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org.hl7.fhir.core
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Merge branch 'master' into Snapshot-issue

This commit is contained in:
Lloyd McKenzie 2019-02-06 23:25:13 -07:00 committed by GitHub
parent 13d22dfcd1 d1c9de3d8b
commit a17754792b
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GPG Key ID: 4AEE18F83AFDEB23
23 changed files with 4966 additions and 4314 deletions
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2
org.hl7.fhir.convertors/pom.xml
View File

@ -5,7 +5,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>org.hl7.fhir.core</artifactId>
<version>3.7.3-SNAPSHOT</version>
<version>3.7.4-SNAPSHOT</version>
<relativePath>../pom.xml</relativePath>
</parent>

13
org.hl7.fhir.convertors/src/main/java/org/hl7/fhir/convertors/VersionConvertor_30_40.java
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@ -33,6 +33,7 @@ import org.hl7.fhir.dstu3.model.Parameters;
import org.hl7.fhir.dstu3.model.Parameters.ParametersParameterComponent;
import org.hl7.fhir.exceptions.FHIRException;
import org.hl7.fhir.r4.model.BooleanType;
import org.hl7.fhir.r4.model.Questionnaire;
import org.hl7.fhir.r4.model.CodeableConcept;
import org.hl7.fhir.r4.model.Enumeration;
import org.hl7.fhir.r4.model.Expression.ExpressionLanguage;
@ -76,7 +77,7 @@ import org.hl7.fhir.utilities.Utilities;
public class VersionConvertor_30_40 {
private static List<String> CANONICAL_URLS = new ArrayList<String>();
private static List<String> CANONICAL_URLS = new ArrayList<>();
static {
CANONICAL_URLS.add("http://hl7.org/fhir/StructureDefinition/11179-permitted-value-conceptmap");
CANONICAL_URLS.add("http://hl7.org/fhir/StructureDefinition/11179-permitted-value-valueset");
@ -16013,6 +16014,7 @@ public class VersionConvertor_30_40 {
tgt.setType(convertQuestionnaireItemType(src.getType()));
for (org.hl7.fhir.dstu3.model.Questionnaire.QuestionnaireItemEnableWhenComponent t : src.getEnableWhen())
tgt.addEnableWhen(convertQuestionnaireItemEnableWhenComponent(t));
tgt.setEnableBehavior(Questionnaire.EnableWhenBehavior.ANY);
if (src.hasRequired())
tgt.setRequired(src.getRequired());
if (src.hasRepeats())
@ -16029,6 +16031,9 @@ public class VersionConvertor_30_40 {
tgt.addInitial().setValue(convertType(src.getInitial()));
for (org.hl7.fhir.dstu3.model.Questionnaire.QuestionnaireItemComponent t : src.getItem())
tgt.addItem(convertQuestionnaireItemComponent(t));
for (org.hl7.fhir.dstu3.model.Extension t : src.getModifierExtension()) {
tgt.addModifierExtension(convertExtension(t));
}
return tgt;
}
@ -16131,8 +16136,10 @@ public class VersionConvertor_30_40 {
tgt.setOperator(org.hl7.fhir.r4.model.Questionnaire.QuestionnaireItemOperator.EXISTS);
tgt.setAnswer(convertType(src.getHasAnswerElement()));
}
else if (src.hasAnswer())
tgt.setAnswer(convertType(src.getAnswer()));
else if (src.hasAnswer()) {
tgt.setOperator(org.hl7.fhir.r4.model.Questionnaire.QuestionnaireItemOperator.EQUAL);
tgt.setAnswer(convertType(src.getAnswer()));
}
return tgt;
}

2
org.hl7.fhir.dstu2/pom.xml
View File

@ -5,7 +5,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>org.hl7.fhir.core</artifactId>
<version>3.7.3-SNAPSHOT</version>
<version>3.7.4-SNAPSHOT</version>
<relativePath>../pom.xml</relativePath>
</parent>

2
org.hl7.fhir.dstu2016may/pom.xml
View File

@ -5,7 +5,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>org.hl7.fhir.core</artifactId>
<version>3.7.3-SNAPSHOT</version>
<version>3.7.4-SNAPSHOT</version>
<relativePath>../pom.xml</relativePath>
</parent>

2
org.hl7.fhir.dstu3/pom.xml
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@ -5,7 +5,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>org.hl7.fhir.core</artifactId>
<version>3.7.3-SNAPSHOT</version>
<version>3.7.4-SNAPSHOT</version>
<relativePath>../pom.xml</relativePath>
</parent>

2
org.hl7.fhir.r4/pom.xml
View File

@ -5,7 +5,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>org.hl7.fhir.core</artifactId>
<version>3.7.3-SNAPSHOT</version>
<version>3.7.4-SNAPSHOT</version>
<relativePath>../pom.xml</relativePath>
</parent>

19
org.hl7.fhir.r4/src/main/java/org/hl7/fhir/r4/conformance/ProfileUtilities.java
View File

@ -650,8 +650,14 @@ public class ProfileUtilities extends TranslatingUtilities {
}
if (outcome.getType().size() > 1)
for (TypeRefComponent t : outcome.getType()) {
if (!t.getCode().equals("Reference"))
throw new DefinitionException(diffMatches.get(0).getPath()+" has children ("+differential.getElement().get(diffCursor).getPath()+") and multiple types ("+typeCode(outcome.getType())+") in profile "+profileName);
if (!t.getCode().equals("Reference")) {
boolean nonExtension = false;
for (ElementDefinition ed : diffMatches)
if (ed != diffMatches.get(0) && !ed.getPath().endsWith(".extension"))
nonExtension = true;
if (nonExtension)
throw new DefinitionException(diffMatches.get(0).getPath()+" has children ("+differential.getElement().get(diffCursor).getPath()+") and multiple types ("+typeCode(outcome.getType())+") in profile "+profileName);
}
}
}
int start = diffCursor;
@ -668,7 +674,7 @@ public class ProfileUtilities extends TranslatingUtilities {
nbl++;
processPaths(indent+" ", result, base, differential, nbc, start - 1, nbl-1, diffCursor - 1, url, profileName, tgt.getPath(), diffMatches.get(0).getPath(), trimDifferential, contextName, resultPathBase, false, redirectorStack(redirector, outcome, cpath));
} else {
StructureDefinition dt = getProfileForDataType(outcome.getType().get(0));
StructureDefinition dt = outcome.getType().size() == 1 ? getProfileForDataType(outcome.getType().get(0)) : getProfileForDataType("Element");
if (dt == null)
throw new DefinitionException(diffMatches.get(0).getPath()+" has children ("+differential.getElement().get(diffCursor).getPath()+") for type "+typeCode(outcome.getType())+" in profile "+profileName+", but can't find type");
contextName = dt.getUrl();
@ -1194,6 +1200,13 @@ public class ProfileUtilities extends TranslatingUtilities {
return sd;
}
private StructureDefinition getProfileForDataType(String type) {
StructureDefinition sd = context.fetchTypeDefinition(type);
if (sd == null)
System.out.println("XX: failed to find profle for type: " + type); // debug GJM
return sd;
}
public static String typeCode(List<TypeRefComponent> types) {
StringBuilder b = new StringBuilder();

3
org.hl7.fhir.r4/src/main/java/org/hl7/fhir/r4/context/SimpleWorkerContext.java
View File

@ -153,6 +153,7 @@ public class SimpleWorkerContext extends BaseWorkerContext implements IWorkerCon
public static SimpleWorkerContext fromPackage(NpmPackage pi, IContextResourceLoader loader) throws FileNotFoundException, IOException, FHIRException {
SimpleWorkerContext res = new SimpleWorkerContext();
res.setAllowLoadingDuplicates(true);
res.version = pi.getNpm().get("version").getAsString();
res.loadFromPackage(pi, loader);
return res;
}
@ -523,7 +524,7 @@ public class SimpleWorkerContext extends BaseWorkerContext implements IWorkerCon
@Override
public String getVersion() {
return version+"-"+revision;
return version;
}

6
org.hl7.fhir.r4/src/main/java/org/hl7/fhir/r4/elementmodel/Element.java
View File

@ -512,12 +512,12 @@ public class Element extends Base {
@SuppressWarnings("unchecked")
List<ElementDecoration> decorations = (List<ElementDecoration>) getUserData("fhir.decorations");
if (decorations == null) {
decorations = new ArrayList<ElementDecoration>();
decorations = new ArrayList<>();
setUserData("fhir.decorations", decorations);
}
decorations.add(new ElementDecoration(DecorationType.TYPE, profile.getUserString("path"), definition.getPath()));
if (tail(definition.getId()).contains(":")) {
String[] details = tail(definition.getId()).split("\\:");
if (definition.getId() != null && tail(definition.getId()).contains(":")) {
String[] details = tail(definition.getId()).split(":");
decorations.add(new ElementDecoration(DecorationType.SLICE, null, details[1]));
}
}

4
org.hl7.fhir.r4/src/main/java/org/hl7/fhir/r4/utils/FHIRPathEngine.java
View File

@ -1906,8 +1906,10 @@ public class FHIRPathEngine {
}
private List<Base> opIn(List<Base> left, List<Base> right) throws FHIRException {
if (left.size() == 0 || right.size() == 0)
if (left.size() == 0)
return new ArrayList<Base>();
if (right.size() == 0)
return makeBoolean(false);
boolean ans = true;
for (Base l : left) {
boolean f = false;

7671
org.hl7.fhir.r4/src/main/resources/snapshot-generation-tests.xml
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File diff suppressed because it is too large Load Diff

