map "http://github.com/hapifhir/org.hl7.fhir.core/org.hl7.fhir.r4.tests/qr2pathumannametwice" = "qr2pathumannametwice"
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uses "http://hl7.org/fhir/StructureDefinition/QuestionnaireResponse" alias QuestionnaireResponse as source
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uses "http://hl7.org/fhir/StructureDefinition/Patient" alias Patient as target
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group entry(source src : QuestionnaireResponse, target tgt : Patient) {
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src.item as item then item(item, tgt);
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}
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group item(source src, target tgt) {
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src.item as item then item(item, tgt);
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src.item as item where linkId.value = 'patient.lastname' -> tgt.name as name then humanNameFamily(item, name);
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src.item as item where linkId.value = 'patient.firstname' -> tgt.name as name then humanNameGiven(item, name);
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src.item as item where linkId.value = 'patient.sex' -> tgt.gender = (item.answer.valueString);
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}
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group humanNameFamily(source src, target tgt: HumanName) {
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src.answer as answer -> tgt.family = (answer.valueString);
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}
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group humanNameGiven(source src, target tgt: HumanName) {
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src.answer as answer -> tgt.given = (answer.valueString);
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}
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group administrativeGender(source src, target tgt: code) {
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src.answer as answer -> tgt = (answer.valueString);
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}
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@ -213,18 +213,26 @@ public class StructureMapUtilities {
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return services.resolveReference(appContext, url);
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}
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private boolean noErrorValidationMessages(List<ValidationMessage> valerrors) {
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boolean ok = true;
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for (ValidationMessage v : valerrors)
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ok = ok && !v.getLevel().isError();
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return ok;
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}
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@Override
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public boolean conformsToProfile(Object appContext, Base item, String url) throws FHIRException {
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IResourceValidator val = worker.newValidator();
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List<ValidationMessage> valerrors = new ArrayList<ValidationMessage>();
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if (item instanceof Resource) {
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val.validate(appContext, valerrors, (Resource) item, url);
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boolean ok = true;
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for (ValidationMessage v : valerrors)
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ok = ok && v.getLevel().isError();
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return ok;
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return noErrorValidationMessages(valerrors);
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}
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throw new NotImplementedException("Not done yet (FFHIRPathHostServices.conformsToProfile), when item is element");
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if (item instanceof Element) {
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val.validate(appContext, valerrors, (Element) item, url);
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return noErrorValidationMessages(valerrors);
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}
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throw new NotImplementedException("Not done yet (FFHIRPathHostServices.conformsToProfile), when item is not element or not resource");
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}
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@Override
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@ -36,8 +36,8 @@ import org.hl7.fhir.utilities.Utilities;
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import org.hl7.fhir.utilities.cache.FilesystemPackageCacheManager;
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import org.hl7.fhir.utilities.cache.ToolsVersion;
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import org.hl7.fhir.utilities.xml.XMLUtil;
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import org.hl7.fhir.validation.instance.InstanceValidatorFactory;
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import org.junit.jupiter.api.BeforeAll;
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import org.junit.jupiter.api.Disabled;
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import org.junit.jupiter.params.ParameterizedTest;
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import org.junit.jupiter.params.provider.Arguments;
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import org.junit.jupiter.params.provider.MethodSource;
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@ -68,14 +68,16 @@ public class FHIRMappingLanguageTests implements ITransformerServices {
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@BeforeAll
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public static void setUp() throws Exception {
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FilesystemPackageCacheManager pcm = new FilesystemPackageCacheManager(true, ToolsVersion.TOOLS_VERSION);
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context = SimpleWorkerContext.fromPackage(pcm.loadPackage("hl7.fhir.core", "4.0.1"));
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context = SimpleWorkerContext.fromPackage(pcm.loadPackage("hl7.fhir.r5.core", "current"));
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if (context.getValidatorFactory() == null) {
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context.setValidatorFactory(new InstanceValidatorFactory());
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}
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jsonParser = new JsonParser();
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jsonParser.setOutputStyle(OutputStyle.PRETTY);
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}
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@ParameterizedTest(name = "{index}: {0}")
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@MethodSource("data")
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@Disabled // Test fails: java.lang.AssertionError: Error, but proper output was expected (This does not appear to be a FHIR resource (unknown name "QuestionnaireResponse")
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public void test(String name, String source, String map, String output) throws Exception {
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InputStream fileSource = TestingUtilities.loadTestResourceStream("r5", "fml", source);
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