Tweak to validator

hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/dstu3/FhirResourceDaoDstu3ValidateTest.java

@@ -1,9 +1,5 @@
 package ca.uhn.fhir.jpa.dao.dstu3;
 
-import static org.hamcrest.Matchers.containsString;
-import static org.junit.Assert.assertThat;
-import static org.junit.Assert.fail;
-
 import ca.uhn.fhir.jpa.util.TestUtil;
 import ca.uhn.fhir.rest.api.EncodingEnum;
 import ca.uhn.fhir.rest.api.MethodOutcome;
@@ -12,21 +8,33 @@ import ca.uhn.fhir.rest.server.exceptions.PreconditionFailedException;
 import ca.uhn.fhir.rest.server.exceptions.ResourceVersionConflictException;
 import ca.uhn.fhir.rest.server.exceptions.UnprocessableEntityException;
 import ca.uhn.fhir.util.StopWatch;
+import ca.uhn.fhir.validation.IValidatorModule;
 import org.apache.commons.io.IOUtils;
+import org.hl7.fhir.dstu3.hapi.validation.FhirInstanceValidator;
 import org.hl7.fhir.dstu3.model.*;
 import org.hl7.fhir.dstu3.model.Bundle.BundleEntryComponent;
 import org.hl7.fhir.dstu3.model.Observation.ObservationStatus;
 import org.hl7.fhir.instance.model.api.IBaseResource;
 import org.hl7.fhir.instance.model.api.IIdType;
+import org.hl7.fhir.r4.utils.IResourceValidator;
+import org.junit.After;
 import org.junit.AfterClass;
 import org.junit.Ignore;
 import org.junit.Test;
+import org.springframework.beans.factory.annotation.Autowired;
+import org.springframework.test.util.AopTestUtils;
 
 import java.io.IOException;
 import java.nio.charset.StandardCharsets;
 
+import static org.hamcrest.Matchers.containsString;
+import static org.junit.Assert.assertThat;
+import static org.junit.Assert.fail;
+
 public class FhirResourceDaoDstu3ValidateTest extends BaseJpaDstu3Test {
 	private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(FhirResourceDaoDstu3ValidateTest.class);
+	@Autowired
+	private IValidatorModule myValidatorModule;
 
 	@Test
 	public void testValidateChangedQuestionnaire() {
@@ -73,6 +81,77 @@ public class FhirResourceDaoDstu3ValidateTest extends BaseJpaDstu3Test {
 
