remove disabled r4 fml tests
This commit is contained in:
Oliver Egger
parent
72d250a40a
commit
ae4c3bbe0c
|
|
@ -1,149 +0,0 @@
|
||||||
package org.hl7.fhir.r4.test;
|
|
||||||
|
|
||||||
import org.hl7.fhir.exceptions.FHIRException;
|
|
||||||
import org.hl7.fhir.r4.context.SimpleWorkerContext;
|
|
||||||
import org.hl7.fhir.r4.elementmodel.Manager;
|
|
||||||
import org.hl7.fhir.r4.elementmodel.Manager.FhirFormat;
|
|
||||||
import org.hl7.fhir.r4.formats.IParser.OutputStyle;
|
|
||||||
import org.hl7.fhir.r4.formats.JsonParser;
|
|
||||||
import org.hl7.fhir.r4.model.*;
|
|
||||||
import org.hl7.fhir.r4.model.StructureDefinition.StructureDefinitionKind;
|
|
||||||
import org.hl7.fhir.r4.terminologies.ConceptMapEngine;
|
|
||||||
import org.hl7.fhir.r4.test.utils.TestingUtilities;
|
|
||||||
import org.hl7.fhir.r4.utils.StructureMapUtilities;
|
|
||||||
import org.hl7.fhir.r4.utils.StructureMapUtilities.ITransformerServices;
|
|
||||||
import org.hl7.fhir.utilities.TextFile;
|
|
||||||
import org.hl7.fhir.utilities.Utilities;
|
|
||||||
import org.hl7.fhir.utilities.cache.FilesystemPackageCacheManager;
|
|
||||||
import org.hl7.fhir.utilities.cache.ToolsVersion;
|
|
||||||
import org.hl7.fhir.utilities.xml.XMLUtil;
|
|
||||||
import org.junit.jupiter.api.BeforeAll;
|
|
||||||
import org.junit.jupiter.api.Disabled;
|
|
||||||
import org.junit.jupiter.params.ParameterizedTest;
|
|
||||||
import org.junit.jupiter.params.provider.Arguments;
|
|
||||||
import org.junit.jupiter.params.provider.MethodSource;
|
|
||||||
import org.w3c.dom.Document;
|
|
||||||
import org.w3c.dom.Element;
|
|
||||||
import org.xml.sax.SAXException;
|
|
||||||
|
|
||||||
import javax.xml.parsers.ParserConfigurationException;
|
|
||||||
import java.io.ByteArrayInputStream;
|
|
||||||
import java.io.ByteArrayOutputStream;
|
|
||||||
import java.io.FileNotFoundException;
|
|
||||||
import java.io.IOException;
|
|
||||||
import java.util.ArrayList;
|
|
||||||
import java.util.List;
|
|
||||||
import java.util.stream.Stream;
|
|
||||||
|
|
||||||
import static org.junit.Assert.assertTrue;
|
|
||||||
|
|
||||||
@Disabled
|
|
||||||
public class FHIRMappingLanguageTests implements ITransformerServices {
|
|
||||||
|
|
||||||
private List<Resource> outputs = new ArrayList<Resource>();
|
|
||||||
|
|
||||||
static private SimpleWorkerContext context;
|
|
||||||
static private JsonParser jsonParser;
|
|
||||||
|
|
||||||
public static Stream<Arguments> data()
|
|
||||||
throws FileNotFoundException, IOException, ParserConfigurationException, SAXException {
|
|
||||||
Document tests = XMLUtil.parseFileToDom(TestingUtilities.resourceNameToFile("fml", "manifest.xml"));
|
|
||||||
Element test = XMLUtil.getFirstChild(tests.getDocumentElement());
|
|
||||||
List<Arguments> objects = new ArrayList();
|
|
||||||
while (test != null && test.getNodeName().equals("test")) {
|
|
||||||
objects.add(Arguments.of(test.getAttribute("name"), test.getAttribute("source"), test.getAttribute("map"),
|
|
||||||
test.getAttribute("output")));
|
|
||||||
test = XMLUtil.getNextSibling(test);
|
|
||||||
}
|
|
||||||
return objects.stream();
|
|
||||||
}
|
|
||||||
|
|
||||||
@BeforeAll
|
|
||||||
static public void setUp() throws Exception {
|
|
||||||
if (context == null) {
|
|
||||||
FilesystemPackageCacheManager pcm = new FilesystemPackageCacheManager(true, ToolsVersion.TOOLS_VERSION);
|
|
