Add validation module for QuestionnaireAnswers

hapi-fhir-base/src/main/java/ca/uhn/fhir/validation/IResourceLoader.java

@@ -0,0 +1,22 @@
+package ca.uhn.fhir.validation;
+
+import org.hl7.fhir.instance.model.api.IBaseResource;
+import org.hl7.fhir.instance.model.api.IIdType;
+
+import ca.uhn.fhir.rest.server.exceptions.ResourceNotFoundException;
+
+public interface IResourceLoader {
+
+	/**
+	 * Load the latest version of a given resource
+	 * 
+	 * @param theType
+	 *           The type of the resource to load
+	 * @param theId
+	 *           The ID of the resource to load
+	 * @throws ResourceNotFoundException
+	 *            If the resource is not known
+	 */
+	public <T extends IBaseResource> T load(Class<T> theType, IIdType theId) throws ResourceNotFoundException;
+
+}

hapi-fhir-base/src/main/java/ca/uhn/fhir/validation/IValidationContext.java

@@ -23,7 +23,7 @@ package ca.uhn.fhir.validation;
 import ca.uhn.fhir.context.FhirContext;
 import ca.uhn.fhir.rest.server.EncodingEnum;
 
-interface IValidationContext<T> {
+public interface IValidationContext<T> {
 
 	FhirContext getFhirContext();
 

hapi-fhir-structures-hl7org-dstu2/pom.xml

@@ -218,7 +218,6 @@
 				<artifactId>maven-compiler-plugin</artifactId>
 				<configuration>
 					<fork>true</fork>
-					<verbose>true</verbose>
 				</configuration>
 			</plugin>
 		</plugins>

hapi-fhir-structures-hl7org-dstu2/src/main/java/ca/uhn/fhir/validation/BaseValidatorBridge.java

@@ -0,0 +1,51 @@
+package ca.uhn.fhir.validation;
+
+import java.util.List;
+
+import org.hl7.fhir.instance.model.api.IBaseResource;
+import org.hl7.fhir.instance.validation.ValidationMessage;
+
+import ca.uhn.fhir.model.api.Bundle;
+
+/**
+ * Base class for a bridge between the RI validation tools and HAPI
+ */
+abstract class BaseValidatorBridge implements IValidator {
+
+	public BaseValidatorBridge() {
+		super();
+	}
+
+	private void doValidate(IValidationContext<?> theCtx) {
+		List<ValidationMessage> messages = validate(theCtx);
+
+		for (ValidationMessage riMessage : messages) {
+			SingleValidationMessage hapiMessage = new SingleValidationMessage();
+			if (riMessage.getCol() != -1) {
+				hapiMessage.setLocationCol(riMessage.getCol());
+			}
+			if (riMessage.getLine() != -1) {
+				hapiMessage.setLocationLine(riMessage.getLine());
+			}
+			hapiMessage.setLocationString(riMessage.getLocation());
+			hapiMessage.setMessage(riMessage.getMessage());
+			if (riMessage.getLevel() != null) {
+				hapiMessage.setSeverity(ResultSeverityEnum.fromCode(riMessage.getLevel().toCode()));
+			}
+			theCtx.addValidationMessage(hapiMessage);
+		}
+	}
+
+	protected abstract List<ValidationMessage> validate(IValidationContext<?> theCtx);
+
+	@Override
+	public void validateBundle(IValidationContext<Bundle> theCtx) {
+		doValidate(theCtx);
+	}
+
+	@Override
+	public void validateResource(IValidationContext<IBaseResource> theCtx) {
+		doValidate(theCtx);
+	}
+
+}

hapi-fhir-structures-hl7org-dstu2/src/main/java/ca/uhn/fhir/validation/FhirInstanceValidator.java