 	}
 
+	@After
+	public void after() {
+		FhirInstanceValidator val = AopTestUtils.getTargetObject(myValidatorModule);
+		val.setBestPracticeWarningLevel(IResourceValidator.BestPracticeWarningLevel.Warning);
+	}
+
+
+	@Test
+	public void testValidateWithCanonicalReference() {
+		FhirInstanceValidator val = AopTestUtils.getTargetObject(myValidatorModule);
+		IResourceValidator.BestPracticeWarningLevel a = IResourceValidator.BestPracticeWarningLevel.Ignore;
+		val.setBestPracticeWarningLevel(a);
+
+		ValueSet vs = new ValueSet();
+		vs.setId("MYVS");
+		vs.setUrl("http://myvs");
+		vs.getCompose()
+			.addInclude()
+			.setSystem("http://hl7.org/fhir/administrative-gender")
+			.addConcept(new ValueSet.ConceptReferenceComponent().setCode("male"))
+			.addConcept(new ValueSet.ConceptReferenceComponent().setCode("female"));
+		myValueSetDao.update(vs);
+
+		Questionnaire q = new Questionnaire();
+		q.setId("MYQ");
+		q.setUrl("http://hl7.org/fhir/Questionnaire/myq");
+		q.addItem()
+			.setLinkId("LINKID")
+			.setType(Questionnaire.QuestionnaireItemType.CHOICE)
+			.setOptions(new Reference().setReference("ValueSet/MYVS"));
+		myQuestionnaireDao.update(q);
+
+		// Validate with matching code
+		QuestionnaireResponse qr = new QuestionnaireResponse();
+		qr.setStatus(QuestionnaireResponse.QuestionnaireResponseStatus.COMPLETED);
+		qr.setQuestionnaire(new Reference("Questionnaire/MYQ"));
+		qr.addItem()
+			.setLinkId("LINKID")
+			.addAnswer()
+			.setValue(new Coding().setSystem("http://hl7.org/fhir/administrative-gender").setCode("aaa").setDisplay("AAAA"));
+
+		// Validate as resource
+		try {
+			MethodOutcome outcome = myQuestionnaireResponseDao.validate(qr, null, null, null, ValidationModeEnum.CREATE, null, mySrd);
+			OperationOutcome oo = (OperationOutcome) outcome.getOperationOutcome();
+			ourLog.info(myFhirCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(oo));
+			fail();
+		} catch (PreconditionFailedException e) {
+			OperationOutcome oo = (OperationOutcome) e.getOperationOutcome();
+			String encoded = myFhirCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(oo);
+			ourLog.info(encoded);
+			assertThat(encoded, containsString("is not in the options value set"));
+		}
+
+		// Validate as string
+		try {
+			String raw = myFhirCtx.newJsonParser().encodeResourceToString(qr);
+			MethodOutcome outcome = myQuestionnaireResponseDao.validate(qr, null, raw, EncodingEnum.JSON, ValidationModeEnum.CREATE, null, mySrd);
+			OperationOutcome oo = (OperationOutcome) outcome.getOperationOutcome();
+			ourLog.info(myFhirCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(oo));
+			fail();
+		} catch (PreconditionFailedException e) {
+			OperationOutcome oo = (OperationOutcome) e.getOperationOutcome();
+			String encoded = myFhirCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(oo);
+			ourLog.info(encoded);
+			assertThat(encoded, containsString("is not in the options value set"));
+		}
+
+	}
+
+
 	@Test
 	public void testValidateStructureDefinition() throws Exception {
 		String input = IOUtils.toString(getClass().getResourceAsStream("/sd-david-dhtest7.json"), StandardCharsets.UTF_8);

hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/r4/FhirResourceDaoR4ValidateTest.java

@@ -1,9 +1,5 @@
 package ca.uhn.fhir.jpa.dao.r4;
 
-import static org.hamcrest.Matchers.containsString;
-import static org.junit.Assert.assertThat;
-import static org.junit.Assert.fail;
-
 import ca.uhn.fhir.rest.api.EncodingEnum;
 import ca.uhn.fhir.rest.api.MethodOutcome;
 import ca.uhn.fhir.rest.api.ValidationModeEnum;
@@ -13,41 +9,40 @@ import ca.uhn.fhir.rest.server.exceptions.ResourceVersionConflictException;
 import ca.uhn.fhir.rest.server.exceptions.UnprocessableEntityException;
 import ca.uhn.fhir.util.StopWatch;
 import ca.uhn.fhir.util.TestUtil;
+import ca.uhn.fhir.validation.IValidatorModule;
 import org.apache.commons.io.IOUtils;
 import org.hl7.fhir.instance.model.api.IBaseResource;
 import org.hl7.fhir.instance.model.api.IIdType;
-import org.hl7.fhir.r4.model.Bundle;
+import org.hl7.fhir.r4.hapi.validation.FhirInstanceValidator;
+import org.hl7.fhir.r4.model.*;
 import org.hl7.fhir.r4.model.Bundle.BundleEntryComponent;
-import org.hl7.fhir.r4.model.CanonicalType;
-import org.hl7.fhir.r4.model.IdType;
-import org.hl7.fhir.r4.model.Observation;
 import org.hl7.fhir.r4.model.Observation.ObservationStatus;
-import org.hl7.fhir.r4.model.OperationOutcome;
+import org.hl7.fhir.r4.utils.IResourceValidator;
-import org.hl7.fhir.r4.model.Organization;
+import org.junit.After;
-import org.hl7.fhir.r4.model.Patient;
-import org.hl7.fhir.r4.model.StructureDefinition;
-import org.hl7.fhir.r4.model.ValueSet;
 import org.junit.AfterClass;
 import org.junit.Ignore;
 import org.junit.Test;
+import org.springframework.beans.factory.annotation.Autowired;
+import org.springframework.test.util.AopTestUtils;
 
 import java.io.IOException;
 import java.nio.charset.StandardCharsets;
 
