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org.hl7.fhir.core
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Merge remote-tracking branch 'origin/master'

This commit is contained in:
Grahame Grieve 2022-05-12 16:46:44 +10:00
parent eddcaba803 8a8bbb7308
commit d3d9f52ea1
5 changed files with 46 additions and 45 deletions
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4
org.hl7.fhir.r4b/src/test/java/org/hl7/fhir/r4b/test/StructureMapUtilitiesTest.java
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@ -31,7 +31,7 @@ public class StructureMapUtilitiesTest implements ITransformerServices {
@Test @Test
public void testParseRuleName() throws IOException, FHIRException { public void testParseRuleName() throws IOException, FHIRException {
StructureMapUtilities scu = new StructureMapUtilities(context, this); StructureMapUtilities scu = new StructureMapUtilities(context, this);
String fileMap = TestingUtilities.loadTestResource("r5", "fml", "ActivityDefinition.map"); String fileMap = TestingUtilities.loadTestResource("r5", "structure-mapping", "ActivityDefinition.map");
StructureMap structureMap = scu.parse(fileMap, "ActivityDefinition3To4"); StructureMap structureMap = scu.parse(fileMap, "ActivityDefinition3To4");
// StructureMap/ActivityDefinition3to4: StructureMap.group[3].rule[2].name error id value '"expression"' is not valid // StructureMap/ActivityDefinition3to4: StructureMap.group[3].rule[2].name error id value '"expression"' is not valid
@ -59,7 +59,7 @@ public class StructureMapUtilitiesTest implements ITransformerServices {
@Test @Test
public void testSyntax() throws IOException, FHIRException { public void testSyntax() throws IOException, FHIRException {
StructureMapUtilities scu = new StructureMapUtilities(context, this); StructureMapUtilities scu = new StructureMapUtilities(context, this);
String fileMap = TestingUtilities.loadTestResource("r5", "fml", "syntax.map"); String fileMap = TestingUtilities.loadTestResource("r5", "structure-mapping", "syntax.map");
System.out.println(fileMap); System.out.println(fileMap);
StructureMap structureMap = scu.parse(fileMap, "Syntax"); StructureMap structureMap = scu.parse(fileMap, "Syntax");

22
org.hl7.fhir.r5/src/main/java/org/hl7/fhir/r5/utils/GraphQLEngine.java
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@ -2,10 +2,7 @@ package org.hl7.fhir.r5.utils;
import java.io.UnsupportedEncodingException; import java.io.UnsupportedEncodingException;
import java.net.URLDecoder; import java.net.URLDecoder;
import java.util.ArrayList; import java.util.*;
import java.util.HashMap;
import java.util.List;
import java.util.Map;
/* /*
Copyright (c) 2011+, HL7, Inc. Copyright (c) 2011+, HL7, Inc.
@ -41,20 +38,9 @@ import java.util.Map;
import org.hl7.fhir.exceptions.FHIRException; import org.hl7.fhir.exceptions.FHIRException;
import org.hl7.fhir.instance.model.api.IBaseResource; import org.hl7.fhir.instance.model.api.IBaseResource;
import org.hl7.fhir.r5.context.IWorkerContext; import org.hl7.fhir.r5.context.IWorkerContext;
import org.hl7.fhir.r5.model.BackboneElement; import org.hl7.fhir.r5.model.*;
import org.hl7.fhir.r5.model.Base;
import org.hl7.fhir.r5.model.Bundle;
import org.hl7.fhir.r5.model.Bundle.BundleEntryComponent; import org.hl7.fhir.r5.model.Bundle.BundleEntryComponent;
import org.hl7.fhir.r5.model.Bundle.BundleLinkComponent; import org.hl7.fhir.r5.model.Bundle.BundleLinkComponent;
import org.hl7.fhir.r5.model.CanonicalType;
import org.hl7.fhir.r5.model.DomainResource;
import org.hl7.fhir.r5.model.Element;
import org.hl7.fhir.r5.model.ExpressionNode;
import org.hl7.fhir.r5.model.IntegerType;
import org.hl7.fhir.r5.model.Property;
import org.hl7.fhir.r5.model.Reference;
import org.hl7.fhir.r5.model.Resource;
import org.hl7.fhir.r5.model.StringType;
import org.hl7.fhir.utilities.Utilities; import org.hl7.fhir.utilities.Utilities;
import org.hl7.fhir.utilities.graphql.Argument; import org.hl7.fhir.utilities.graphql.Argument;
import org.hl7.fhir.utilities.graphql.Argument.ArgumentListStatus; import org.hl7.fhir.utilities.graphql.Argument.ArgumentListStatus;
@ -571,6 +557,10 @@ public class GraphQLEngine implements IGraphQLEngine {
if (!isPrimitive(prop.getTypeCode()) && sel.getField().getName().startsWith("_")) if (!isPrimitive(prop.getTypeCode()) && sel.getField().getName().startsWith("_"))
throw new EGraphQLException("Unknown property "+sel.getField().getName()+" on "+source.fhirType()); throw new EGraphQLException("Unknown property "+sel.getField().getName()+" on "+source.fhirType());
if ("id".equals(prop.getName()) && context != null) {
prop.getValues().set(0, new IdType(context.getIdPart()));
}
List<Base> vl = filter(context, prop, sel.getField().getName(), sel.getField().getArguments(), prop.getValues(), sel.getField().getName().startsWith("_")); List<Base> vl = filter(context, prop, sel.getField().getName(), sel.getField().getArguments(), prop.getValues(), sel.getField().getName().startsWith("_"));
if (!vl.isEmpty()) if (!vl.isEmpty())
processValues(context, sel, prop, target, vl, sel.getField().getName().startsWith("_"), inheritedList, suffix); processValues(context, sel, prop, target, vl, sel.getField().getName().startsWith("_"), inheritedList, suffix);