915
org.hl7.fhir.r4/src/test/java/org/hl7/fhir/r4/test/SnapShotGenerationTests.java
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@ -1,451 +1,464 @@
package org.hl7.fhir.r4.test;
import java.io.File;
import java.io.FileInputStream;
import java.io.FileOutputStream;
import java.io.IOException;
import java.util.ArrayList;
import java.util.HashMap;
import java.util.HashSet;
import java.util.List;
import java.util.Map;
import java.util.Set;
import javax.xml.parsers.ParserConfigurationException;
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.SimpleWorkerContext;
import org.hl7.fhir.r4.formats.IParser.OutputStyle;
import org.hl7.fhir.r4.formats.XmlParser;
import org.hl7.fhir.r4.model.Base;
import org.hl7.fhir.r4.model.Coding;
import org.hl7.fhir.r4.model.ElementDefinition.ElementDefinitionBindingComponent;
import org.hl7.fhir.r4.model.ExpressionNode.CollectionStatus;
import org.hl7.fhir.r4.model.MetadataResource;
import org.hl7.fhir.r4.model.Resource;
import org.hl7.fhir.r4.model.StructureDefinition;
import org.hl7.fhir.r4.model.StructureDefinition.StructureDefinitionKind;
import org.hl7.fhir.r4.model.StructureDefinition.TypeDerivationRule;
import org.hl7.fhir.r4.model.TestScript;
import org.hl7.fhir.r4.model.TestScript.SetupActionAssertComponent;
import org.hl7.fhir.r4.model.TestScript.SetupActionOperationComponent;
import org.hl7.fhir.r4.model.TestScript.TestActionComponent;
import org.hl7.fhir.r4.model.TestScript.TestScriptFixtureComponent;
import org.hl7.fhir.r4.model.TestScript.TestScriptTestComponent;
import org.hl7.fhir.r4.test.utils.TestingUtilities;
import org.hl7.fhir.r4.model.TypeDetails;
import org.hl7.fhir.r4.utils.CodingUtilities;
import org.hl7.fhir.r4.utils.FHIRPathEngine;
import org.hl7.fhir.r4.utils.FHIRPathEngine.IEvaluationContext;
import org.hl7.fhir.r4.utils.IResourceValidator;
import org.hl7.fhir.r4.utils.NarrativeGenerator;
import org.hl7.fhir.utilities.Utilities;
import org.hl7.fhir.utilities.validation.ValidationMessage;
import org.junit.Test;
import org.junit.runner.RunWith;
import org.junit.runners.Parameterized;
import org.junit.runners.Parameterized.Parameters;
import junit.framework.Assert;
@RunWith(Parameterized.class)
public class SnapShotGenerationTests {
public class TestPKP implements ProfileKnowledgeProvider {
@Override
public boolean isDatatype(String name) {
StructureDefinition sd = TestingUtilities.context().fetchTypeDefinition(name);
return (sd != null) && (sd.getDerivation() == TypeDerivationRule.SPECIALIZATION) && (sd.getKind() == StructureDefinitionKind.PRIMITIVETYPE || sd.getKind() == StructureDefinitionKind.COMPLEXTYPE);
}
@Override
public boolean isResource(String typeSimple) {
StructureDefinition sd = TestingUtilities.context().fetchTypeDefinition(name);
return (sd != null) && (sd.getDerivation() == TypeDerivationRule.SPECIALIZATION) && (sd.getKind() == StructureDefinitionKind.RESOURCE);
}
@Override
public boolean hasLinkFor(String typeSimple) {
return isDatatype(name);
}
@Override
public String getLinkFor(String corePath, String typeSimple) {
return Utilities.pathURL(corePath, "datatypes.html#"+typeSimple);
}
@Override
public BindingResolution resolveBinding(StructureDefinition def, ElementDefinitionBindingComponent binding, String path) throws FHIRException {
BindingResolution br = new BindingResolution();
br.url = path+"/something.html";
br.display = "something";
return br;
}
@Override
public String getLinkForProfile(StructureDefinition profile, String url) {
StructureDefinition sd = TestingUtilities.context().fetchResource(StructureDefinition.class, url);
if (sd == null)
return url+"|"+url;
else
return sd.getId()+".html|"+sd.present();
}
@Override
public boolean prependLinks() {
return false;
}
}
private static class SnapShotGenerationTestsContext implements IEvaluationContext {
private Map<String, Resource> fixtures;
private Map<String, StructureDefinition> snapshots = new HashMap<String, StructureDefinition>();
public TestScript tests;
public void checkTestsDetails() {
if (!"http://hl7.org/fhir/tests/snapshotgeneration".equals(tests.getUrl()))
throw new Error("Wrong URL on test script");
if (!tests.getSetup().isEmpty())
throw new Error("Setup is not supported");
if (!tests.getTeardown().isEmpty())
throw new Error("Teardown is not supported");
Set<String> ids = new HashSet<String>();
Set<String> urls = new HashSet<String>();
for (Resource r : tests.getContained()) {
if (ids.contains(r.getId()))
throw new Error("Unsupported: duplicate contained resource on fixture id "+r.getId());
ids.add(r.getId());
if (r instanceof MetadataResource) {
MetadataResource md = (MetadataResource) r;
if (urls.contains(md.getUrl()))
throw new Error("Unsupported: duplicate canonical url "+md.getUrl()+" on fixture id "+r.getId());
urls.add(md.getUrl());
}
}
for (TestScriptFixtureComponent r : tests.getFixture()) {
if (ids.contains(r.getId()))
throw new Error("Unsupported: duplicate contained resource or fixture id "+r.getId());
ids.add(r.getId());
}
Set<String> names = new HashSet<String>();
for (TestScriptTestComponent test : tests.getTest()) {
if (names.contains(test.getName()))
throw new Error("Unsupported: duplicate name "+test.getName());
names.add(test.getName());
if (test.getAction().size() < 2)
throw new Error("Unsupported: multiple actions required");
if (!test.getActionFirstRep().hasOperation())
throw new Error("Unsupported: first action must be an operation");
for (int i = 0; i < test.getAction().size(); i++) {
// if (!test.getAction().get(i).hasAssert())
// throw new Error("Unsupported: following actions must be an asserts");
TestActionComponent action = test.getAction().get(i);
if (action.hasOperation()) {
SetupActionOperationComponent op = test.getActionFirstRep().getOperation();
if (!CodingUtilities.matches(op.getType(), "http://hl7.org/fhir/testscript-operation-codes", "snapshot")
&& !CodingUtilities.matches(op.getType(), "http://hl7.org/fhir/testscript-operation-codes", "sortDifferential"))
throw new Error("Unsupported action operation type "+CodingUtilities.present(op.getType()));
if (!"StructureDefinition".equals(op.getResource()))
throw new Error("Unsupported action operation resource "+op.getResource());
if (!op.hasResponseId())
throw new Error("Unsupported action operation: no response id");
if (!op.hasSourceId())
throw new Error("Unsupported action operation: no source id");
if (!hasSource(op.getSourceId()))
throw new Error("Unsupported action operation: source id could not be resolved");
} else if (action.hasAssert()) {
SetupActionAssertComponent a = action.getAssert();
if (!a.hasLabel())
throw new Error("Unsupported: actions must have a label");
if (!a.hasDescription())
throw new Error("Unsupported: actions must have a description");
if (!a.hasExpression() && !(a.hasResponse() && a.getResponse().equals(TestScript.AssertionResponseTypes.BAD)))
throw new Error("Unsupported: actions must have an expression or a response type of 'bad'");
} else {
throw new Error("Unsupported: Unrecognized action type");
}
}
}
}
private boolean hasSource(String sourceId) {
for (TestScriptFixtureComponent ds : tests.getFixture()) {
if (sourceId.equals(ds.getId()))
return true;
}
for (Resource r : tests.getContained()) {
if (sourceId.equals(r.getId()))
return true;
}
return false;
}
public Resource fetchFixture(String id) {
if (fixtures.containsKey(id))
return fixtures.get(id);
for (TestScriptFixtureComponent ds : tests.getFixture()) {
if (id.equals(ds.getId()))
throw new Error("not done yet");
}
for (Resource r : tests.getContained()) {
if (id.equals(r.getId()))
return r;
}
return null;
}
// FHIRPath methods
@Override
public Base resolveConstant(Object appContext, String name, boolean beforeContext) throws PathEngineException {
return null;
}
@Override
public TypeDetails resolveConstantType(Object appContext, String name) throws PathEngineException {
return null;
}
@Override
public boolean log(String argument, List<Base> focus) {
System.out.println(argument+": "+fp.convertToString(focus));
return true;
}
@Override
public FunctionDetails resolveFunction(String functionName) {
if ("fixture".equals(functionName))
return new FunctionDetails("Access a fixture defined in the testing context", 0, 1);
return null;
}
@Override
public TypeDetails checkFunction(Object appContext, String functionName, List<TypeDetails> parameters) throws PathEngineException {
if ("fixture".equals(functionName))
return new TypeDetails(CollectionStatus.SINGLETON, TestingUtilities.context().getResourceNamesAsSet());
return null;
}
@Override
public List<Base> executeFunction(Object appContext, String functionName, List<List<Base>> parameters) {
if ("fixture".equals(functionName)) {
String id = fp.convertToString(parameters.get(0));
Resource res = fetchFixture(id);
if (res != null) {
List<Base> list = new ArrayList<Base>();
list.add(res);
return list;
}
}
return null;
}
@Override
public Base resolveReference(Object appContext, String url) {
// TODO Auto-generated method stub
return null;
}
@Override
public boolean conformsToProfile(Object appContext, Base item, String url) throws FHIRException {
IResourceValidator val = TestingUtilities.context().newValidator();
List<ValidationMessage> valerrors = new ArrayList<ValidationMessage>();
if (item instanceof Resource) {
val.validate(appContext, valerrors, (Resource) item, url);
boolean ok = true;
for (ValidationMessage v : valerrors)
ok = ok && v.getLevel().isError();
return ok;
}
throw new NotImplementedException("Not done yet (IGPublisherHostServices.SnapShotGenerationTestsContext), when item is element");
}
}
private static FHIRPathEngine fp;
@Parameters(name = "{index}: file {0}")
public static Iterable<Object[]> data() throws ParserConfigurationException, IOException, FHIRFormatError {
SnapShotGenerationTestsContext context = new SnapShotGenerationTestsContext();
context.tests = (TestScript) new XmlParser().parse(new FileInputStream(TestingUtilities.resourceNameToFile("snapshot-generation-tests.xml")));
context.checkTestsDetails();
List<Object[]> objects = new ArrayList<Object[]>(context.tests.getTest().size());
for (TestScriptTestComponent e : context.tests.getTest()) {
objects.add(new Object[] { e.getName(), e, context });
}
return objects;
}
private final TestScriptTestComponent test;
private final String name;
private SnapShotGenerationTestsContext context;
public SnapShotGenerationTests(String name, TestScriptTestComponent e, SnapShotGenerationTestsContext context) {
this.name = name;
this.test = e;
this.context = context;
}
@SuppressWarnings("deprecation")
@Test
public void test() throws FHIRException {
try {
for (Resource cr : context.tests.getContained()) {
if (cr instanceof StructureDefinition) {
StructureDefinition sd = (StructureDefinition) cr;
if (sd.getType().equals("Extension")) {
if (TestingUtilities.context().fetchResource(StructureDefinition.class, sd.getUrl()) == null) {
sd.setUserData("path", "test-"+sd.getId()+".html");
StructureDefinition extd = TestingUtilities.context().fetchResource(StructureDefinition.class, sd.getBaseDefinition());
new ProfileUtilities(TestingUtilities.context(), null, null).generateSnapshot(extd, sd, sd.getUrl(), sd.getName());
TestingUtilities.context().cacheResource(sd);
debugSaveResource(sd);
