fix R4 compilation error and update pr for R5
This commit is contained in:
Oliver Egger
parent
1c73a3771e
commit
f659b67307
|
|
@ -80,9 +80,8 @@ public class FHIRMappingLanguageTests implements ITransformerServices {
|
|||
@BeforeClass
|
||||
static public void setUp() throws Exception {
|
||||
if (context == null) {
|
||||
context = new SimpleWorkerContext();
|
||||
PackageCacheManager pcm = new PackageCacheManager(true, ToolsVersion.TOOLS_VERSION);
|
||||
context.loadFromPackage(pcm.loadPackageCacheLatest("hl7.fhir.core"), null, "StructureDefinition");
|
||||
context = SimpleWorkerContext.fromPackage(pcm.loadPackage("hl7.fhir.core", "4.0.0"));
|
||||
jsonParser = new JsonParser();
|
||||
jsonParser.setOutputStyle(OutputStyle.PRETTY);
|
||||
}
|
||||
|
|
|
|||
|
|
@ -1170,11 +1170,13 @@ public class StructureMapUtilities {
|
|||
target.addListMode(StructureMapTargetListMode.SHARE);
|
||||
lexer.next();
|
||||
target.setListRuleId(lexer.take());
|
||||
} else if (lexer.getCurrent().equals("first"))
|
||||
target.addListMode(StructureMapTargetListMode.FIRST);
|
||||
else
|
||||
target.addListMode(StructureMapTargetListMode.LAST);
|
||||
lexer.next();
|
||||
} else {
|
||||
if (lexer.getCurrent().equals("first"))
|
||||
target.addListMode(StructureMapTargetListMode.FIRST);
|
||||
else
|
||||
target.addListMode(StructureMapTargetListMode.LAST);
|
||||
lexer.next();
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
|
|
@ -1219,7 +1221,7 @@ public class StructureMapUtilities {
|
|||
}
|
||||
|
||||
public enum VariableMode {
|
||||
INPUT, OUTPUT
|
||||
INPUT, OUTPUT, SHARED
|
||||
}
|
||||
|
||||
public class Variable {
|
||||
|
|
@ -1277,16 +1279,25 @@ public class StructureMapUtilities {
|
|||
return null;
|
||||
}
|
||||
|
||||
public String summary() {
|
||||
CommaSeparatedStringBuilder s = new CommaSeparatedStringBuilder();
|
||||
CommaSeparatedStringBuilder t = new CommaSeparatedStringBuilder();
|
||||
for (Variable v : list)
|
||||
if (v.mode == VariableMode.INPUT)
|
||||
s.append(v.summary());
|
||||
else
|
||||
t.append(v.summary());
|
||||
return "source variables ["+s.toString()+"], target variables ["+t.toString()+"]";
|
||||
}
|
||||
public String summary() {
|
||||
CommaSeparatedStringBuilder s = new CommaSeparatedStringBuilder();
|
||||
CommaSeparatedStringBuilder t = new CommaSeparatedStringBuilder();
|
||||
CommaSeparatedStringBuilder sh = new CommaSeparatedStringBuilder();
|
||||
for (Variable v : list)
|
||||
switch(v.mode) {
|
||||
case INPUT:
|
||||
s.append(v.summary());
|
||||
break;
|
||||
case OUTPUT:
|
||||
t.append(v.summary());
|
||||
break;
|
||||
case SHARED:
|
||||
sh.append(v.summary());
|
||||
break;
|
||||
}
|
||||
return "source variables ["+s.toString()+"], target variables ["+t.toString()+"], shared variables ["+sh.toString()+"]";
|
||||
}
|
||||
|
||||
}
|
||||
|
||||
public class TransformContext {
|
||||
|
|
@ -1379,7 +1390,7 @@ public class StructureMapUtilities {
|
|||
if (source != null) {
|
||||
for (Variables v : source) {
|
||||
for (StructureMapGroupRuleTargetComponent t : rule.getTarget()) {
|
||||
processTarget(rule.getName(), context, v, map, group, t, rule.getSource().size() == 1 ? rule.getSourceFirstRep().getVariable() : null, atRoot);
|
||||
processTarget(rule.getName(), context, v, map, group, t, rule.getSource().size() == 1 ? rule.getSourceFirstRep().getVariable() : null, atRoot, vars);
|
||||
}
|
||||
if (rule.hasRule()) {
|
||||
for (StructureMapGroupRuleComponent childrule : rule.getRule()) {