+import static org.hamcrest.Matchers.containsString;
+import static org.junit.Assert.assertThat;
+import static org.junit.Assert.fail;
+
 public class FhirResourceDaoR4ValidateTest extends BaseJpaR4Test {
 	private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(FhirResourceDaoR4ValidateTest.class);
-
+	@Autowired
-	@AfterClass
+	private IValidatorModule myValidatorModule;
-	public static void afterClassClearContext() {
-		TestUtil.clearAllStaticFieldsForUnitTest();
-	}
 
 	@Test
 	public void testValidateStructureDefinition() throws Exception {
 		String input = IOUtils.toString(getClass().getResourceAsStream("/r4/sd-david-dhtest7.json"), StandardCharsets.UTF_8);
 		StructureDefinition sd = myFhirCtx.newJsonParser().parseResource(StructureDefinition.class, input);
-		
+
-		
+
 		ourLog.info("Starting validation");
 		try {
 			myStructureDefinitionDao.validate(sd, null, null, null, ValidationModeEnum.UPDATE, null, mySrd);
@@ -55,7 +50,7 @@ public class FhirResourceDaoR4ValidateTest extends BaseJpaR4Test {
 			ourLog.info(myFhirCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(e.getOperationOutcome()));
 		}
 		ourLog.info("Done validation");
-		
+
 		StopWatch sw = new StopWatch();
 		ourLog.info("Starting validation");
 		try {
@@ -66,13 +61,13 @@ public class FhirResourceDaoR4ValidateTest extends BaseJpaR4Test {
 		ourLog.info("Done validation in {}ms", sw.getMillis());
 
 	}
-	
+
 	@Test
 	public void testValidateDocument() throws Exception {
 		String input = IOUtils.toString(getClass().getResourceAsStream("/r4/document-bundle.json"), StandardCharsets.UTF_8);
 		Bundle document = myFhirCtx.newJsonParser().parseResource(Bundle.class, input);
-		
+
-		
+
 		ourLog.info("Starting validation");
 		try {
 			MethodOutcome outcome = myBundleDao.validate(document, null, null, null, ValidationModeEnum.CREATE, null, mySrd);
@@ -80,7 +75,7 @@ public class FhirResourceDaoR4ValidateTest extends BaseJpaR4Test {
 			ourLog.info(myFhirCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(e.getOperationOutcome()));
 		}
 		ourLog.info("Done validation");
-		
+
 //		ourLog.info(myFhirCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(outcome.getOperationOutcome()));
 	}
 
@@ -139,24 +134,24 @@ public class FhirResourceDaoR4ValidateTest extends BaseJpaR4Test {
 		MethodOutcome outcome = null;
 		ValidationModeEnum mode = ValidationModeEnum.CREATE;
 		switch (enc) {
-		case JSON:
+			case JSON:
-			encoded = myFhirCtx.newJsonParser().encodeResourceToString(input);
+				encoded = myFhirCtx.newJsonParser().encodeResourceToString(input);
-			try {
+				try {
-				myObservationDao.validate(input, null, encoded, EncodingEnum.JSON, mode, null, mySrd);
+					myObservationDao.validate(input, null, encoded, EncodingEnum.JSON, mode, null, mySrd);
-				fail();
+					fail();
-			} catch (PreconditionFailedException e) {
+				} catch (PreconditionFailedException e) {
-				return (OperationOutcome) e.getOperationOutcome();
+					return (OperationOutcome) e.getOperationOutcome();
-			}
+				}
-			break;
+				break;
-		case XML:
+			case XML:
-			encoded = myFhirCtx.newXmlParser().encodeResourceToString(input);
+				encoded = myFhirCtx.newXmlParser().encodeResourceToString(input);
-			try {
+				try {
-				myObservationDao.validate(input, null, encoded, EncodingEnum.XML, mode, null, mySrd);
+					myObservationDao.validate(input, null, encoded, EncodingEnum.XML, mode, null, mySrd);
-				fail();
+					fail();
-			} catch (PreconditionFailedException e) {
+				} catch (PreconditionFailedException e) {
-				return (OperationOutcome) e.getOperationOutcome();
+					return (OperationOutcome) e.getOperationOutcome();
-			}
+				}
-			break;
+				break;
 		}
 