}
}
}
}
if (fp == null)
fp = new FHIRPathEngine(TestingUtilities.context());
fp.setHostServices(context);
resolveFixtures();
for (int i = 0; i < test.getAction().size(); i++) {
TestActionComponent action = test.getAction().get(i);
try {
if (action.hasOperation()) {
SetupActionOperationComponent op = action.getOperation();
Coding opType = op.getType();
if (opType.getSystem().equals("http://hl7.org/fhir/testscript-operation-codes") && opType.getCode().equals("snapshot")) {
StructureDefinition source = (StructureDefinition) context.fetchFixture(op.getSourceId());
StructureDefinition base = getSD(source.getBaseDefinition());
StructureDefinition output = source.copy();
ProfileUtilities pu = new ProfileUtilities(TestingUtilities.context(), null, new TestPKP());
pu.setIds(source, false);
if ("sort=true".equals(op.getParams())) {
List<String> errors = new ArrayList<String>();
pu.sortDifferential(base, output, source.getName(), errors);
if (errors.size() > 0)
throw new FHIRException("Sort failed: "+errors.toString());
}
pu.generateSnapshot(base, output, source.getUrl(), source.getName());
debugSaveResource(output);
context.fixtures.put(op.getResponseId(), output);
context.snapshots.put(output.getUrl(), output);
new XmlParser().setOutputStyle(OutputStyle.PRETTY).compose(new FileOutputStream(Utilities.path(System.getProperty("java.io.tmpdir"), op.getResponseId()+".xml")), output);
if (output.getDifferential().hasElement())
new NarrativeGenerator("", "http://hl7.org/fhir", TestingUtilities.context()).setPkp(new TestPKP()).generate(output, null);
new XmlParser().setOutputStyle(OutputStyle.PRETTY).compose(new FileOutputStream(Utilities.path(System.getProperty("java.io.tmpdir"), op.getResponseId()+"-d.xml")), output);
} else if (opType.getSystem().equals("http://hl7.org/fhir/testscript-operation-codes") && opType.getCode().equals("sortDifferential")) {
StructureDefinition source = (StructureDefinition) context.fetchFixture(op.getSourceId());
StructureDefinition base = getSD(source.getBaseDefinition());
StructureDefinition output = source.copy();
ProfileUtilities pu = new ProfileUtilities(TestingUtilities.context(), null, null);
pu.setIds(source, false);
List<String> errors = new ArrayList<String>();
pu.sortDifferential(base, output, output.getUrl(), errors);
if (!errors.isEmpty())
throw new FHIRException(errors.get(0));
context.fixtures.put(op.getResponseId(), output);
context.snapshots.put(output.getUrl(), output);
new XmlParser().setOutputStyle(OutputStyle.PRETTY).compose(new FileOutputStream(Utilities.path(System.getProperty("java.io.tmpdir"), op.getResponseId()+".xml")), output);
} else {
throw new Error("Unsupported operation: " + opType.getSystem() + " : " + opType.getCode());
}
} else if (action.hasAssert()) {
SetupActionAssertComponent a = action.getAssert();
if (a.hasResponse() && a.getResponse().equals(TestScript.AssertionResponseTypes.BAD))
Assert.fail(action.getAssert().getLabel()+": "+action.getAssert().getDescription());
else {
boolean ok = fp.evaluateToBoolean(new StructureDefinition(), new StructureDefinition(), a.getExpression());
Assert.assertTrue(a.getLabel()+": "+a.getDescription(), ok);
}
}
} catch (Exception e) {
boolean ok = false;
for (int j = i+1;i < test.getAction().size(); i++) {
TestActionComponent followAction = test.getAction().get(j);
if (followAction.hasAssert() && followAction.getAssert().hasResponse() && followAction.getAssert().getResponse().equals(TestScript.AssertionResponseTypes.BAD)) {
ok = true;
break;
}
}
if (!ok)
throw e;
else
break;
}
}
} catch (Exception e) {
e.printStackTrace();
throw new FHIRException(e);
}
}
private void debugSaveResource(Resource r) throws IOException {
String dir = System.getProperty("java.io.tmpdir");
if (new File("c:\\temp").exists())
dir = "c:\\temp";
String fn = Utilities.path(dir, r.fhirType()+"-"+r.getId()+".xml");
new XmlParser().setOutputStyle(OutputStyle.PRETTY).compose(new FileOutputStream(fn), r);
}
private StructureDefinition getSD(String url) throws DefinitionException, FHIRException, IOException {
StructureDefinition sd = context.snapshots.get(url);
if (sd == null)
sd = findContainedProfile(url);
if (sd == null)
sd = TestingUtilities.context().fetchResource(StructureDefinition.class, url);
return sd;
}
private StructureDefinition findContainedProfile(String url) throws DefinitionException, FHIRException, IOException {
for (Resource r : context.tests.getContained()) {
if (r instanceof StructureDefinition) {
StructureDefinition sd = (StructureDefinition) r;
if (sd.getUrl().equals(url)) {
StructureDefinition p = sd.copy();
ProfileUtilities pu = new ProfileUtilities(TestingUtilities.context(), null, null);
pu.setIds(p, false);
List<String> errors = new ArrayList<String>();
pu.sortDifferential(getSD(p.getBaseDefinition()), p, url, errors);
if (!errors.isEmpty())
throw new FHIRException(errors.get(0));
pu.generateSnapshot(getSD(p.getBaseDefinition()), p, p.getUrl(), p.getName());
debugSaveResource(p);
return p;
}
}
}
return null;
}
private void resolveFixtures() {
if (context.fixtures == null) {
context.fixtures = new HashMap<String, Resource>();
for (TestScriptFixtureComponent fd : context.tests.getFixture()) {
Resource r = TestingUtilities.context().fetchResource(Resource.class, fd.getResource().getReference());
context.fixtures.put(fd.getId(), r);
}
}
}
}
package org.hl7.fhir.r4.test;
import java.io.File;
import java.io.FileInputStream;
import java.io.FileOutputStream;
import java.io.IOException;
import java.util.ArrayList;
import java.util.HashMap;
import java.util.HashSet;
import java.util.List;
import java.util.Map;
import java.util.Set;
import javax.xml.parsers.ParserConfigurationException;
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.SimpleWorkerContext;
import org.hl7.fhir.r4.formats.IParser.OutputStyle;
import org.hl7.fhir.r4.formats.XmlParser;
import org.hl7.fhir.r4.model.Base;
import org.hl7.fhir.r4.model.Coding;
import org.hl7.fhir.r4.model.ElementDefinition.ElementDefinitionBindingComponent;
import org.hl7.fhir.r4.model.ExpressionNode.CollectionStatus;
import org.hl7.fhir.r4.model.MetadataResource;
import org.hl7.fhir.r4.model.Resource;
import org.hl7.fhir.r4.model.StructureDefinition;
import org.hl7.fhir.r4.model.StructureDefinition.StructureDefinitionKind;
import org.hl7.fhir.r4.model.StructureDefinition.TypeDerivationRule;
import org.hl7.fhir.r4.model.TestScript;
import org.hl7.fhir.r4.model.TestScript.AssertionResponseTypes;
import org.hl7.fhir.r4.model.TestScript.SetupActionAssertComponent;
import org.hl7.fhir.r4.model.TestScript.SetupActionOperationComponent;
import org.hl7.fhir.r4.model.TestScript.TestActionComponent;
import org.hl7.fhir.r4.model.TestScript.TestScriptFixtureComponent;
import org.hl7.fhir.r4.model.TestScript.TestScriptTestComponent;
import org.hl7.fhir.r4.test.utils.TestingUtilities;
import org.hl7.fhir.r4.model.TypeDetails;
import org.hl7.fhir.r4.utils.CodingUtilities;
import org.hl7.fhir.r4.utils.FHIRPathEngine;
import org.hl7.fhir.r4.utils.FHIRPathEngine.IEvaluationContext;
import org.hl7.fhir.r4.utils.IResourceValidator;
import org.hl7.fhir.r4.utils.NarrativeGenerator;
import org.hl7.fhir.utilities.Utilities;
import org.hl7.fhir.utilities.validation.ValidationMessage;
import org.junit.Test;
import org.junit.runner.RunWith;
import org.junit.runners.Parameterized;
import org.junit.runners.Parameterized.Parameters;
import junit.framework.Assert;
@RunWith(Parameterized.class)
public class SnapShotGenerationTests {
public class TestPKP implements ProfileKnowledgeProvider {
@Override
public boolean isDatatype(String name) {
StructureDefinition sd = TestingUtilities.context().fetchTypeDefinition(name);
return (sd != null) && (sd.getDerivation() == TypeDerivationRule.SPECIALIZATION) && (sd.getKind() == StructureDefinitionKind.PRIMITIVETYPE || sd.getKind() == StructureDefinitionKind.COMPLEXTYPE);
}
@Override
public boolean isResource(String typeSimple) {
StructureDefinition sd = TestingUtilities.context().fetchTypeDefinition(name);
return (sd != null) && (sd.getDerivation() == TypeDerivationRule.SPECIALIZATION) && (sd.getKind() == StructureDefinitionKind.RESOURCE);
}
@Override
public boolean hasLinkFor(String typeSimple) {
return isDatatype(name);
}
@Override
public String getLinkFor(String corePath, String typeSimple) {
return Utilities.pathURL(corePath, "datatypes.html#"+typeSimple);
}
@Override
public BindingResolution resolveBinding(StructureDefinition def, ElementDefinitionBindingComponent binding, String path) throws FHIRException {
BindingResolution br = new BindingResolution();
br.url = path+"/something.html";
br.display = "something";
return br;
}
@Override
public String getLinkForProfile(StructureDefinition profile, String url) {
StructureDefinition sd = TestingUtilities.context().fetchResource(StructureDefinition.class, url);
if (sd == null)
return url+"|"+url;
else
return sd.getId()+".html|"+sd.present();
}
@Override
public boolean prependLinks() {
return false;
}
}
private static class SnapShotGenerationTestsContext implements IEvaluationContext {
private Map<String, Resource> fixtures;
private Map<String, StructureDefinition> snapshots = new HashMap<String, StructureDefinition>();
public TestScript tests;
public void checkTestsDetails() {
if (!"http://hl7.org/fhir/tests/snapshotgeneration".equals(tests.getUrl()))
throw new Error("Wrong URL on test script");
if (!tests.getSetup().isEmpty())
throw new Error("Setup is not supported");
if (!tests.getTeardown().isEmpty())
throw new Error("Teardown is not supported");
Set<String> ids = new HashSet<String>();
Set<String> urls = new HashSet<String>();
for (Resource r : tests.getContained()) {
if (ids.contains(r.getId()))
throw new Error("Unsupported: duplicate contained resource on fixture id "+r.getId());
ids.add(r.getId());
if (r instanceof MetadataResource) {
MetadataResource md = (MetadataResource) r;
if (urls.contains(md.getUrl()))
throw new Error("Unsupported: duplicate canonical url "+md.getUrl()+" on fixture id "+r.getId());
urls.add(md.getUrl());
}
}
for (TestScriptFixtureComponent r : tests.getFixture()) {
if (ids.contains(r.getId()))
throw new Error("Unsupported: duplicate contained resource or fixture id "+r.getId());
ids.add(r.getId());
}
Set<String> names = new HashSet<String>();
for (TestScriptTestComponent test : tests.getTest()) {
if (names.contains(test.getName()))
throw new Error("Unsupported: duplicate name "+test.getName());
names.add(test.getName());
if (test.getAction().size() < 2)
throw new Error("Unsupported: multiple actions required");
if (!test.getActionFirstRep().hasOperation())
throw new Error("Unsupported: first action must be an operation");
for (int i = 0; i < test.getAction().size(); i++) {
// if (!test.getAction().get(i).hasAssert())
// throw new Error("Unsupported: following actions must be an asserts");
TestActionComponent action = test.getAction().get(i);
if (action.hasOperation()) {
SetupActionOperationComponent op = test.getActionFirstRep().getOperation();
if (!CodingUtilities.matches(op.getType(), "http://hl7.org/fhir/testscript-operation-codes", "snapshot")
&& !CodingUtilities.matches(op.getType(), "http://hl7.org/fhir/testscript-operation-codes", "sortDifferential"))