||||||
context = SimpleWorkerContext.fromPackage(pcm.loadPackage("hl7.fhir.core", "4.0.0"));
|
|
||||||
jsonParser = new JsonParser();
|
|
||||||
jsonParser.setOutputStyle(OutputStyle.PRETTY);
|
|
||||||
}
|
|
||||||
}
|
|
||||||
|
|
||||||
@ParameterizedTest(name = "{index}: {0}")
|
|
||||||
@MethodSource("data")
|
|
||||||
public void test(String name, String source, String map, String output) throws Exception {
|
|
||||||
|
|
||||||
String fileSource = TestingUtilities.resourceNameToFile("fml", source);
|
|
||||||
String fileMap = TestingUtilities.resourceNameToFile("fml", map);
|
|
||||||
String fileOutput = TestingUtilities.resourceNameToFile("fml", output);
|
|
||||||
String fileOutputRes = TestingUtilities.resourceNameToFile("fml", output) + ".out";
|
|
||||||
|
|
||||||
outputs.clear();
|
|
||||||
|
|
||||||
boolean ok = false;
|
|
||||||
String msg = null;
|
|
||||||
Resource resource = null;
|
|
||||||
try {
|
|
||||||
StructureMapUtilities scu = new StructureMapUtilities(context, this);
|
|
||||||
org.hl7.fhir.r4.elementmodel.Element src = Manager.parse(context,
|
|
||||||
new ByteArrayInputStream(TextFile.fileToBytes(fileSource)), FhirFormat.JSON);
|
|
||||||
StructureMap structureMap = scu.parse(TextFile.fileToString(fileMap), name);
|
|
||||||
String typeName = scu.getTargetType(structureMap).getType();
|
|
||||||
resource = ResourceFactory.createResource(typeName);
|
|
||||||
scu.transform(null, src, structureMap, resource);
|
|
||||||
ok = true;
|
|
||||||
} catch (Exception e) {
|
|
||||||
ok = false;
|
|
||||||
msg = e.getMessage();
|
|
||||||
}
|
|
||||||
if (ok) {
|
|
||||||
ByteArrayOutputStream boas = new ByteArrayOutputStream();
|
|
||||||
jsonParser.compose(boas, resource);
|
|
||||||
log(boas.toString());
|
|
||||||
TextFile.bytesToFile(boas.toByteArray(), fileOutputRes);
|
|
||||||
msg = TestingUtilities.checkJsonIsSame(fileOutputRes, fileOutput);
|
|
||||||
assertTrue(msg, Utilities.noString(msg));
|
|
||||||
} else
|
|
||||||
assertTrue("Error, but proper output was expected (" + msg + ")", output.equals("$error"));
|
|
||||||
}
|
|
||||||
|
|
||||||
@Override
|
|
||||||
public void log(String message) {
|
|
||||||
System.out.println(message);
|
|
||||||
}
|
|
||||||
|
|
||||||
@Override
|
|
||||||
public Base createType(Object appInfo, String name) throws FHIRException {
|
|
||||||
StructureDefinition sd = context.fetchResource(StructureDefinition.class, name);
|
|
||||||
if (sd != null && sd.getKind() == StructureDefinitionKind.LOGICAL) {
|
|
||||||
return Manager.build(context, sd);
|
|
||||||
} else {
|
|
||||||
if (name.startsWith("http://hl7.org/fhir/StructureDefinition/"))
|
|
||||||
name = name.substring("http://hl7.org/fhir/StructureDefinition/".length());
|
|
||||||
return ResourceFactory.createResourceOrType(name);
|
|
||||||
}
|
|
||||||
}
|
|
||||||
|
|
||||||
@Override
|
|
||||||
public Base createResource(Object appInfo, Base res, boolean atRootofTransform) {
|
|
||||||
if (atRootofTransform)
|
|
||||||
outputs.add((Resource) res);
|
|
||||||
return res;
|
|
||||||
}
|
|
||||||
|
|
||||||
@Override
|
|
||||||
public Coding translate(Object appInfo, Coding source, String conceptMapUrl) throws FHIRException {
|
|
||||||
ConceptMapEngine cme = new ConceptMapEngine(context);
|
|
||||||
return cme.translate(source, conceptMapUrl);
|
|
||||||
}
|
|
||||||
|
|
||||||
@Override
|
|
||||||