@@ -14,7 +14,6 @@ import javax.xml.parsers.DocumentBuilderFactory;
 import org.apache.commons.io.IOUtils;
 import org.hl7.fhir.instance.model.OperationOutcome.IssueSeverity;
 import org.hl7.fhir.instance.model.StructureDefinition;
-import org.hl7.fhir.instance.model.api.IBaseResource;
 import org.hl7.fhir.instance.utils.WorkerContext;
 import org.hl7.fhir.instance.validation.ValidationMessage;
 import org.w3c.dom.Document;
@@ -24,7 +23,6 @@ import org.xml.sax.InputSource;
 
 import ca.uhn.fhir.context.ConfigurationException;
 import ca.uhn.fhir.context.FhirContext;
-import ca.uhn.fhir.model.api.Bundle;
 import ca.uhn.fhir.rest.server.EncodingEnum;
 import ca.uhn.fhir.rest.server.exceptions.InternalErrorException;
 
@@ -32,9 +30,9 @@ import com.google.gson.Gson;
 import com.google.gson.GsonBuilder;
 import com.google.gson.JsonObject;
 
-public class FhirInstanceValidator implements IValidator {
+public class FhirInstanceValidator extends BaseValidatorBridge implements IValidator {
 
-	private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(FhirInstanceValidator.class);
+	static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(FhirInstanceValidator.class);
 
 	private DocumentBuilderFactory myDocBuilderFactory;
 
@@ -43,7 +41,39 @@ public class FhirInstanceValidator implements IValidator {
 		myDocBuilderFactory.setNamespaceAware(true);
 	}
 
-	List<ValidationMessage> validate(FhirContext theCtx, String theInput, EncodingEnum theEncoding) {
+	private String determineResourceName(Document theDocument) {
+		Element root = null;
+
+		NodeList list = theDocument.getChildNodes();
+		for (int i = 0; i < list.getLength(); i++) {
+			if (list.item(i) instanceof Element) {
+				root = (Element) list.item(i);
+				break;
+			}
+		}
+		root = theDocument.getDocumentElement();
+		return root.getLocalName();
+	}
+
+	private StructureDefinition loadProfileOrReturnNull(List<ValidationMessage> theMessages, FhirContext theCtx, String theResourceName) {
+		if (isBlank(theResourceName)) {
+			theMessages.add(new ValidationMessage().setLevel(IssueSeverity.FATAL).setMessage("Could not determine resource type from request. Content appears invalid."));
+			return null;
+		}
+
+		String profileCpName = "/org/hl7/fhir/instance/model/profile/" + theResourceName.toLowerCase() + ".profile.xml";
+		String profileText;
+		try {
+			profileText = IOUtils.toString(FhirInstanceValidator.class.getResourceAsStream(profileCpName), "UTF-8");
+		} catch (IOException e1) {
+			theMessages.add(new ValidationMessage().setLevel(IssueSeverity.FATAL).setMessage("No profile found for resource type " + theResourceName));
+			return null;
+		}
+		StructureDefinition profile = theCtx.newXmlParser().parseResource(StructureDefinition.class, profileText);
+		return profile;
+	}
+
+	protected List<ValidationMessage> validate(FhirContext theCtx, String theInput, EncodingEnum theEncoding) {
 		WorkerContext workerContext = new WorkerContext();
 		org.hl7.fhir.instance.validation.InstanceValidator v;
 		try {
@@ -97,61 +127,9 @@ public class FhirInstanceValidator implements IValidator {
 		return messages;
 	}
 