throw new Error("Unsupported action operation type "+CodingUtilities.present(op.getType()));
if (!"StructureDefinition".equals(op.getResource()))
throw new Error("Unsupported action operation resource "+op.getResource());
if (!op.hasResponseId())
throw new Error("Unsupported action operation: no response id");
if (!op.hasSourceId())
throw new Error("Unsupported action operation: no source id");
if (!hasSource(op.getSourceId()))
throw new Error("Unsupported action operation: source id could not be resolved");
} else if (action.hasAssert()) {
SetupActionAssertComponent a = action.getAssert();
if (!a.hasLabel())
throw new Error("Unsupported: actions must have a label");
if (!a.hasDescription())
throw new Error("Unsupported: actions must have a description");
if (!a.hasExpression() && !a.hasResponse())
throw new Error("Unsupported: actions must have an expression or a response");
} else {
throw new Error("Unsupported: Unrecognized action type");
}
}
}
}
private boolean hasSource(String sourceId) {
for (TestScriptFixtureComponent ds : tests.getFixture()) {
if (sourceId.equals(ds.getId()))
return true;
}
for (Resource r : tests.getContained()) {
if (sourceId.equals(r.getId()))
return true;
}
return false;
}
public Resource fetchFixture(String id) {
if (fixtures.containsKey(id))
return fixtures.get(id);
for (TestScriptFixtureComponent ds : tests.getFixture()) {
if (id.equals(ds.getId()))
throw new Error("not done yet");
}
for (Resource r : tests.getContained()) {
if (id.equals(r.getId()))
return r;
}
return null;
}
// FHIRPath methods
@Override
public Base resolveConstant(Object appContext, String name, boolean beforeContext) throws PathEngineException {
return null;
}
@Override
public TypeDetails resolveConstantType(Object appContext, String name) throws PathEngineException {
return null;
}
@Override
public boolean log(String argument, List<Base> focus) {
System.out.println(argument+": "+fp.convertToString(focus));
return true;
}
@Override
public FunctionDetails resolveFunction(String functionName) {
if ("fixture".equals(functionName))
return new FunctionDetails("Access a fixture defined in the testing context", 0, 1);
return null;
}
@Override
public TypeDetails checkFunction(Object appContext, String functionName, List<TypeDetails> parameters) throws PathEngineException {
if ("fixture".equals(functionName))
return new TypeDetails(CollectionStatus.SINGLETON, TestingUtilities.context().getResourceNamesAsSet());
return null;
}
@Override
public List<Base> executeFunction(Object appContext, String functionName, List<List<Base>> parameters) {
if ("fixture".equals(functionName)) {
String id = fp.convertToString(parameters.get(0));
Resource res = fetchFixture(id);
if (res != null) {
List<Base> list = new ArrayList<Base>();
list.add(res);
return list;
}
}
return null;
}
@Override
public Base resolveReference(Object appContext, String url) {
// TODO Auto-generated method stub
return null;
}
@Override
public boolean conformsToProfile(Object appContext, Base item, String url) throws FHIRException {
IResourceValidator val = TestingUtilities.context().newValidator();
List<ValidationMessage> valerrors = new ArrayList<ValidationMessage>();
if (item instanceof Resource) {
val.validate(appContext, valerrors, (Resource) item, url);
boolean ok = true;
for (ValidationMessage v : valerrors)
ok = ok && v.getLevel().isError();
return ok;
}
throw new NotImplementedException("Not done yet (IGPublisherHostServices.SnapShotGenerationTestsContext), when item is element");
}
}
private static FHIRPathEngine fp;
@Parameters(name = "{index}: file {0}")
public static Iterable<Object[]> data() throws ParserConfigurationException, IOException, FHIRFormatError {
SnapShotGenerationTestsContext context = new SnapShotGenerationTestsContext();
context.tests = (TestScript) new XmlParser().parse(new FileInputStream(TestingUtilities.resourceNameToFile("snapshot-generation-tests.xml")));
context.checkTestsDetails();
List<Object[]> objects = new ArrayList<Object[]>(context.tests.getTest().size());
for (TestScriptTestComponent e : context.tests.getTest()) {
objects.add(new Object[] { e.getName(), e, context });
}
return objects;
}
private final TestScriptTestComponent test;
private final String name;
private SnapShotGenerationTestsContext context;
public SnapShotGenerationTests(String name, TestScriptTestComponent e, SnapShotGenerationTestsContext context) {
this.name = name;
this.test = e;
this.context = context;
}
@SuppressWarnings("deprecation")
@Test
public void test() throws FHIRException {
try {
for (Resource cr : context.tests.getContained()) {
if (cr instanceof StructureDefinition) {
StructureDefinition sd = (StructureDefinition) cr;
if (sd.getType().equals("Extension")) {
if (TestingUtilities.context().fetchResource(StructureDefinition.class, sd.getUrl()) == null) {
sd.setUserData("path", "test-"+sd.getId()+".html");
StructureDefinition extd = TestingUtilities.context().fetchResource(StructureDefinition.class, sd.getBaseDefinition());
new ProfileUtilities(TestingUtilities.context(), null, null).generateSnapshot(extd, sd, sd.getUrl(), sd.getName());
TestingUtilities.context().cacheResource(sd);
debugSaveResource(sd);
}
}
}
}
if (fp == null)
fp = new FHIRPathEngine(TestingUtilities.context());
fp.setHostServices(context);
resolveFixtures();
TestScript.AssertionResponseTypes lastOpOutcome = null;
for (int i = 0; i < test.getAction().size(); i++) {
TestActionComponent action = test.getAction().get(i);
if (action.hasOperation()) {
lastOpOutcome = AssertionResponseTypes.OKAY;
try {
SetupActionOperationComponent op = action.getOperation();
Coding opType = op.getType();
if (opType.getSystem().equals("http://hl7.org/fhir/testscript-operation-codes") && opType.getCode().equals("snapshot")) {
StructureDefinition source = (StructureDefinition) context.fetchFixture(op.getSourceId());
StructureDefinition base = getSD(source.getBaseDefinition());
StructureDefinition output = source.copy();
ProfileUtilities pu = new ProfileUtilities(TestingUtilities.context(), null, new TestPKP());
pu.setIds(source, false);
if ("sort=true".equals(op.getParams())) {
List<String> errors = new ArrayList<String>();
pu.sortDifferential(base, output, source.getName(), errors);
if (errors.size() > 0)
throw new FHIRException("Sort failed: "+errors.toString());
}
pu.generateSnapshot(base, output, source.getUrl(), source.getName());
debugSaveResource(output);
context.fixtures.put(op.getResponseId(), output);
context.snapshots.put(output.getUrl(), output);
new XmlParser().setOutputStyle(OutputStyle.PRETTY).compose(new FileOutputStream(Utilities.path(System.getProperty("java.io.tmpdir"), op.getResponseId()+".xml")), output);
if (output.getDifferential().hasElement())
new NarrativeGenerator("", "http://hl7.org/fhir", TestingUtilities.context()).setPkp(new TestPKP()).generate(output, null);
new XmlParser().setOutputStyle(OutputStyle.PRETTY).compose(new FileOutputStream(Utilities.path(System.getProperty("java.io.tmpdir"), op.getResponseId()+"-d.xml")), output);
} else if (opType.getSystem().equals("http://hl7.org/fhir/testscript-operation-codes") && opType.getCode().equals("sortDifferential")) {
StructureDefinition source = (StructureDefinition) context.fetchFixture(op.getSourceId());
StructureDefinition base = getSD(source.getBaseDefinition());
StructureDefinition output = source.copy();
ProfileUtilities pu = new ProfileUtilities(TestingUtilities.context(), null, null);
pu.setIds(source, false);
List<String> errors = new ArrayList<String>();
pu.sortDifferential(base, output, output.getUrl(), errors);
if (!errors.isEmpty())
throw new FHIRException(errors.get(0));
context.fixtures.put(op.getResponseId(), output);
context.snapshots.put(output.getUrl(), output);
new XmlParser().setOutputStyle(OutputStyle.PRETTY).compose(new FileOutputStream(Utilities.path(System.getProperty("java.io.tmpdir"), op.getResponseId()+".xml")), output);
new XmlParser().setOutputStyle(OutputStyle.PRETTY).compose(new FileOutputStream(Utilities.path(System.getProperty("java.io.tmpdir"), op.getResponseId()+".xml")), output);
} else {
throw new Error("Unsupported operation: " + opType.getSystem() + " : " + opType.getCode());
}
} else if (action.hasAssert()) {
SetupActionAssertComponent a = action.getAssert();
if (a.hasResponse() && a.getResponse().equals(TestScript.AssertionResponseTypes.BAD))
Assert.fail(action.getAssert().getLabel()+": "+action.getAssert().getDescription());
else {
boolean ok = fp.evaluateToBoolean(new StructureDefinition(), new StructureDefinition(), a.getExpression());
Assert.assertTrue(a.getLabel()+": "+a.getDescription(), ok);
}
}
} catch (Exception e) {
boolean ok = false;
for (int j = i+1;i < test.getAction().size(); i++) {
TestActionComponent followAction = test.getAction().get(j);
if (followAction.hasAssert() && followAction.getAssert().hasResponse() && followAction.getAssert().getResponse().equals(TestScript.AssertionResponseTypes.BAD)) {
ok = true;
break;
}
}
} catch (Exception e) {
lastOpOutcome = AssertionResponseTypes.BAD;
}
} else if (action.hasAssert()) {
SetupActionAssertComponent a = action.getAssert();
if (a.getResponse() != null) {
Assert.assertTrue(a.getLabel()+" (response): "+a.getDescription(), a.getResponse() == lastOpOutcome);
}
if (a.hasExpression()) {
boolean ok = fp.evaluateToBoolean(new StructureDefinition(), new StructureDefinition(), a.getExpression());
Assert.assertTrue(a.getLabel()+": "+a.getDescription(), ok);
}
}
}
} catch (Exception e) {
e.printStackTrace();
throw new FHIRException(e);
}
}
private void debugSaveResource(Resource r) throws IOException {
String dir = System.getProperty("java.io.tmpdir");
if (new File("c:\\temp").exists())
dir = "c:\\temp";
String fn = Utilities.path(dir, r.fhirType()+"-"+r.getId()+".xml");
new XmlParser().setOutputStyle(OutputStyle.PRETTY).compose(new FileOutputStream(fn), r);
}
private StructureDefinition getSD(String url) throws DefinitionException, FHIRException, IOException {
StructureDefinition sd = context.snapshots.get(url);
if (sd == null)
sd = findContainedProfile(url);
if (sd == null)
sd = TestingUtilities.context().fetchResource(StructureDefinition.class, url);
return sd;
}
private StructureDefinition findContainedProfile(String url) throws DefinitionException, FHIRException, IOException {
for (Resource r : context.tests.getContained()) {
if (r instanceof StructureDefinition) {
StructureDefinition sd = (StructureDefinition) r;
if (sd.getUrl().equals(url)) {
StructureDefinition p = sd.copy();
ProfileUtilities pu = new ProfileUtilities(TestingUtilities.context(), null, null);
pu.setIds(p, false);
List<String> errors = new ArrayList<String>();
pu.sortDifferential(getSD(p.getBaseDefinition()), p, url, errors);
if (!errors.isEmpty())
throw new FHIRException(errors.get(0));
pu.generateSnapshot(getSD(p.getBaseDefinition()), p, p.getUrl(), p.getName());
debugSaveResource(p);
return p;
}
}
}
return null;
}
private void resolveFixtures() {
if (context.fixtures == null) {
context.fixtures = new HashMap<String, Resource>();
for (TestScriptFixtureComponent fd : context.tests.getFixture()) {
Resource r = TestingUtilities.context().fetchResource(Resource.class, fd.getResource().getReference());
context.fixtures.put(fd.getId(), r);
}
}
}
}