|
||||
|
|
@ -1781,7 +1792,7 @@ public class StructureMapUtilities {
|
|||
return false;
|
||||
}
|
||||
|
||||
private void processTarget(String ruleId, TransformContext context, Variables vars, StructureMap map, StructureMapGroupComponent group, StructureMapGroupRuleTargetComponent tgt, String srcVar, boolean atRoot) throws FHIRException {
|
||||
private void processTarget(String ruleId, TransformContext context, Variables vars, StructureMap map, StructureMapGroupComponent group, StructureMapGroupRuleTargetComponent tgt, String srcVar, boolean atRoot, Variables sharedVars) throws FHIRException {
|
||||
Base dest = null;
|
||||
if (tgt.hasContext()) {
|
||||
dest = vars.get(VariableMode.OUTPUT, tgt.getContext());
|
||||
|
|
@ -1795,8 +1806,17 @@ public class StructureMapUtilities {
|
|||
v = runTransform(ruleId, context, map, group, tgt, vars, dest, tgt.getElement(), srcVar, atRoot);
|
||||
if (v != null && dest != null)
|
||||
v = dest.setProperty(tgt.getElement().hashCode(), tgt.getElement(), v); // reset v because some implementations may have to rewrite v when setting the value
|
||||
} else if (dest != null)
|
||||
v = dest.makeProperty(tgt.getElement().hashCode(), tgt.getElement());
|
||||
} else if (dest != null) {
|
||||
if (tgt.hasListMode(StructureMapTargetListMode.SHARE)) {
|
||||
v = sharedVars.get(VariableMode.SHARED, tgt.getListRuleId());
|
||||
if (v == null) {
|
||||
v = dest.makeProperty(tgt.getElement().hashCode(), tgt.getElement());
|
||||
sharedVars.add(VariableMode.SHARED, tgt.getListRuleId(), v);
|
||||
}
|
||||
} else {
|
||||
v = dest.makeProperty(tgt.getElement().hashCode(), tgt.getElement());
|
||||
}
|
||||
}
|
||||
if (tgt.hasVariable() && v != null)
|
||||
vars.add(VariableMode.OUTPUT, tgt.getVariable(), v);
|
||||
}
|
||||
|
|
|
|||
|
|
@ -0,0 +1 @@
|
|||
*.out
|
||||
|
|
@ -0,0 +1,6 @@
|
|||
<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>
|
||||
|
|
@ -0,0 +1,39 @@
|
|||
{
|
||||
"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"
|
||||
}
|
||||
]
|
||||
}
|
||||
]
|
||||
}
|
||||
]
|
||||
}
|
||||
|
|
@ -0,0 +1,4 @@
|
|||
{
|
||||
"resourceType" : "Patient",
|
||||
"gender" : "female"
|
||||
}
|
||||
|
|
@ -0,0 +1,8 @@
|
|||
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";
|
||||
}
|
||||
|
|
@ -0,0 +1,4 @@
|
|||
{
|
||||
"resourceType" : "Patient",
|
||||
"gender" : "female"
|
||||
}
|
||||
|
|
@ -0,0 +1,12 @@
|
|||
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);
|
||||
}
|
||||
|
|
@ -0,0 +1,8 @@
|
|||
{
|
||||
"resourceType" : "Patient",
|
||||
"name" : [{
|
||||
"family" : "Brönnimann-Bertholet",
|
||||
"given" : ["Elisabeth"]
|
||||
}],
|
||||
"gender" : "female"
|
||||
}
|
||||
|
|
@ -0,0 +1,26 @@
|
|||
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);
|
||||
}
|
||||
|
|
@ -0,0 +1,10 @@
|
|||
{
|
||||
"resourceType" : "Patient",
|
||||
"name" : [{
|
||||
"family" : "Brönnimann-Bertholet"
|
||||
},
|
||||
{
|
||||
"given" : ["Elisabeth"]
|
||||
}],
|
||||
"gender" : "female"
|
||||
}
|
||||
|
|
@ -0,0 +1,26 @@
|
|||
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);
|
||||
}
|
||||
|
|
@ -0,0 +1,167 @@
|
|||
package org.hl7.fhir.r5.test;
|
||||
|
||||
import static org.junit.Assert.assertTrue;
|
||||
|
||||
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 javax.xml.parsers.ParserConfigurationException;
|
||||
|
||||
import org.hl7.fhir.exceptions.FHIRException;
|
||||
import org.hl7.fhir.r5.context.SimpleWorkerContext;