-	private StructureDefinition loadProfileOrReturnNull(List<ValidationMessage> theMessages, FhirContext theCtx, String theResourceName) {
-		if (isBlank(theResourceName)) {
-			theMessages.add(new ValidationMessage().setLevel(IssueSeverity.FATAL).setMessage("Could not determine resource type from request. Content appears invalid."));
-			return null;
-		}
-
-		String profileCpName = "/org/hl7/fhir/instance/model/profile/" + theResourceName.toLowerCase() + ".profile.xml";
-		String profileText;
-		try {
-			profileText = IOUtils.toString(FhirInstanceValidator.class.getResourceAsStream(profileCpName), "UTF-8");
-		} catch (IOException e1) {
-			theMessages.add(new ValidationMessage().setLevel(IssueSeverity.FATAL).setMessage("No profile found for resource type " + theResourceName));
-			return null;
-		}
-		StructureDefinition profile = theCtx.newXmlParser().parseResource(StructureDefinition.class, profileText);
-		return profile;
-	}
-
-	private String determineResourceName(Document theDocument) {
-		Element root = null;
-
-		NodeList list = theDocument.getChildNodes();
-		for (int i = 0; i < list.getLength(); i++) {
-			if (list.item(i) instanceof Element) {
-				root = (Element) list.item(i);
-				break;
-			}
-		}
-		root = theDocument.getDocumentElement();
-		return root.getLocalName();
-	}
-
 	@Override
-	public void validateResource(IValidationContext<IBaseResource> theCtx) {
+	protected List<ValidationMessage> validate(IValidationContext<?> theCtx) {
-		List<ValidationMessage> messages = validate(theCtx.getFhirContext(), theCtx.getResourceAsString(), theCtx.getResourceAsStringEncoding());
+		return validate(theCtx.getFhirContext(), theCtx.getResourceAsString(), theCtx.getResourceAsStringEncoding());
-		for (ValidationMessage riMessage : messages) {
-			SingleValidationMessage hapiMessage = new SingleValidationMessage();
-			if (riMessage.getCol() != -1) {
-				hapiMessage.setLocationCol(riMessage.getCol());
-			}
-			if (riMessage.getLine() != -1) {
-				hapiMessage.setLocationLine(riMessage.getLine());
-			}
-			hapiMessage.setLocationString(riMessage.getLocation());
-			hapiMessage.setMessage(riMessage.getMessage());
-			if (riMessage.getLevel() != null) {
-				hapiMessage.setSeverity(ResultSeverityEnum.fromCode(riMessage.getLevel().toCode()));
-			}
-			theCtx.addValidationMessage(hapiMessage);
-		}
-	}
-
-	@Override
-	public void validateBundle(IValidationContext<Bundle> theContext) {
-		// nothing for now
 	}
 
 }

hapi-fhir-structures-hl7org-dstu2/src/main/java/ca/uhn/fhir/validation/FhirQuestionnaireAnswersValidator.java