2
org.hl7.fhir.utilities/pom.xml
View File

@ -5,7 +5,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>org.hl7.fhir.core</artifactId>
<version>3.7.3-SNAPSHOT</version>
<version>3.7.4-SNAPSHOT</version>
<relativePath>../pom.xml</relativePath>
</parent>

59
org.hl7.fhir.validation.cli/pom.xml
View File

@ -5,7 +5,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>org.hl7.fhir.core</artifactId>
<version>3.7.3-SNAPSHOT</version>
<version>3.7.4-SNAPSHOT</version>
<relativePath>../pom.xml</relativePath>
</parent>
@ -55,28 +55,63 @@
<build>
<plugins>
<!--
Build a fatjar containing all depenedncies
-->
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-shade-plugin</artifactId>
<version>3.2.1</version>
<artifactId>maven-dependency-plugin</artifactId>
<executions>
<execution>
<phase>package</phase>
<id>unpack-dependencies</id>
<phase>process-classes</phase>
<goals>
<goal>shade</goal>
<goal>unpack-dependencies</goal>
</goals>
<configuration>
<shadedClassifierName/>
<transformers>
<transformer implementation="org.apache.maven.plugins.shade.resource.ManifestResourceTransformer">
<mainClass>org.hl7.fhir.r4.validation.Validator</mainClass>
</transformer>
</transformers>
<shadedArtifactAttached>true</shadedArtifactAttached>
<excludes>**/module-info.class</excludes>
<outputDirectory>${project.build.directory}/classes</outputDirectory>
<overWriteReleases>false</overWriteReleases>
<overWriteSnapshots>true</overWriteSnapshots>
<excludeScope>test</excludeScope>
<includeScope>compile</includeScope>
</configuration>
</execution>
</executions>
</plugin>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-jar-plugin</artifactId>
<configuration>
<archive>
<manifest>
<addClasspath>true</addClasspath>
<mainClass>org.hl7.fhir.r4.validation.Validator</mainClass>
</manifest>
</archive>
</configuration>
</plugin>
<!--
These two plugins provide quality checks that don't make sense to perform
on a fatjar.
-->
<plugin>
<groupId>org.codehaus.mojo</groupId>
<artifactId>animal-sniffer-maven-plugin</artifactId>
<configuration>
<skip>true</skip>
</configuration>
</plugin>
<plugin>
<groupId>org.basepom.maven</groupId>
<artifactId>duplicate-finder-maven-plugin</artifactId>
<configuration>
<skip>true</skip>
</configuration>
</plugin>
</plugins>
</build>

0
org.hl7.fhir.validation.cli/src/main/java/.keep.16
View File

103
org.hl7.fhir.validation/.classpath
View File

@ -1,52 +1,51 @@
<?xml version="1.0" encoding="UTF-8"?>
<classpath>
<classpathentry kind="src" path="src/test/java" output="target/test-classes" including="**/*.java"/>
<classpathentry kind="src" path="src/test/resources" output="target/test-classes" excluding="**/*.java"/>
<classpathentry kind="src" path="src/main/java" including="**/*.java"/>
<classpathentry kind="src" path="src/main/resources" excluding="**/*.java"/>
<classpathentry kind="output" path="target/classes"/>
<classpathentry kind="var" path="M2_REPO/javax/xml/bind/jaxb-api/2.3.1/jaxb-api-2.3.1.jar" sourcepath="M2_REPO/javax/xml/bind/jaxb-api/2.3.1/jaxb-api-2.3.1-sources.jar"/>
<classpathentry kind="var" path="M2_REPO/javax/activation/javax.activation-api/1.2.0/javax.activation-api-1.2.0.jar" sourcepath="M2_REPO/javax/activation/javax.activation-api/1.2.0/javax.activation-api-1.2.0-sources.jar"/>
<classpathentry kind="con" path="org.eclipse.jdt.launching.JRE_CONTAINER/org.eclipse.jdt.internal.debug.ui.launcher.StandardVMType/JavaSE-1.8"/>
<classpathentry kind="var" path="M2_REPO/ca/uhn/hapi/fhir/hapi-fhir-base/3.7.0-SNAPSHOT/hapi-fhir-base-3.7.0-SNAPSHOT.jar" sourcepath="M2_REPO/ca/uhn/hapi/fhir/hapi-fhir-base/3.7.0-SNAPSHOT/hapi-fhir-base-3.7.0-SNAPSHOT-sources.jar"/>
<classpathentry kind="var" path="M2_REPO/com/google/code/gson/gson/2.8.5/gson-2.8.5.jar" sourcepath="M2_REPO/com/google/code/gson/gson/2.8.5/gson-2.8.5-sources.jar"/>
<classpathentry kind="var" path="M2_REPO/org/apache/commons/commons-lang3/3.8.1/commons-lang3-3.8.1.jar" sourcepath="M2_REPO/org/apache/commons/commons-lang3/3.8.1/commons-lang3-3.8.1-sources.jar"/>
<classpathentry kind="var" path="M2_REPO/org/apache/commons/commons-text/1.6/commons-text-1.6.jar" sourcepath="M2_REPO/org/apache/commons/commons-text/1.6/commons-text-1.6-sources.jar"/>
<classpathentry kind="var" path="M2_REPO/commons-codec/commons-codec/1.11/commons-codec-1.11.jar" sourcepath="M2_REPO/commons-codec/commons-codec/1.11/commons-codec-1.11-sources.jar"/>
<classpathentry kind="var" path="M2_REPO/commons-io/commons-io/2.6/commons-io-2.6.jar" sourcepath="M2_REPO/commons-io/commons-io/2.6/commons-io-2.6-sources.jar"/>
<classpathentry kind="var" path="M2_REPO/com/google/guava/guava/25.0-jre/guava-25.0-jre.jar" sourcepath="M2_REPO/com/google/guava/guava/25.0-jre/guava-25.0-jre-sources.jar"/>
<classpathentry kind="var" path="M2_REPO/com/google/code/findbugs/jsr305/1.3.9/jsr305-1.3.9.jar"/>
<classpathentry kind="var" path="M2_REPO/org/checkerframework/checker-compat-qual/2.0.0/checker-compat-qual-2.0.0.jar" sourcepath="M2_REPO/org/checkerframework/checker-compat-qual/2.0.0/checker-compat-qual-2.0.0-sources.jar"/>
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2
org.hl7.fhir.validation/pom.xml
View File

@ -5,7 +5,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>org.hl7.fhir.core</artifactId>
<version>3.7.3-SNAPSHOT</version>
<version>3.7.4-SNAPSHOT</version>
<relativePath>../pom.xml</relativePath>
</parent>

126
org.hl7.fhir.validation/src/main/java/org/hl7/fhir/r4/validation/BaseValidator.java
View File

