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[GF#20324] FML support for share in Target Transform

This commit is contained in:
Oliver Egger 2019-01-31 13:11:39 +01:00
parent aa5e132307
commit 1c73a3771e
14 changed files with 361 additions and 28 deletions
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74
org.hl7.fhir.r4/src/main/java/org/hl7/fhir/r4/utils/StructureMapUtilities.java
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@ -34,11 +34,6 @@ import java.util.Map;
import java.util.Set;
import java.util.UUID;
import org.apache.commons.lang3.NotImplementedException;
import org.hl7.fhir.exceptions.DefinitionException;
import org.hl7.fhir.exceptions.FHIRException;
import org.hl7.fhir.exceptions.FHIRFormatError;
import org.hl7.fhir.exceptions.PathEngineException;
import org.hl7.fhir.r4.conformance.ProfileUtilities;
import org.hl7.fhir.r4.conformance.ProfileUtilities.ProfileKnowledgeProvider;
import org.hl7.fhir.r4.context.IWorkerContext;
@ -91,10 +86,10 @@ import org.hl7.fhir.r4.model.StructureMap.StructureMapGroupRuleTargetComponent;
import org.hl7.fhir.r4.model.StructureMap.StructureMapGroupRuleTargetParameterComponent;
import org.hl7.fhir.r4.model.StructureMap.StructureMapGroupTypeMode;
import org.hl7.fhir.r4.model.StructureMap.StructureMapInputMode;
import org.hl7.fhir.r4.model.StructureMap.StructureMapModelMode;
import org.hl7.fhir.r4.model.StructureMap.StructureMapSourceListMode;
import org.hl7.fhir.r4.model.StructureMap.StructureMapStructureComponent;
import org.hl7.fhir.r4.model.StructureMap.StructureMapTargetListMode;
import org.hl7.fhir.r4.model.StructureMap.StructureMapModelMode;
import org.hl7.fhir.r4.model.StructureMap.StructureMapStructureComponent;
import org.hl7.fhir.r4.model.StructureMap.StructureMapTransform;
import org.hl7.fhir.r4.model.Type;
import org.hl7.fhir.r4.model.TypeDetails;
@ -105,6 +100,11 @@ import org.hl7.fhir.r4.model.ValueSet.ValueSetExpansionContainsComponent;
import org.hl7.fhir.r4.terminologies.ValueSetExpander.ValueSetExpansionOutcome;
import org.hl7.fhir.r4.utils.FHIRLexer.FHIRLexerException;
import org.hl7.fhir.r4.utils.FHIRPathEngine.IEvaluationContext;
import org.apache.commons.lang3.NotImplementedException;
import org.hl7.fhir.exceptions.DefinitionException;
import org.hl7.fhir.exceptions.FHIRException;
import org.hl7.fhir.exceptions.FHIRFormatError;
import org.hl7.fhir.exceptions.PathEngineException;
import org.hl7.fhir.utilities.CommaSeparatedStringBuilder;
import org.hl7.fhir.utilities.Utilities;
import org.hl7.fhir.utilities.validation.ValidationMessage;
@ -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);
}

1
org.hl7.fhir.r4/src/main/resources/fml/.gitignore vendored Normal file
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@ -0,0 +1 @@
*.out

6
org.hl7.fhir.r4/src/main/resources/fml/manifest.xml Normal file
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@ -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>

39
org.hl7.fhir.r4/src/main/resources/fml/qr.json Normal file
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@ -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"
}
]
}
]
}
]
}

4
org.hl7.fhir.r4/src/main/resources/fml/qr2pat-assignment-res.json Normal file
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@ -0,0 +1,4 @@
{
"resourceType" : "Patient",
"gender" : "female"
}

8
org.hl7.fhir.r4/src/main/resources/fml/qr2pat-assignment.map Normal file
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@ -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";
}

4
org.hl7.fhir.r4/src/main/resources/fml/qr2pat-gender-res.json Normal file
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@ -0,0 +1,4 @@
{
"resourceType" : "Patient",
"gender" : "female"
}

12
org.hl7.fhir.r4/src/main/resources/fml/qr2pat-gender.map Normal file
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@ -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);
}

8
org.hl7.fhir.r4/src/main/resources/fml/qr2pat-humannameshared-res.json Normal file
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@ -0,0 +1,8 @@
{
"resourceType" : "Patient",
"name" : [{
"family" : "Brönnimann-Bertholet",
"given" : ["Elisabeth"]
}],
"gender" : "female"
}

26
org.hl7.fhir.r4/src/main/resources/fml/qr2pat-humannameshared.map Normal file
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@ -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);
}

10
org.hl7.fhir.r4/src/main/resources/fml/qr2pat-humannametwice-res.json Normal file
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@ -0,0 +1,10 @@
{
"resourceType" : "Patient",
"name" : [{
"family" : "Brönnimann-Bertholet"
},
{
"given" : ["Elisabeth"]
}],
"gender" : "female"
}

26
org.hl7.fhir.r4/src/main/resources/fml/qr2pat-humannametwice.map Normal file
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@ -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);
}

3
org.hl7.fhir.r4/src/test/java/org/hl7/fhir/r4/test/AllTests.java
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@ -18,7 +18,8 @@ import org.junit.runners.Suite.SuiteClasses;
NarrativeGeneratorTests.class,
ShexGeneratorTests.class,
BaseDateTimeTypeTest.class,
SnapShotGenerationTests.class})
SnapShotGenerationTests.class,
FHIRMappingLanguageTests.class})
public class AllTests {
}

168
org.hl7.fhir.r4/src/test/java/org/hl7/fhir/r4/test/FHIRMappingLanguageTests.java Normal file
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@ -0,0 +1,168 @@
package org.hl7.fhir.r4.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.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.Base;
import org.hl7.fhir.r4.model.Coding;
import org.hl7.fhir.r4.model.Resource;
import org.hl7.fhir.r4.model.ResourceFactory;
import org.hl7.fhir.r4.model.StructureDefinition;
import org.hl7.fhir.r4.model.StructureDefinition.StructureDefinitionKind;
import org.hl7.fhir.r4.model.StructureMap;
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.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) {
context = new SimpleWorkerContext();
PackageCacheManager pcm = new PackageCacheManager(true, ToolsVersion.TOOLS_VERSION);
context.loadFromPackage(pcm.loadPackageCacheLatest("hl7.fhir.core"), null, "StructureDefinition");
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.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");
}
}