@@ -0,0 +1,139 @@
+package ca.uhn.fhir.validation;
+
+import java.util.ArrayList;
+import java.util.Collections;
+import java.util.List;
+
+import org.hl7.fhir.instance.model.OperationOutcome.IssueSeverity;
+import org.hl7.fhir.instance.model.Questionnaire;
+import org.hl7.fhir.instance.model.QuestionnaireAnswers;
+import org.hl7.fhir.instance.model.ValueSet;
+import org.hl7.fhir.instance.model.api.IBaseResource;
+import org.hl7.fhir.instance.model.api.IIdType;
+import org.hl7.fhir.instance.utils.WorkerContext;
+import org.hl7.fhir.instance.validation.QuestionnaireAnswersValidator;
+import org.hl7.fhir.instance.validation.ValidationMessage;
+
+import ca.uhn.fhir.context.RuntimeResourceDefinition;
+import ca.uhn.fhir.parser.IParser;
+import ca.uhn.fhir.rest.server.exceptions.ResourceNotFoundException;
+import ca.uhn.fhir.util.ResourceReferenceInfo;
+
+public class FhirQuestionnaireAnswersValidator extends BaseValidatorBridge {
+
+	private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(FhirQuestionnaireAnswersValidator.class);
+	private IResourceLoader myResourceLoader;
+
+	/**
+	 * Set the class which will be used to load linked resources from the <code>QuestionnaireAnswers</code>. Specifically, if the <code>QuestionnaireAnswers</code> refers to an external (non-contained)
+	 * <code>Questionnaire</code>, or to any external (non-contained) <code>ValueSet</code>, the resource loader will be used to fetch those resources during the validation.
+	 * 
+	 * @param theResourceLoader
+	 *           The resourceloader to use. May be <code>null</code> if no resource loader should be used (in which case any <code>QuestionaireAnswers</code> with external references will fail to
+	 *           validate.)
+	 */
+	public void setResourceLoader(IResourceLoader theResourceLoader) {
+		myResourceLoader = theResourceLoader;
+	}
+
+	@Override
+	protected List<ValidationMessage> validate(IValidationContext<?> theCtx) {
+		Object resource = theCtx.getResource();
+		if (!(theCtx.getResource() instanceof IBaseResource)) {
+			ourLog.debug("Not validating object of type {}", theCtx.getResource().getClass());
+			return Collections.emptyList();
+		}
+
+		if (resource instanceof QuestionnaireAnswers) {
+			return doValidate(theCtx, (QuestionnaireAnswers) resource);
+		}
+
+		RuntimeResourceDefinition def = theCtx.getFhirContext().getResourceDefinition((IBaseResource) resource);
+		if ("QuestionnaireAnswers".equals(def.getName()) == false) {
+			return Collections.emptyList();
+		}
+
+		/*
+		 * If we have a non-RI structure, convert it
+		 */
+
+		IParser p = theCtx.getFhirContext().newJsonParser();
+		String string = p.encodeResourceToString((IBaseResource) resource);
+		QuestionnaireAnswers qa = p.parseResource(QuestionnaireAnswers.class, string);
+
+		return doValidate(theCtx, qa);
+	}
+
+	private List<ValidationMessage> doValidate(IValidationContext<?> theValCtx, QuestionnaireAnswers theResource) {
+
+		WorkerContext workerCtx = new WorkerContext();
+		ArrayList<ValidationMessage> retVal = new ArrayList<ValidationMessage>();
+
+		if (!loadReferences(theResource, workerCtx, theValCtx, retVal)) {
+			return retVal;
+		}
+
+		QuestionnaireAnswersValidator val = new QuestionnaireAnswersValidator(workerCtx);
+
+		val.validate(retVal, theResource);
+		return retVal;
+	}
+
+	private boolean loadReferences(IBaseResource theResource, WorkerContext theWorkerCtx, IValidationContext<?> theValCtx, ArrayList<ValidationMessage> theMessages) {
+		List<ResourceReferenceInfo> refs = theValCtx.getFhirContext().newTerser().getAllResourceReferences(theResource);
+
+		List<IBaseResource> newResources = new ArrayList<IBaseResource>();
+
+		for (ResourceReferenceInfo nextRefInfo : refs) {
+			IIdType nextRef = nextRefInfo.getResourceReference().getReferenceElement();
+			String resourceType = nextRef.getResourceType();
+			if ("ValueSet".equals(resourceType)) {
+				if (!theWorkerCtx.getValueSets().containsKey(nextRef.getValue())) {
+					ValueSet resource = tryToLoad(ValueSet.class, nextRef, theMessages);
+					if (resource == null) {
+						return false;
+					}
+					theWorkerCtx.getValueSets().put(nextRef.getValue(), resource);
+					newResources.add(resource);
+				}
+			} else if ("Questionnaire".equals(resourceType)) {
+				if (!theWorkerCtx.getQuestionnaires().containsKey(nextRef.getValue())) {
+					Questionnaire resource = tryToLoad(Questionnaire.class, nextRef, theMessages);
+					if (resource == null) {
+						return false;
+					}
+					theWorkerCtx.getQuestionnaires().put(nextRef.getValue(), resource);
+					newResources.add(resource);
+				}
+			}
+		}
+
+		for (IBaseResource nextAddedResource : newResources) {
+			boolean outcome = loadReferences(nextAddedResource, theWorkerCtx, theValCtx, theMessages);
+			if (!outcome) {
+				return false;
+			}
+		}
+
+		return true;
+	}
+
+	private <T extends IBaseResource> T tryToLoad(Class<T> theType, IIdType theReference, List<ValidationMessage> theMessages) {
+		if (myResourceLoader == null) {
+			theMessages.add(new ValidationMessage().setLevel(IssueSeverity.FATAL).setMessage("No resource loader present, could not load " + theReference));
+			return null;
+		}
+
+		try {
+			T retVal = myResourceLoader.load(theType, theReference);
+			if (retVal == null) {
+				throw new IllegalStateException("ResourceLoader returned null. This is a bug with the resourceloader. Reference was: " + theReference);
+			}
+			return retVal;
+		} catch (ResourceNotFoundException e) {
+			theMessages.add(new ValidationMessage().setLevel(IssueSeverity.FATAL).setMessage("Reference could not be found: " + theReference));
+			return null;
+		}
+	}
+
+}