@ -72,8 +72,8 @@ public class BaseValidator {
*/
protected boolean fail(List<ValidationMessage> errors, IssueType type, int line, int col, String path, boolean thePass, String msg) {
if (!thePass) {
errors.add(new ValidationMessage(source, type, line, col, path, msg, IssueSeverity.FATAL));
}
addValidationMessage(errors, type, line, col, path, msg, IssueSeverity.FATAL);
}
return thePass;
}
@ -87,8 +87,8 @@ public class BaseValidator {
protected boolean fail(List<ValidationMessage> errors, IssueType type, List<String> pathParts, boolean thePass, String msg) {
if (!thePass) {
String path = toPath(pathParts);
errors.add(new ValidationMessage(source, type, -1, -1, path, msg, IssueSeverity.FATAL));
}
addValidationMessage(errors, type, -1, -1, path, msg, IssueSeverity.FATAL);
}
return thePass;
}
@ -102,8 +102,8 @@ public class BaseValidator {
protected boolean fail(List<ValidationMessage> errors, IssueType type, List<String> pathParts, boolean thePass, String theMessage, Object... theMessageArguments) {
if (!thePass) {
String path = toPath(pathParts);
errors.add(new ValidationMessage(source, type, -1, -1, path, formatMessage(theMessage, theMessageArguments), IssueSeverity.FATAL));
}
addValidationMessage(errors, type, -1, -1, path, formatMessage(theMessage, theMessageArguments), IssueSeverity.FATAL);
}
return thePass;
}
@ -116,8 +116,8 @@ public class BaseValidator {
*/
protected boolean fail(List<ValidationMessage> errors, IssueType type, String path, boolean thePass, String msg) {
if (!thePass) {
errors.add(new ValidationMessage(source, type, -1, -1, path, msg, IssueSeverity.FATAL));
}
addValidationMessage(errors, type, -1, -1, path, msg, IssueSeverity.FATAL);
}
return thePass;
}
@ -145,8 +145,8 @@ public class BaseValidator {
*/
protected boolean hint(List<ValidationMessage> errors, IssueType type, int line, int col, String path, boolean thePass, String msg) {
if (!thePass) {
errors.add(new ValidationMessage(source, type, line, col, path, msg, IssueSeverity.INFORMATION));
}
addValidationMessage(errors, type, line, col, path, msg, IssueSeverity.INFORMATION);
}
return thePass;
}
@ -160,15 +160,16 @@ public class BaseValidator {
protected boolean hint(List<ValidationMessage> errors, IssueType type, int line, int col, String path, boolean thePass, String theMessage, Object... theMessageArguments) {
if (!thePass) {
String message = formatMessage(theMessage, theMessageArguments);
errors.add(new ValidationMessage(source, type, line, col, path, message, IssueSeverity.INFORMATION));
}
addValidationMessage(errors, type, line, col, path, message, IssueSeverity.INFORMATION);
}
return thePass;
}
protected boolean txHint(List<ValidationMessage> errors, String txLink, IssueType type, int line, int col, String path, boolean thePass, String theMessage, Object... theMessageArguments) {
if (!thePass) {
String message = formatMessage(theMessage, theMessageArguments);
errors.add(new ValidationMessage(Source.TerminologyEngine, type, line, col, path, message, IssueSeverity.INFORMATION).setTxLink(txLink));
addValidationMessage(errors, type, line, col, path, message, IssueSeverity.INFORMATION, Source.TerminologyEngine)
.setTxLink(txLink);
}
return thePass;
}
@ -184,8 +185,8 @@ public class BaseValidator {
if (!thePass) {
String path = toPath(pathParts);
String message = formatMessage(theMessage, theMessageArguments);
errors.add(new ValidationMessage(source, type, -1, -1, path, message, IssueSeverity.INFORMATION));
}
addValidationMessage(errors, type, -1, -1, path, message, IssueSeverity.INFORMATION);
}
return thePass;
}
@ -198,8 +199,8 @@ public class BaseValidator {
*/
protected boolean hint(List<ValidationMessage> errors, IssueType type, String path, boolean thePass, String msg) {
if (!thePass) {
errors.add(new ValidationMessage(source, type, -1, -1, path, msg, IssueSeverity.INFORMATION));
}
addValidationMessage(errors, type, -1, -1, path, msg, IssueSeverity.INFORMATION);
}
return thePass;
}
@ -213,8 +214,8 @@ public class BaseValidator {
protected boolean rule(List<ValidationMessage> errors, IssueType type, int line, int col, String path, boolean thePass, String theMessage, Object... theMessageArguments) {
if (!thePass) {
String message = formatMessage(theMessage, theMessageArguments);
errors.add(new ValidationMessage(source, type, line, col, path, message, IssueSeverity.ERROR));
}
addValidationMessage(errors, type, line, col, path, message, IssueSeverity.ERROR);
}
return thePass;
}
@ -236,8 +237,8 @@ public class BaseValidator {
protected boolean rule(List<ValidationMessage> errors, IssueType type, List<String> pathParts, boolean thePass, String msg) {
if (!thePass) {
String path = toPath(pathParts);
errors.add(new ValidationMessage(source, type, -1, -1, path, msg, IssueSeverity.ERROR));
}
addValidationMessage(errors, type, -1, -1, path, msg, IssueSeverity.ERROR);
}
return thePass;
}
@ -252,8 +253,8 @@ public class BaseValidator {
if (!thePass) {
String path = toPath(pathParts);
String message = formatMessage(theMessage, theMessageArguments);
errors.add(new ValidationMessage(source, type, -1, -1, path, message, IssueSeverity.ERROR));
}
addValidationMessage(errors, type, -1, -1, path, message, IssueSeverity.ERROR);
}
return thePass;
}
@ -266,15 +267,15 @@ public class BaseValidator {
*/
protected boolean rule(List<ValidationMessage> errors, IssueType type, String path, boolean thePass, String msg) {
if (!thePass) {
errors.add(new ValidationMessage(source, type, -1, -1, path, msg, IssueSeverity.ERROR));
}
addValidationMessage(errors, type, -1, -1, path, msg, IssueSeverity.ERROR);
}
return thePass;
}
static public boolean rule(List<ValidationMessage> errors, Source source, IssueType type, String path, boolean thePass, String msg) {
public boolean rule(List<ValidationMessage> errors, Source source, IssueType type, String path, boolean thePass, String msg) {
if (!thePass) {
errors.add(new ValidationMessage(source, type, -1, -1, path, msg, IssueSeverity.ERROR));
}
addValidationMessage(errors, type, -1, -1, path, msg, IssueSeverity.ERROR, source);
}
return thePass;
}
@ -287,8 +288,8 @@ public class BaseValidator {
*/
protected boolean rule(List<ValidationMessage> errors, IssueType type, String path, boolean thePass, String msg, String html) {
if (!thePass) {
errors.add(new ValidationMessage(source, type, -1, -1, path, msg, html, IssueSeverity.ERROR));
}
addValidationMessage(errors, type, path, msg, html, IssueSeverity.ERROR);
}
return thePass;
}
@ -330,13 +331,25 @@ public class BaseValidator {
protected boolean warning(List<ValidationMessage> errors, IssueType type, int line, int col, String path, boolean thePass, String msg, Object... theMessageArguments) {
if (!thePass) {
msg = formatMessage(msg, theMessageArguments);
errors.add(new ValidationMessage(source, type, line, col, path, msg, IssueSeverity.WARNING));
}
IssueSeverity severity = IssueSeverity.WARNING;
addValidationMessage(errors, type, line, col, path, msg, severity);
}
return thePass;
}
/**
protected void addValidationMessage(List<ValidationMessage> errors, IssueType type, int line, int col, String path, String msg, IssueSeverity theSeverity) {
Source source = this.source;
addValidationMessage(errors, type, line, col, path, msg, theSeverity, source);
}
protected ValidationMessage addValidationMessage(List<ValidationMessage> errors, IssueType type, int line, int col, String path, String msg, IssueSeverity theSeverity, Source theSource) {
ValidationMessage validationMessage = new ValidationMessage(theSource, type, line, col, path, msg, theSeverity);
errors.add(validationMessage);
return validationMessage;
}
/**
* Test a rule and add a {@link IssueSeverity#WARNING} validation message if the validation fails
*
* @param thePass
@ -355,8 +368,8 @@ public class BaseValidator {
protected boolean warningOrError(boolean isError, List<ValidationMessage> errors, IssueType type, int line, int col, String path, boolean thePass, String msg, Object... theMessageArguments) {
if (!thePass) {
msg = formatMessage(msg, theMessageArguments);
errors.add(new ValidationMessage(source, type, line, col, path, msg, isError ? IssueSeverity.ERROR : IssueSeverity.WARNING));
}
addValidationMessage(errors, type, line, col, path, msg, isError ? IssueSeverity.ERROR : IssueSeverity.WARNING);
}
return thePass;
}
@ -372,8 +385,8 @@ public class BaseValidator {
if (!thePass) {
String path = toPath(pathParts);
String message = formatMessage(theMessage, theMessageArguments);
errors.add(new ValidationMessage(source, type, -1, -1, path, message, IssueSeverity.WARNING));
}
addValidationMessage(errors, type, -1, -1, path, message, IssueSeverity.WARNING);
}
return thePass;
}
@ -386,8 +399,8 @@ public class BaseValidator {
*/
protected boolean warning(List<ValidationMessage> errors, IssueType type, String path, boolean thePass, String msg) {
if (!thePass) {
errors.add(new ValidationMessage(source, type, -1, -1, path, msg, IssueSeverity.WARNING));
}
addValidationMessage(errors, type, -1, -1, path, msg, IssueSeverity.WARNING);
}
return thePass;
}
@ -400,8 +413,8 @@ public class BaseValidator {
*/
protected boolean warning(List<ValidationMessage> errors, IssueType type, String path, boolean thePass, String msg, String html) {
if (!thePass) {
errors.add(new ValidationMessage(source, type, -1, -1, path, msg, html, IssueSeverity.WARNING));
}
addValidationMessage(errors, type, path, msg, html, IssueSeverity.WARNING);
}
return thePass;
}
@ -415,8 +428,8 @@ public class BaseValidator {
protected boolean warning(List<ValidationMessage> errors, IssueType type, String path, boolean thePass, String msg, String html, Object... theMessageArguments) {
if (!thePass) {
msg = formatMessage(msg, theMessageArguments);
errors.add(new ValidationMessage(source, type, -1, -1, path, msg, html, IssueSeverity.WARNING));
}
addValidationMessage(errors, type, path, msg, html, IssueSeverity.WARNING);
}
return thePass;
}
@ -431,8 +444,8 @@ public class BaseValidator {
protected boolean suppressedwarning(List<ValidationMessage> errors, IssueType type, int line, int col, String path, boolean thePass, String msg, Object... theMessageArguments) {
if (!thePass) {
msg = formatMessage(msg, theMessageArguments);
errors.add(new ValidationMessage(source, type, line, col, path, msg, IssueSeverity.INFORMATION));
}
addValidationMessage(errors, type, line, col, path, msg, IssueSeverity.INFORMATION);
}
return thePass;
}
@ -448,8 +461,8 @@ public class BaseValidator {
if (!thePass) {
String path = toPath(pathParts);
String message = formatMessage(theMessage, theMessageArguments);
errors.add(new ValidationMessage(source, type, -1, -1, path, message, IssueSeverity.INFORMATION));
}
addValidationMessage(errors, type, -1, -1, path, message, IssueSeverity.INFORMATION);
}
return thePass;
}
@ -462,8 +475,8 @@ public class BaseValidator {
*/
protected boolean suppressedwarning(List<ValidationMessage> errors, IssueType type, String path, boolean thePass, String msg) {
if (!thePass) {
errors.add(new ValidationMessage(source, type, -1, -1, path, msg, IssueSeverity.INFORMATION));
}
addValidationMessage(errors, type, -1, -1, path, msg, IssueSeverity.INFORMATION);
}
return thePass;
}
@ -476,12 +489,17 @@ public class BaseValidator {
*/
protected boolean suppressedwarning(List<ValidationMessage> errors, IssueType type, String path, boolean thePass, String msg, String html) {
if (!thePass) {
errors.add(new ValidationMessage(source, type, -1, -1, path, msg, html, IssueSeverity.INFORMATION));
}
IssueSeverity severity = IssueSeverity.INFORMATION;
addValidationMessage(errors, type, path, msg, html, severity);
}
return thePass;
}
/**
protected void addValidationMessage(List<ValidationMessage> errors, IssueType type, String path, String msg, String html, IssueSeverity theSeverity) {
errors.add(new ValidationMessage(source, type, -1, -1, path, msg, html, theSeverity));
}
/**
* Test a rule and add a {@link IssueSeverity#WARNING} validation message if the validation fails
*
* @param thePass
@ -491,8 +509,8 @@ public class BaseValidator {
protected boolean suppressedwarning(List<ValidationMessage> errors, IssueType type, String path, boolean thePass, String msg, String html, Object... theMessageArguments) {
if (!thePass) {
msg = formatMessage(msg, theMessageArguments);
errors.add(new ValidationMessage(source, type, -1, -1, path, msg, html, IssueSeverity.INFORMATION));
}
addValidationMessage(errors, type, path, msg, html, IssueSeverity.INFORMATION);
}
return thePass;
}

216
org.hl7.fhir.validation/src/main/java/org/hl7/fhir/r4/validation/DefaultEnableWhenEvaluator.java Normal file
View File