public Base resolveReference(Object appContext, String url) throws FHIRException {
|
|
||||||
throw new FHIRException("resolveReference is not supported yet");
|
|
||||||
}
|
|
||||||
|
|
||||||
@Override
|
|
||||||
public List<Base> performSearch(Object appContext, String url) throws FHIRException {
|
|
||||||
throw new FHIRException("performSearch is not supported yet");
|
|
||||||
}
|
|
||||||
|
|
||||||
}
|
|
||||||
|
|
@ -1 +0,0 @@
|
||||||
*.out
|
|
||||||
|
|
@ -1,6 +0,0 @@
|
||||||
<fml-tests>
|
|
||||||
<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" />
|
|
||||||
<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" />
|
|
||||||
<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" />
|
|
||||||
<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" />
|
|
||||||
</fml-tests>
|
|
||||||
|
|
@ -1,39 +0,0 @@
|
||||||
{
|
|
||||||
"resourceType": "QuestionnaireResponse",
|
|
||||||
"status": "in-progress",
|
|
||||||
"item": [
|
|
||||||
{
|
|
||||||
"linkId": "patient",
|
|
||||||
"text": "Patient",
|
|
||||||
"item": [
|
|
||||||
{
|
|
||||||
"linkId": "patient.lastname",
|
|
||||||
"text": "Name",
|
|
||||||
"answer": [
|
|
||||||
{
|
|
||||||
"valueString": "Brönnimann-Bertholet"
|
|
||||||
}
|
|
||||||
]
|
|
||||||
},
|
|
||||||
{
|
|
||||||
"linkId": "patient.firstname",
|
|
||||||
"text": "Vorname",
|
|
||||||
"answer": [
|
|
||||||
{
|
|
||||||
"valueString": "Elisabeth"
|
|
||||||
}
|
|
||||||
]
|
|
||||||
},
|
|
||||||
{
|
|
||||||
"linkId": "patient.sex",
|
|
||||||
"text": "Geschlecht",
|
|
||||||
"answer": [
|
|
||||||
{
|
|
||||||
"valueString": "female"
|
|
||||||
}
|
|
||||||
]
|
|
||||||
}
|
|
||||||
]
|
|
||||||
}
|
|
||||||
]
|
|
||||||
}
|
|
||||||
|
|
@ -1,4 +0,0 @@
|
||||||
{
|
|
||||||
"resourceType" : "Patient",
|
|
||||||
"gender" : "female"
|
|
||||||
}
|
|
||||||
|
|
@ -1,8 +0,0 @@
|
||||||
map "http://github.com/hapifhir/org.hl7.fhir.core/org.hl7.fhir.r4.tests/qr2patassignment" = "qr2patassignment"
|
|
||||||
|
|
||||||
uses "http://hl7.org/fhir/StructureDefinition/QuestionnaireResponse" alias QuestionnaireResponse as source
|
|
||||||
uses "http://hl7.org/fhir/StructureDefinition/Patient" alias Patient as target
|
|
||||||
|
|
||||||
group QuestionnaireResponse(source src : QuestionnaireResponse, target tgt : Patient) {
|
|
||||||
src -> tgt.gender = 'female' "Simple Assignment";
|
|
||||||
}
|
|
||||||
|
|
@ -1,4 +0,0 @@
|
||||||
{
|
|
||||||
"resourceType" : "Patient",
|
|
||||||
"gender" : "female"
|
|
||||||
}
|
|
||||||
|
|
@ -1,12 +0,0 @@
|
||||||
map "http://github.com/hapifhir/org.hl7.fhir.core/org.hl7.fhir.r4.tests/qr2patgender" = "qr2patgender"
|
|
||||||
|
|
||||||
uses "http://hl7.org/fhir/StructureDefinition/QuestionnaireResponse" alias QuestionnaireResponse as source
|
|
||||||
uses "http://hl7.org/fhir/StructureDefinition/Patient" alias Patient as target
|
|
||||||
|
|
||||||
group QuestionnaireResponse(source src : QuestionnaireResponse, target tgt : Patient) {
|
|
||||||
src.item as item -> tgt as patient then item(item, patient);
|
|
||||||
}
|
|
||||||
|
|
||||||
group item(source src, target tgt: Patient) {
|
|
||||||
src.item as item where linkId.value in ('patient.sex') -> tgt.gender = (item.answer.valueString);
|
|
||||||
}
|
|
||||||
|
|
@ -1,8 +0,0 @@
|
||||||
{
|
|
||||||
"resourceType" : "Patient",
|
|
||||||
"name" : [{
|
|
||||||
"family" : "Brönnimann-Bertholet",
|
|