hapi-fhir-structures-hl7org-dstu2/src/test/java/ca/uhn/fhir/validation/QuestionnaireAnswersValidatorIntegrationTest.java

@@ -0,0 +1,124 @@
+package ca.uhn.fhir.validation;
+
+import static org.hamcrest.Matchers.containsString;
+import static org.junit.Assert.*;
+import static org.mockito.Mockito.mock;
+import static org.mockito.Mockito.when;
+
+import java.io.IOException;
+import java.util.ArrayList;
+import java.util.List;
+
+import org.apache.commons.io.IOUtils;
+import org.hl7.fhir.instance.model.Coding;
+import org.hl7.fhir.instance.model.IdType;
+import org.hl7.fhir.instance.model.Questionnaire;
+import org.hl7.fhir.instance.model.QuestionnaireAnswers;
+import org.hl7.fhir.instance.model.Reference;
+import org.hl7.fhir.instance.model.StringType;
+import org.hl7.fhir.instance.model.ValueSet;
+import org.hl7.fhir.instance.model.Questionnaire.AnswerFormat;
+import org.hl7.fhir.instance.utils.WorkerContext;
+import org.hl7.fhir.instance.validation.QuestionnaireAnswersValidator;
+import org.hl7.fhir.instance.validation.ValidationMessage;
+import org.junit.Before;
+import org.junit.Test;
+import org.mockito.Mockito;
+
+import ca.uhn.fhir.context.FhirContext;
+import ca.uhn.fhir.rest.server.exceptions.ResourceNotFoundException;
+
+public class QuestionnaireAnswersValidatorIntegrationTest {
+	private static final FhirContext ourCtx = FhirContext.forDstu2Hl7Org();
+	
+	private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(QuestionnaireAnswersValidatorIntegrationTest.class);
+
+	private IResourceLoader myResourceLoaderMock;
+
+	private FhirValidator myVal;
+	
+	@Before
+	public void before() {
+		myResourceLoaderMock = mock(IResourceLoader.class);
+		
+		FhirQuestionnaireAnswersValidator qaVal = new FhirQuestionnaireAnswersValidator();
+		qaVal.setResourceLoader(myResourceLoaderMock);
+		
+		myVal = ourCtx.newValidator();
+		myVal.setValidateAgainstStandardSchema(false);
+		myVal.setValidateAgainstStandardSchematron(false);
+		myVal.registerValidator(qaVal);
+	}
+	
+	@Test
+	public void testAnswerWithWrongType() {
+		Questionnaire q = new Questionnaire();
+		q.getGroup().addQuestion().setLinkId("link0").setRequired(true).setType(AnswerFormat.BOOLEAN);
+		
+		when(myResourceLoaderMock.load(Mockito.eq(Questionnaire.class), Mockito.eq(new IdType("http://example.com/Questionnaire/q1")))).thenReturn(q);
+		
+		QuestionnaireAnswers qa = new QuestionnaireAnswers();
+		qa.getQuestionnaire().setReference("http://example.com/Questionnaire/q1");
+		qa.getGroup().addQuestion().setLinkId("link0").addAnswer().setValue(new StringType("FOO"));
+
+		ValidationResult result = myVal.validateWithResult(qa);
+		ourLog.info(result.getMessages().toString());
+		assertThat(result.getMessages().toString(), containsString("Answer to question with linkId[link0] found of type [StringType] but this is invalid for question of type [boolean]"));
+	}
+
+	@Test
+	public void testCodedAnswer() {