24
org.hl7.fhir.r5/src/main/java/org/hl7/fhir/r5/utils/structuremap/StructureMapUtilities.java
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@ -338,18 +338,19 @@ public class StructureMapUtilities {
for (int i = 0; i < indent; i++) for (int i = 0; i < indent; i++)
b.append(' '); b.append(' ');
boolean canBeAbbreviated = checkisSimple(r); boolean canBeAbbreviated = checkisSimple(r);
{
boolean first = true; boolean first = true;
for (StructureMapGroupRuleSourceComponent rs : r.getSource()) { for (StructureMapGroupRuleSourceComponent rs : r.getSource()) {
if (first) if (first)
first = false; first = false;
else else
b.append(", "); b.append(", ");
renderSource(b, rs, canBeAbbreviated); renderSource(b, rs, canBeAbbreviated);
}
} }
if (r.getTarget().size() > 1) { if (r.getTarget().size() > 1) {
b.append(" -> "); b.append(" -> ");
first = true; boolean first = true;
for (StructureMapGroupRuleTargetComponent rt : r.getTarget()) { for (StructureMapGroupRuleTargetComponent rt : r.getTarget()) {
if (first) if (first)
first = false; first = false;
@ -379,7 +380,7 @@ public class StructureMapUtilities {
} else { } else {
if (r.hasDependent()) { if (r.hasDependent()) {
b.append(" then "); b.append(" then ");
first = true; boolean first = true;
for (StructureMapGroupRuleDependentComponent rd : r.getDependent()) { for (StructureMapGroupRuleDependentComponent rd : r.getDependent()) {
if (first) if (first)
first = false; first = false;
@ -524,6 +525,7 @@ public class StructureMapUtilities {
b.append(rt.getTransform().toCode()); b.append(rt.getTransform().toCode());
b.append("("); b.append("(");
b.append(((IdType) rt.getParameter().get(0).getValue()).asStringValue()); b.append(((IdType) rt.getParameter().get(0).getValue()).asStringValue());
b.append(", ");
b.append(((StringType) rt.getParameter().get(1).getValue()).asStringValue()); b.append(((StringType) rt.getParameter().get(1).getValue()).asStringValue());
b.append(")"); b.append(")");
} else { } else {
@ -1679,7 +1681,7 @@ public class StructureMapUtilities {
case EVALUATE: case EVALUATE:
ExpressionNode expr = (ExpressionNode) tgt.getUserData(MAP_EXPRESSION); ExpressionNode expr = (ExpressionNode) tgt.getUserData(MAP_EXPRESSION);
if (expr == null) { if (expr == null) {
expr = fpe.parse(getParamStringNoNull(vars, tgt.getParameter().get(0), tgt.toString())); expr = fpe.parse(getParamStringNoNull(vars, tgt.getParameter().get(1), tgt.toString()));
tgt.setUserData(MAP_WHERE_EXPRESSION, expr); tgt.setUserData(MAP_WHERE_EXPRESSION, expr);
} }
List<Base> v = fpe.evaluate(vars, null, null, tgt.getParameter().size() == 2 ? getParam(vars, tgt.getParameter().get(0)) : new BooleanType(false), expr); List<Base> v = fpe.evaluate(vars, null, null, tgt.getParameter().size() == 2 ? getParam(vars, tgt.getParameter().get(0)) : new BooleanType(false), expr);