@ -0,0 +1,216 @@
package org.hl7.fhir.r4.validation;
import java.util.*;
import java.util.stream.*;
import org.hl7.fhir.exceptions.FHIRException;
import org.hl7.fhir.r4.elementmodel.Element;
import org.hl7.fhir.r4.model.*;
import org.hl7.fhir.r4.model.Questionnaire.*;
import ca.uhn.fhir.rest.server.exceptions.UnprocessableEntityException;
/**
* Evaluates Questionnaire.item.enableWhen against a QuestionnaireResponse.
* Ignores possible modifierExtensions and extensions.
*
*/
public class DefaultEnableWhenEvaluator implements IEnableWhenEvaluator {
public static final String LINKID_ELEMENT = "linkId";
public static final String ITEM_ELEMENT = "item";
public static final String ANSWER_ELEMENT = "answer";
@Override
public boolean isQuestionEnabled(QuestionnaireItemComponent questionnaireItem, Element questionnaireResponse) {
if (!questionnaireItem.hasEnableWhen()) {
return true;
}
List<EnableWhenResult> evaluationResults = questionnaireItem.getEnableWhen()
.stream()
.map(enableCondition -> evaluateCondition(enableCondition, questionnaireResponse,
questionnaireItem.getLinkId()))
.collect(Collectors.toList());
return checkConditionResults(evaluationResults, questionnaireItem);
}
public boolean checkConditionResults(List<EnableWhenResult> evaluationResults,
QuestionnaireItemComponent questionnaireItem) {
if (questionnaireItem.hasEnableBehavior() && questionnaireItem.getEnableBehavior() == EnableWhenBehavior.ANY){
return evaluationResults.stream().anyMatch(EnableWhenResult::isEnabled);
} if (questionnaireItem.hasEnableBehavior() && questionnaireItem.getEnableBehavior() == EnableWhenBehavior.ALL){
return evaluationResults.stream().allMatch(EnableWhenResult::isEnabled);
}
//TODO: Throw exception? enableBehavior is mandatory when there are multiple conditions
return true;
}
protected EnableWhenResult evaluateCondition(QuestionnaireItemEnableWhenComponent enableCondition,
Element questionnaireResponse, String linkId) {
//TODO: Fix EnableWhenResult stuff
List<Element> answerItems = findQuestionAnswers(questionnaireResponse,
enableCondition.getQuestion());
QuestionnaireItemOperator operator = enableCondition.getOperator();
if (operator == QuestionnaireItemOperator.EXISTS){
Type answer = enableCondition.getAnswer();
if (!(answer instanceof BooleanType)){
throw new UnprocessableEntityException("Exists-operator requires answerBoolean");
}
return new EnableWhenResult(((BooleanType)answer).booleanValue() != answerItems.isEmpty(),
linkId, enableCondition, questionnaireResponse);
}
boolean result = answerItems
.stream()
.anyMatch(answer -> evaluateAnswer(answer, enableCondition.getAnswer(), enableCondition.getOperator()));
return new EnableWhenResult(result, linkId, enableCondition, questionnaireResponse);
}
public Type convertToType(Element element) throws FHIRException {
Type b = new Factory().create(element.fhirType());
if (b instanceof PrimitiveType) {
((PrimitiveType<?>) b).setValueAsString(element.primitiveValue());
} else {
for (Element child : element.getChildren()) {
if (!isExtension(child)) {
b.setProperty(child.getName(), convertToType(child));
}
}
}
return b;
}
private boolean isExtension(Element element) {
return "Extension".equals(element.fhirType());
}
protected boolean evaluateAnswer(Element answer, Type expectedAnswer, QuestionnaireItemOperator questionnaireItemOperator) {
Type actualAnswer;
if (isExtension(answer)) {
return false;
}
try {
actualAnswer = convertToType(answer);
} catch (FHIRException e) {
throw new UnprocessableEntityException("Unexpected answer type", e);
}
if (!actualAnswer.getClass().equals(expectedAnswer.getClass())) {
throw new UnprocessableEntityException("Expected answer and actual answer have incompatible types");
}
if (expectedAnswer instanceof Coding) {
return compareCodingAnswer((Coding)expectedAnswer, (Coding)actualAnswer, questionnaireItemOperator);
} else if ((expectedAnswer instanceof PrimitiveType)) {
return comparePrimitiveAnswer((PrimitiveType<?>)actualAnswer, (PrimitiveType<?>)expectedAnswer, questionnaireItemOperator);
} else if (expectedAnswer instanceof Quantity) {
return compareQuantityAnswer((Quantity)actualAnswer, (Quantity)expectedAnswer, questionnaireItemOperator);
}
// TODO: Attachment, reference?
throw new UnprocessableEntityException("Unimplemented answer type: " + expectedAnswer.getClass());
}
private boolean compareQuantityAnswer(Quantity actualAnswer, Quantity expectedAnswer, QuestionnaireItemOperator questionnaireItemOperator) {
return compareComparable(actualAnswer.getValue(), expectedAnswer.getValue(), questionnaireItemOperator);
}
private boolean comparePrimitiveAnswer(PrimitiveType<?> actualAnswer, PrimitiveType<?> expectedAnswer, QuestionnaireItemOperator questionnaireItemOperator) {
if (actualAnswer.getValue() instanceof Comparable){
return compareComparable((Comparable)actualAnswer.getValue(), (Comparable) expectedAnswer.getValue(), questionnaireItemOperator);
} else if (questionnaireItemOperator == QuestionnaireItemOperator.EQUAL){
return actualAnswer.equalsShallow(expectedAnswer);
} else if (questionnaireItemOperator == QuestionnaireItemOperator.NOT_EQUAL){
return !actualAnswer.equalsShallow(expectedAnswer);
}
throw new UnprocessableEntityException("Bad operator for PrimitiveType comparison");
}
@SuppressWarnings({ "rawtypes", "unchecked" })
private boolean compareComparable(Comparable actual, Comparable expected,
QuestionnaireItemOperator questionnaireItemOperator) {
int result = actual.compareTo(expected);
if (questionnaireItemOperator == QuestionnaireItemOperator.EQUAL){
return result == 0;
} else if (questionnaireItemOperator == QuestionnaireItemOperator.NOT_EQUAL){
return result != 0;
} else if (questionnaireItemOperator == QuestionnaireItemOperator.GREATER_OR_EQUAL){
return result >= 0;
} else if (questionnaireItemOperator == QuestionnaireItemOperator.LESS_OR_EQUAL){
return result <= 0;
} else if (questionnaireItemOperator == QuestionnaireItemOperator.LESS_THAN){
return result < 0;
} else if (questionnaireItemOperator == QuestionnaireItemOperator.GREATER_THAN){
return result > 0;
}
throw new UnprocessableEntityException("Bad operator for PrimitiveType comparison");
}
private List<Element> findQuestionAnswers(Element questionnaireResponse, String question) {
List<Element> matchingItems = questionnaireResponse.getChildren(ITEM_ELEMENT)
.stream()
.flatMap(i -> findSubItems(i).stream())
.filter(i -> hasLinkId(i, question))
.collect(Collectors.toList());
return matchingItems
.stream()
.flatMap(e -> extractAnswer(e).stream())
.collect(Collectors.toList());
}
private List<Element> extractAnswer(Element item) {
return item.getChildrenByName(ANSWER_ELEMENT)
.stream()
.flatMap(c -> c.getChildren().stream())
.collect(Collectors.toList());
}
private boolean compareCodingAnswer(Coding expectedAnswer, Coding actualAnswer, QuestionnaireItemOperator questionnaireItemOperator) {
boolean result = compareSystems(expectedAnswer, actualAnswer) && compareCodes(expectedAnswer, actualAnswer);
if (questionnaireItemOperator == QuestionnaireItemOperator.EQUAL){
return result == true;
} else if (questionnaireItemOperator == QuestionnaireItemOperator.NOT_EQUAL){
return result == false;
}
throw new UnprocessableEntityException("Bad operator for Coding comparison");
}
private boolean compareCodes(Coding expectedCoding, Coding value) {
if (expectedCoding.hasCode() != value.hasCode()) {
return false;
}
if (expectedCoding.hasCode()) {
return expectedCoding.getCode().equals(value.getCode());
}
return true;
}
private boolean compareSystems(Coding expectedCoding, Coding value) {
if (expectedCoding.hasSystem() && !value.hasSystem()) {
return false;
}
if (expectedCoding.hasSystem()) {
return expectedCoding.getSystem().equals(value.getSystem());
}
return true;
}
private List<Element> findSubItems(Element item) {
List<Element> results = item.getChildren(LINKID_ELEMENT)
.stream()
.flatMap(i -> findSubItems(i).stream())
.collect(Collectors.toList());
results.add(item);
return results;
}
private boolean hasLinkId(Element item, String linkId) {
Element linkIdChild = item.getNamedChild(LINKID_ELEMENT);
if (linkIdChild != null && linkIdChild.getValue().equals(linkId)){
return true;
}
return false;
}
}

48
org.hl7.fhir.validation/src/main/java/org/hl7/fhir/r4/validation/EnableWhenResult.java Normal file
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@ -0,0 +1,48 @@
package org.hl7.fhir.r4.validation;
import org.hl7.fhir.r4.elementmodel.Element;
import org.hl7.fhir.r4.model.Questionnaire.QuestionnaireItemEnableWhenComponent;
public class EnableWhenResult {
private final boolean enabled;
private final QuestionnaireItemEnableWhenComponent enableWhenCondition;
private final Element answerItem;
private final String linkId;
/**
* Evaluation result of enableWhen condition
*
* @param enabled
* Evaluation result
* @param linkId
* LinkId of the questionnaire item
* @param enableWhenCondition
* Evaluated enableWhen condition
* @param responseItem
* item in QuestionnaireResponse
*/
public EnableWhenResult(boolean enabled, String linkId, QuestionnaireItemEnableWhenComponent enableWhenCondition,
Element answerItem) {
this.enabled = enabled;
this.linkId = linkId;
this.answerItem = answerItem;
this.enableWhenCondition = enableWhenCondition;
}
public boolean isEnabled() {
return enabled;
}
public String getLinkId() {
return linkId;
}
public Element getAnswerItem() {
return answerItem;
}
public QuestionnaireItemEnableWhenComponent getEnableWhenCondition() {
return enableWhenCondition;
}
}

10
org.hl7.fhir.validation/src/main/java/org/hl7/fhir/r4/validation/IEnableWhenEvaluator.java Normal file
View File

@ -0,0 +1,10 @@
package org.hl7.fhir.r4.validation;
import org.hl7.fhir.r4.elementmodel.Element;
import org.hl7.fhir.r4.model.Questionnaire.QuestionnaireItemComponent;
public interface IEnableWhenEvaluator {
public boolean isQuestionEnabled(QuestionnaireItemComponent questionnaireItem,
Element questionnaireResponse);
}

71
org.hl7.fhir.validation/src/main/java/org/hl7/fhir/r4/validation/InstanceValidator.java
View File