+		String questionnaireRef = "http://example.com/Questionnaire/q1";
+		
+		Questionnaire q = new Questionnaire();
+		q.getGroup().addQuestion().setLinkId("link0").setRequired(false).setType(AnswerFormat.CHOICE).setOptions(new Reference("http://somevalueset/ValueSet/123"));
+		when(myResourceLoaderMock.load(Mockito.eq(Questionnaire.class), Mockito.eq(new IdType("http://example.com/Questionnaire/q1")))).thenReturn(q);
+				
+		ValueSet options = new ValueSet();
+		options.getDefine().setSystem("urn:system").addConcept().setCode("code0");
+		when(myResourceLoaderMock.load(Mockito.eq(ValueSet.class), Mockito.eq(new IdType("http://somevalueset/ValueSet/123")))).thenReturn(options);
+		
+		QuestionnaireAnswers qa;
+		
+		// Good code
+		
+		qa = new QuestionnaireAnswers();
+		qa.getQuestionnaire().setReference(questionnaireRef);
+		qa.getGroup().addQuestion().setLinkId("link0").addAnswer().setValue(new Coding().setSystem("urn:system").setCode("code0"));
+		ValidationResult result = myVal.validateWithResult(qa);
+		assertEquals(result.getMessages().toString(), 0, result.getMessages().size());
+		
+		// Bad code
+		
+		qa = new QuestionnaireAnswers();
+		qa.getQuestionnaire().setReference(questionnaireRef);
+		qa.getGroup().addQuestion().setLinkId("link0").addAnswer().setValue(new Coding().setSystem("urn:system").setCode("code1"));
+		result = myVal.validateWithResult(qa);
+		ourLog.info(result.getMessages().toString());
+		assertThat(result.getMessages().toString(), containsString("myLocationString=QuestionnaireAnswers.group(0).question(0).answer(0)"));
+		assertThat(result.getMessages().toString(), containsString("myMessage=Question with linkId[link0] has answer with system[urn:system] and code[code1] but this is not a valid answer for ValueSet[http://somevalueset/ValueSet/123]"));
+	}
+
+
+	@Test
+	public void testUnknownValueSet() {
+		String questionnaireRef = "http://example.com/Questionnaire/q1";
+		
+		Questionnaire q = new Questionnaire();
+		q.getGroup().addQuestion().setLinkId("link0").setRequired(false).setType(AnswerFormat.CHOICE).setOptions(new Reference("http://somevalueset/ValueSet/123"));
+		when(myResourceLoaderMock.load(Mockito.eq(Questionnaire.class), Mockito.eq(new IdType("http://example.com/Questionnaire/q1")))).thenReturn(q);
+				
+		when(myResourceLoaderMock.load(Mockito.eq(ValueSet.class), Mockito.eq(new IdType("http://somevalueset/ValueSet/123")))).thenThrow(new ResourceNotFoundException("Unknown"));
+		
+		QuestionnaireAnswers qa;
+		
+		// Bad code
+		
+		qa = new QuestionnaireAnswers();
+		qa.getQuestionnaire().setReference(questionnaireRef);
+		qa.getGroup().addQuestion().setLinkId("link0").addAnswer().setValue(new Coding().setSystem("urn:system").setCode("code1"));
+		ValidationResult result = myVal.validateWithResult(qa);
+		assertThat(result.getMessages().toString(), containsString("myMessage=Reference could not be found: http://some"));
+	}
+
+}