6
org.hl7.fhir.r5/src/test/java/org/hl7/fhir/r5/test/StructureMapUtilitiesTest.java
View File

@ -31,7 +31,7 @@ public class StructureMapUtilitiesTest implements ITransformerServices {
@Test @Test
public void testParseRuleName() throws IOException, FHIRException { public void testParseRuleName() throws IOException, FHIRException {
StructureMapUtilities scu = new StructureMapUtilities(context, this); StructureMapUtilities scu = new StructureMapUtilities(context, this);
String fileMap = TestingUtilities.loadTestResource("r5", "fml", "ActivityDefinition.map"); String fileMap = TestingUtilities.loadTestResource("r5", "structure-mapping", "ActivityDefinition.map");
StructureMap structureMap = scu.parse(fileMap, "ActivityDefinition3To4"); StructureMap structureMap = scu.parse(fileMap, "ActivityDefinition3To4");
// StructureMap/ActivityDefinition3to4: StructureMap.group[3].rule[2].name error id value '"expression"' is not valid // StructureMap/ActivityDefinition3to4: StructureMap.group[3].rule[2].name error id value '"expression"' is not valid
@ -59,7 +59,7 @@ public class StructureMapUtilitiesTest implements ITransformerServices {
@Test @Test
public void testSyntax() throws IOException, FHIRException { public void testSyntax() throws IOException, FHIRException {
StructureMapUtilities scu = new StructureMapUtilities(context, this); StructureMapUtilities scu = new StructureMapUtilities(context, this);
String fileMap = TestingUtilities.loadTestResource("r5", "fml", "syntax.map"); String fileMap = TestingUtilities.loadTestResource("r5", "structure-mapping", "syntax.map");
System.out.println(fileMap); System.out.println(fileMap);
StructureMap structureMap = scu.parse(fileMap, "Syntax"); StructureMap structureMap = scu.parse(fileMap, "Syntax");
@ -71,6 +71,8 @@ public class StructureMapUtilitiesTest implements ITransformerServices {
assertSerializeDeserialize(map); assertSerializeDeserialize(map);
} }
@Override @Override
public void log(String message) { public void log(String message) {
} }

35
org.hl7.fhir.validation/src/test/java/org/hl7/fhir/r5/test/FHIRMappingLanguageTests.java → org.hl7.fhir.validation/src/test/java/org/hl7/fhir/r5/test/StructureMappingTests.java
View File