@ -35,6 +35,8 @@ import java.util.UUID;
import org.apache.commons.lang3.NotImplementedException;
import org.apache.commons.lang3.StringUtils;
import org.hl7.fhir.r4.model.Reference;
import org.hl7.fhir.exceptions.*;
import org.hl7.fhir.convertors.VersionConvertorConstants;
import org.hl7.fhir.exceptions.DefinitionException;
import org.hl7.fhir.exceptions.FHIRException;
@ -274,6 +276,8 @@ public class InstanceValidator extends BaseValidator implements IResourceValidat
private IEvaluationContext externalHostServices;
private boolean noExtensibleWarnings;
private String serverBase;
private IEnableWhenEvaluator myEnableWhenEvaluator = new DefaultEnableWhenEvaluator();
/*
* Keeps track of whether a particular profile has been checked or not yet
@ -2498,6 +2502,10 @@ public class InstanceValidator extends BaseValidator implements IResourceValidat
public void setAllowXsiLocation(boolean allowXsiLocation) {
this.allowXsiLocation = allowXsiLocation;
}
public void setEnableWhenEvaluator(IEnableWhenEvaluator myEnableWhenEvaluator) {
this.myEnableWhenEvaluator = myEnableWhenEvaluator;
}
/**
*
@ -2776,21 +2784,21 @@ public class InstanceValidator extends BaseValidator implements IResourceValidat
sdTime = sdTime + (System.nanoTime() - t);
if (warning(errors, IssueType.REQUIRED, q.line(), q.col(), stack.getLiteralPath(), qsrc != null, "The questionnaire \""+questionnaire+"\" could not be resolved, so no validation can be performed against the base questionnaire")) {
boolean inProgress = "in-progress".equals(element.getNamedChildValue("status"));
validateQuestionannaireResponseItems(qsrc, qsrc.getItem(), errors, element, stack, inProgress);
validateQuestionannaireResponseItems(qsrc, qsrc.getItem(), errors, element, stack, inProgress, element);
}
}
}
private void validateQuestionannaireResponseItem(Questionnaire qsrc, QuestionnaireItemComponent qItem, List<ValidationMessage> errors, Element element, NodeStack stack, boolean inProgress) {
private void validateQuestionannaireResponseItem(Questionnaire qsrc, QuestionnaireItemComponent qItem, List<ValidationMessage> errors, Element element, NodeStack stack, boolean inProgress, Element questionnaireResponseRoot) {
String text = element.getNamedChildValue("text");
rule(errors, IssueType.INVALID, element.line(), element.col(), stack.getLiteralPath(), Utilities.noString(text) || text.equals(qItem.getText()), "If text exists, it must match the questionnaire definition for linkId "+qItem.getLinkId());
List<Element> answers = new ArrayList<Element>();
element.getNamedChildren("answer", answers);
if (inProgress)
warning(errors, IssueType.REQUIRED, element.line(), element.col(), stack.getLiteralPath(), (answers.size() > 0) || !qItem.getRequired(), "No response answer found for required item "+qItem.getLinkId());
warning(errors, IssueType.REQUIRED, element.line(), element.col(), stack.getLiteralPath(), isAnswerRequirementFulfilled(qItem, answers), "No response answer found for required item "+qItem.getLinkId());
else
rule(errors, IssueType.REQUIRED, element.line(), element.col(), stack.getLiteralPath(), (answers.size() > 0) || !qItem.getRequired(), "No response answer found for required item "+qItem.getLinkId());
rule(errors, IssueType.REQUIRED, element.line(), element.col(), stack.getLiteralPath(), isAnswerRequirementFulfilled(qItem, answers), "No response answer found for required item "+qItem.getLinkId());
if (answers.size() > 1)
rule(errors, IssueType.INVALID, answers.get(1).line(), answers.get(1).col(), stack.getLiteralPath(), qItem.getRepeats(), "Only one response answer item with this linkId allowed");
@ -2865,7 +2873,7 @@ public class InstanceValidator extends BaseValidator implements IResourceValidat
// no validation
break;
}
validateQuestionannaireResponseItems(qsrc, qItem.getItem(), errors, answer, stack, inProgress);
validateQuestionannaireResponseItems(qsrc, qItem.getItem(), errors, answer, stack, inProgress, questionnaireResponseRoot);
}
if (qItem.getType() == null) {
fail(errors, IssueType.REQUIRED, element.line(), element.col(), stack.getLiteralPath(), false, "Definition for item "+qItem.getLinkId() + " does not contain a type");
@ -2874,16 +2882,20 @@ public class InstanceValidator extends BaseValidator implements IResourceValidat
element.getNamedChildren("item", items);
rule(errors, IssueType.STRUCTURE, element.line(), element.col(), stack.getLiteralPath(), items.isEmpty(), "Items not of type DISPLAY should not have items - linkId {0}", qItem.getLinkId());
} else {
validateQuestionannaireResponseItems(qsrc, qItem.getItem(), errors, element, stack, inProgress);
validateQuestionannaireResponseItems(qsrc, qItem.getItem(), errors, element, stack, inProgress, questionnaireResponseRoot);
}
}
private void validateQuestionannaireResponseItem(Questionnaire qsrc, QuestionnaireItemComponent qItem, List<ValidationMessage> errors, List<Element> elements, NodeStack stack, boolean inProgress) {
private boolean isAnswerRequirementFulfilled(QuestionnaireItemComponent qItem, List<Element> answers) {
return !answers.isEmpty() || !qItem.getRequired() || qItem.getType() == QuestionnaireItemType.GROUP;
}
private void validateQuestionannaireResponseItem(Questionnaire qsrc, QuestionnaireItemComponent qItem, List<ValidationMessage> errors, List<Element> elements, NodeStack stack, boolean inProgress, Element questionnaireResponseRoot) {
if (elements.size() > 1)
rule(errors, IssueType.INVALID, elements.get(1).line(), elements.get(1).col(), stack.getLiteralPath(), qItem.getRepeats(), "Only one response item with this linkId allowed - " + qItem.getLinkId());
for (Element element : elements) {
NodeStack ns = stack.push(element, -1, null, null);
validateQuestionannaireResponseItem(qsrc, qItem, errors, element, ns, inProgress);
validateQuestionannaireResponseItem(qsrc, qItem, errors, element, ns, inProgress, questionnaireResponseRoot);
}
}
@ -2894,8 +2906,8 @@ public class InstanceValidator extends BaseValidator implements IResourceValidat
}
return -1;
}
private void validateQuestionannaireResponseItems(Questionnaire qsrc, List<QuestionnaireItemComponent> qItems, List<ValidationMessage> errors, Element element, NodeStack stack, boolean inProgress) {
private void validateQuestionannaireResponseItems(Questionnaire qsrc, List<QuestionnaireItemComponent> qItems, List<ValidationMessage> errors, Element element, NodeStack stack, boolean inProgress, Element questionnaireResponseRoot) {
List<Element> items = new ArrayList<Element>();
element.getNamedChildren("item", items);
// now, sort into stacks
@ -2908,9 +2920,9 @@ public class InstanceValidator extends BaseValidator implements IResourceValidat
if (index == -1) {
QuestionnaireItemComponent qItem = findQuestionnaireItem(qsrc, linkId);
if (qItem != null) {
rule(errors, IssueType.STRUCTURE, item.line(), item.col(), stack.getLiteralPath(), index > -1, "Structural Error: item is in the wrong place");
rule(errors, IssueType.STRUCTURE, item.line(), item.col(), stack.getLiteralPath(), index > -1, misplacedItemError(qItem));
NodeStack ns = stack.push(item, -1, null, null);
validateQuestionannaireResponseItem(qsrc, qItem, errors, element, ns, inProgress);
validateQuestionannaireResponseItem(qsrc, qItem, errors, item, ns, inProgress, questionnaireResponseRoot);
}
else
rule(errors, IssueType.NOTFOUND, item.line(), item.col(), stack.getLiteralPath(), index > -1, "LinkId \""+linkId+"\" not found in questionnaire");
@ -2919,11 +2931,9 @@ public class InstanceValidator extends BaseValidator implements IResourceValidat
{
rule(errors, IssueType.STRUCTURE, item.line(), item.col(), stack.getLiteralPath(), index >= lastIndex, "Structural Error: items are out of order");
lastIndex = index;
List<Element> mapItem = map.get(linkId);
if (mapItem == null) {
mapItem = new ArrayList<Element>();
map.put(linkId, mapItem);
}
List<Element> mapItem = map.computeIfAbsent(linkId, key -> new ArrayList<>());
mapItem.add(item);
}
}
@ -2932,13 +2942,25 @@ public class InstanceValidator extends BaseValidator implements IResourceValidat
// ok, now we have a list of known items, grouped by linkId. We"ve made an error for anything out of order
for (QuestionnaireItemComponent qItem : qItems) {
List<Element> mapItem = map.get(qItem.getLinkId());
if (mapItem != null)
validateQuestionannaireResponseItem(qsrc, qItem, errors, mapItem, stack, inProgress);
else
rule(errors, IssueType.REQUIRED, element.line(), element.col(), stack.getLiteralPath(), !qItem.getRequired(), "No response found for required item "+qItem.getLinkId());
if (mapItem != null){
rule(errors, IssueType.INVALID, element.line(), element.col(), stack.getLiteralPath(), myEnableWhenEvaluator.isQuestionEnabled(qItem, questionnaireResponseRoot), "Item has answer, even though it is not enabled "+qItem.getLinkId());
validateQuestionannaireResponseItem(qsrc, qItem, errors, mapItem, stack, inProgress, questionnaireResponseRoot);
} else {
//item is missing, is the question enabled?
if (myEnableWhenEvaluator.isQuestionEnabled(qItem, questionnaireResponseRoot)) {
rule(errors, IssueType.REQUIRED, element.line(), element.col(), stack.getLiteralPath(), !qItem.getRequired(), "No response found for required item "+qItem.getLinkId());
}
}
}
}
private String misplacedItemError(QuestionnaireItemComponent qItem) {
return qItem.hasLinkId() ?
String.format("Structural Error: item with linkid %s is in the wrong place", qItem.getLinkId())
:
"Structural Error: item is in the wrong place";
}
private void validateQuestionnaireResponseItemQuantity( List<ValidationMessage> errors, Element answer, NodeStack stack) {
}
@ -3009,8 +3031,11 @@ public class InstanceValidator extends BaseValidator implements IResourceValidat
long t = System.nanoTime();
ValidationResult res = context.validateCode(c, vs);
txTime = txTime + (System.nanoTime() - t);
if (!res.isOk())
txRule(errors, res.getTxLink(), IssueType.CODEINVALID, value.line(), value.col(), stack.getLiteralPath(), false, "The value provided ("+c.getSystem()+"::"+c.getCode()+") is not in the options value set in the questionnaire");
if (!res.isOk()) {
txRule(errors, res.getTxLink(), IssueType.CODEINVALID, value.line(), value.col(), stack.getLiteralPath(), false, "The value provided (" + c.getSystem() + "::" + c.getCode() + ") is not in the options value set in the questionnaire");
} else if (res.getSeverity() != null) {
super.addValidationMessage(errors, IssueType.CODEINVALID, value.line(), value.col(), stack.getLiteralPath(), res.getMessage(), res.getSeverity(), Source.TerminologyEngine);
}
} catch (Exception e) {
warning(errors, IssueType.CODEINVALID, value.line(), value.col(), stack.getLiteralPath(), false, "Error " + e.getMessage() + " validating Coding against Questionnaire Options");
}

2
pom.xml
View File

@ -13,7 +13,7 @@
each other. It is fine to bump the point version of this POM without affecting
HAPI FHIR.
-->
<version>3.7.3-SNAPSHOT</version>
<version>3.7.4-SNAPSHOT</version>
<properties>
<hapi_fhir_version>3.7.0-SNAPSHOT</hapi_fhir_version>