||||||
"given" : ["Elisabeth"]
|
|
||||||
}],
|
|
||||||
"gender" : "female"
|
|
||||||
}
|
|
||||||
|
|
@ -1,26 +0,0 @@
|
||||||
map "http://github.com/hapifhir/org.hl7.fhir.core/org.hl7.fhir.r4.tests/qr2pathumannameshared" = "qr2pathumannametwice"
|
|
||||||
|
|
||||||
uses "http://hl7.org/fhir/StructureDefinition/QuestionnaireResponse" alias QuestionnaireResponse as source
|
|
||||||
uses "http://hl7.org/fhir/StructureDefinition/Patient" alias Patient as target
|
|
||||||
|
|
||||||
group entry(source src : QuestionnaireResponse, target tgt : Patient) {
|
|
||||||
src.item as item then item(item, tgt);
|
|
||||||
}
|
|
||||||
|
|
||||||
group item(source src, target tgt) {
|
|
||||||
src.item as item then item(item, tgt);
|
|
||||||
src.item as item where linkId.value = 'patient.lastname' -> tgt.name as name share patientName then humanNameFamily(item, name);
|
|
||||||
src.item as item where linkId.value = 'patient.firstname' -> tgt.name as name share patientName then humanNameGiven(item, name);
|
|
||||||
src.item as item where linkId.value = 'patient.sex' -> tgt.gender = (item.answer.valueString);
|
|
||||||
}
|
|
||||||
|
|
||||||
group humanNameFamily(source src, target tgt: HumanName) {
|
|
||||||
src.answer as answer -> tgt.family = (answer.valueString);
|
|
||||||
}
|
|
||||||
group humanNameGiven(source src, target tgt: HumanName) {
|
|
||||||
src.answer as answer -> tgt.given = (answer.valueString);
|
|
||||||
}
|
|
||||||
|
|
||||||
group administrativeGender(source src, target tgt: code) {
|
|
||||||
src.answer as answer -> tgt = (answer.valueString);
|
|
||||||
}
|
|
||||||
|
|
@ -1,10 +0,0 @@
|
||||||
{
|
|
||||||
"resourceType" : "Patient",
|
|
||||||
"name" : [{
|
|
||||||
"family" : "Brönnimann-Bertholet"
|
|
||||||
},
|
|
||||||
{
|
|
||||||
"given" : ["Elisabeth"]
|
|
||||||
}],
|
|
||||||
"gender" : "female"
|
|
||||||
}
|
|
||||||
|
|
@ -1,26 +0,0 @@
|
||||||
map "http://github.com/hapifhir/org.hl7.fhir.core/org.hl7.fhir.r4.tests/qr2pathumannametwice" = "qr2pathumannametwice"
|
|
||||||
|
|
||||||
uses "http://hl7.org/fhir/StructureDefinition/QuestionnaireResponse" alias QuestionnaireResponse as source
|
|
||||||
uses "http://hl7.org/fhir/StructureDefinition/Patient" alias Patient as target
|
|
||||||
|
|
||||||
group entry(source src : QuestionnaireResponse, target tgt : Patient) {
|
|
||||||
src.item as item then item(item, tgt);
|
|
||||||
}
|
|
||||||
|
|
||||||
group item(source src, target tgt) {
|
|
||||||
src.item as item then item(item, tgt);
|
|
||||||
src.item as item where linkId.value = 'patient.lastname' -> tgt.name as name then humanNameFamily(item, name);
|
|
||||||
src.item as item where linkId.value = 'patient.firstname' -> tgt.name as name then humanNameGiven(item, name);
|
|
||||||
src.item as item where linkId.value = 'patient.sex' -> tgt.gender = (item.answer.valueString);
|
|
||||||
}
|
|
||||||
|
|
||||||
group humanNameFamily(source src, target tgt: HumanName) {
|
|
||||||
src.answer as answer -> tgt.family = (answer.valueString);
|
|
||||||
}
|
|
||||||
group humanNameGiven(source src, target tgt: HumanName) {
|
|
||||||
src.answer as answer -> tgt.given = (answer.valueString);
|
|
||||||
}
|
|
||||||
|
|
||||||
group administrativeGender(source src, target tgt: code) {
|
|
||||||
src.answer as answer -> tgt = (answer.valueString);
|
|
||||||
}
|
|
||||||
Loading…
Reference in New Issue