|
||||
import org.hl7.fhir.r5.elementmodel.Manager;
|
||||
import org.hl7.fhir.r5.elementmodel.Manager.FhirFormat;
|
||||
import org.hl7.fhir.r5.formats.IParser.OutputStyle;
|
||||
import org.hl7.fhir.r5.formats.JsonParser;
|
||||
import org.hl7.fhir.r5.model.Base;
|
||||
import org.hl7.fhir.r5.model.Coding;
|
||||
import org.hl7.fhir.r5.model.Resource;
|
||||
import org.hl7.fhir.r5.model.ResourceFactory;
|
||||
import org.hl7.fhir.r5.model.StructureDefinition;
|
||||
import org.hl7.fhir.r5.model.StructureDefinition.StructureDefinitionKind;
|
||||
import org.hl7.fhir.r5.model.StructureMap;
|
||||
import org.hl7.fhir.r5.terminologies.ConceptMapEngine;
|
||||
import org.hl7.fhir.r5.test.utils.TestingUtilities;
|
||||
import org.hl7.fhir.r5.utils.StructureMapUtilities;
|
||||
import org.hl7.fhir.r5.utils.StructureMapUtilities.ITransformerServices;
|
||||
import org.hl7.fhir.utilities.TextFile;
|
||||
import org.hl7.fhir.utilities.Utilities;
|
||||
import org.hl7.fhir.utilities.cache.PackageCacheManager;
|
||||
import org.hl7.fhir.utilities.cache.ToolsVersion;
|
||||
import org.hl7.fhir.utilities.xml.XMLUtil;
|
||||
import org.junit.BeforeClass;
|
||||
import org.junit.Test;
|
||||
import org.junit.runner.RunWith;
|
||||
import org.junit.runners.Parameterized;
|
||||
import org.junit.runners.Parameterized.Parameters;
|
||||
import org.w3c.dom.Document;
|
||||
import org.w3c.dom.Element;
|
||||
import org.xml.sax.SAXException;
|
||||
|
||||
@RunWith(Parameterized.class)
|
||||
|
||||
public class FHIRMappingLanguageTests implements ITransformerServices {
|
||||
|
||||
private List<Resource> outputs = new ArrayList<Resource>();
|
||||
|
||||
static private SimpleWorkerContext context;
|
||||
static private JsonParser jsonParser;
|
||||
|
||||
@Parameters(name = "{index}: {0}")
|
||||
public static Iterable<Object[]> data()
|
||||
throws FileNotFoundException, IOException, ParserConfigurationException, SAXException {
|
||||
Document tests = XMLUtil.parseFileToDom(TestingUtilities.resourceNameToFile("fml", "manifest.xml"));
|
||||
Element test = XMLUtil.getFirstChild(tests.getDocumentElement());
|
||||
List<Object[]> objects = new ArrayList<Object[]>();
|
||||
while (test != null && test.getNodeName().equals("test")) {
|
||||
objects.add(new Object[] { test.getAttribute("name"), test.getAttribute("source"), test.getAttribute("map"),
|
||||
test.getAttribute("output") });
|
||||
test = XMLUtil.getNextSibling(test);
|
||||
}
|
||||
return objects;
|
||||
}
|
||||
|
||||
private final String name;
|
||||
private String source;
|
||||
private String output;
|
||||
private String map;
|
||||
|
||||
public FHIRMappingLanguageTests(String name, String source, String map, String output) {
|
||||
this.name = name;
|
||||
this.source = source;
|
||||
this.output = output;
|
||||
this.map = map;
|
||||
}
|
||||
|
||||
@BeforeClass
|
||||
static public void setUp() throws Exception {
|
||||
if (context == null) {
|
||||
PackageCacheManager pcm = new PackageCacheManager(true, ToolsVersion.TOOLS_VERSION);
|
||||
context = SimpleWorkerContext.fromPackage(pcm.loadPackage("hl7.fhir.core", "4.0.0"));
|
||||
jsonParser = new JsonParser();
|
||||
jsonParser.setOutputStyle(OutputStyle.PRETTY);
|
||||
}
|
||||
}
|
||||
|
||||
@Test
|
||||
public void test() 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.r5.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");
|
||||
}
|
||||
|
||||
}
|
||||
Loading…
Reference in New Issue