@ -1,11 +1,9 @@
package org.hl7.fhir.r5.test; package org.hl7.fhir.r5.test;
import static org.junit.Assert.assertTrue; import static org.junit.Assert.assertTrue;
import static org.junit.jupiter.api.Assertions.fail;
import java.io.ByteArrayOutputStream; import java.io.*;
import java.io.FileInputStream;
import java.io.FileNotFoundException;
import java.io.IOException;
import java.util.ArrayList; import java.util.ArrayList;
import java.util.List; import java.util.List;
import java.util.stream.Stream; import java.util.stream.Stream;
@ -34,7 +32,7 @@ import org.w3c.dom.Document;
import org.w3c.dom.Element; import org.w3c.dom.Element;
import org.xml.sax.SAXException; import org.xml.sax.SAXException;
public class FHIRMappingLanguageTests { public class StructureMappingTests {
private List<Resource> outputs = new ArrayList<Resource>(); private List<Resource> outputs = new ArrayList<Resource>();
@ -44,7 +42,7 @@ public class FHIRMappingLanguageTests {
public static Stream<Arguments> data() public static Stream<Arguments> data()
throws FileNotFoundException, IOException, ParserConfigurationException, SAXException { throws FileNotFoundException, IOException, ParserConfigurationException, SAXException {
Document tests = XMLUtil.parseToDom(TestingUtilities.loadTestResource("r5", "fml", "manifest.xml")); Document tests = XMLUtil.parseToDom(TestingUtilities.loadTestResource("r5", "structure-mapping", "manifest.xml"));
Element test = XMLUtil.getFirstChild(tests.getDocumentElement()); Element test = XMLUtil.getFirstChild(tests.getDocumentElement());
List<Arguments> objects = new ArrayList<>(); List<Arguments> objects = new ArrayList<>();
while (test != null && test.getNodeName().equals("test")) { while (test != null && test.getNodeName().equals("test")) {
@ -76,22 +74,30 @@ public class FHIRMappingLanguageTests {
context.setValidatorFactory(new InstanceValidatorFactory()); context.setValidatorFactory(new InstanceValidatorFactory());
} }
} }
private StructureMap loadStructureMap(String map) throws Exception {
String stringMap = TestingUtilities.loadTestResource("r5", "structure-mapping", map);
if (map.endsWith(".json")) {
return (StructureMap) new org.hl7.fhir.r5.formats.JsonParser().parse(stringMap);
} else if (map.endsWith(".map")) {
return new StructureMapUtilities(context).parse(stringMap, map);
}
throw new Exception("File extension for StuctureMap is not a recognized type (should be one of: '.map', '.json')");
}
@ParameterizedTest(name = "{index}: {0}") @ParameterizedTest(name = "{index}: {0}")
@MethodSource("data") @MethodSource("data")
public void test(String name, String source, String map, String output) throws Exception { public void test(String name, String source, String map, String output) throws Exception {
byte[] byteSource = TestingUtilities.loadTestResourceBytes("r5", "fml", source); byte[] byteSource = TestingUtilities.loadTestResourceBytes("r5", "structure-mapping", source);
String stringMap = TestingUtilities.loadTestResource("r5", "fml", map);
String outputJson = TestingUtilities.loadTestResource("r5", "fml", output); String outputJson = TestingUtilities.loadTestResource("r5", "structure-mapping", output);
String fileOutputRes = TestingUtilities.tempFile("fml", output) + ".out"; String fileOutputRes = TestingUtilities.tempFile("structure-mapping", output) + ".out";
String fileOutputResOrig = TestingUtilities.tempFile("fml", output) + ".orig.out"; String fileOutputResOrig = TestingUtilities.tempFile("structure-mapping", output) + ".orig.out";
ByteArrayOutputStream s = null; ByteArrayOutputStream s = null;
outputs.clear(); outputs.clear();
String msg = null; String msg = null;
try { try {
StructureMap r = new StructureMapUtilities(context).parse(stringMap, map); StructureMap r = loadStructureMap(map);
context.cacheResource(r); context.cacheResource(r);
org.hl7.fhir.r5.elementmodel.Element element = validationEngine.transform(byteSource, FhirFormat.JSON, r.getUrl()); org.hl7.fhir.r5.elementmodel.Element element = validationEngine.transform(byteSource, FhirFormat.JSON, r.getUrl());
s = new ByteArrayOutputStream(); s = new ByteArrayOutputStream();
@ -101,7 +107,8 @@ public class FHIRMappingLanguageTests {
new org.hl7.fhir.r5.elementmodel.XmlParser(context).compose(element, s, IParser.OutputStyle.PRETTY, null); new org.hl7.fhir.r5.elementmodel.XmlParser(context).compose(element, s, IParser.OutputStyle.PRETTY, null);
context.dropResource(r); context.dropResource(r);
} catch (Exception e) { } catch (Exception e) {
assertTrue(e.getMessage(), false); e.printStackTrace();
fail(e.getMessage());
} }
if (output.endsWith("json")) { if (output.endsWith("json")) {
msg = CompareUtilities.checkJsonSrcIsSame(s.toString(), outputJson); msg = CompareUtilities.checkJsonSrcIsSame(s.toString(), outputJson);