 		throw new IllegalStateException(); // shouldn't get here
@@ -185,6 +180,57 @@ public class FhirResourceDaoR4ValidateTest extends BaseJpaR4Test {
 
 	}
 
+	@Test
+	public void testValidateWithCanonicalReference() {
+		FhirInstanceValidator val = AopTestUtils.getTargetObject(myValidatorModule);
+		val.setBestPracticeWarningLevel(IResourceValidator.BestPracticeWarningLevel.Ignore);
+
+		ValueSet vs = new ValueSet();
+		vs.setId("MYVS");
+		vs.setUrl("http://myvs");
+		vs.getCompose()
+			.addInclude()
+			.setSystem("http://hl7.org/fhir/administrative-gender")
+			.addConcept(new ValueSet.ConceptReferenceComponent().setCode("male"))
+			.addConcept(new ValueSet.ConceptReferenceComponent().setCode("female"));
+		myValueSetDao.update(vs);
+
+		Questionnaire q = new Questionnaire();
+		q.setId("MYQ");
+		q.setUrl("http://myquestionnaire");
+		q.addItem()
+			.setLinkId("LINKID")
+			.setType(Questionnaire.QuestionnaireItemType.CHOICE)
+			.setAnswerValueSet("ValueSet/MYVS");
+		myQuestionnaireDao.update(q);
+
+		// Validate with matching code
+		QuestionnaireResponse qr = new QuestionnaireResponse();
+		qr.setStatus(QuestionnaireResponse.QuestionnaireResponseStatus.COMPLETED);
+		qr.setQuestionnaire("Questionnaire/MYQ");
+		qr.addItem()
+			.setLinkId("LINKID")
+			.addAnswer()
+			.setValue(new Coding().setSystem("http://hl7.org/fhir/administrative-gender").setCode("aaa"));
+		try {
+			MethodOutcome outcome = myQuestionnaireResponseDao.validate(qr, null, null, null, ValidationModeEnum.CREATE, null, mySrd);
+			OperationOutcome oo = (OperationOutcome) outcome.getOperationOutcome();
+			ourLog.info(myFhirCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(oo));
+			fail();
+		} catch (PreconditionFailedException e) {
+			OperationOutcome oo = (OperationOutcome) e.getOperationOutcome();
+			String encoded = myFhirCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(oo);
+			ourLog.info(encoded);
+			assertThat(encoded, containsString("is not in the options value set"));
+		}
+	}
+
+	@After
+	public void after() {
+		FhirInstanceValidator val = AopTestUtils.getTargetObject(myValidatorModule);
+		val.setBestPracticeWarningLevel(IResourceValidator.BestPracticeWarningLevel.Warning);
+	}
+
 	@Test
 	public void testValidateForCreate() {
 		String methodName = "testValidateForCreate";
@@ -337,18 +383,18 @@ public class FhirResourceDaoR4ValidateTest extends BaseJpaR4Test {
 		}
 		return retVal;
 	}
-	
+
 	/**
 	 * Format has changed, this is out of date
 	 */
 	@Test
 	@Ignore
 	public void testValidateNewQuestionnaireFormat() throws Exception {
-		String input =IOUtils.toString(FhirResourceDaoR4ValidateTest.class.getResourceAsStream("/questionnaire_r4.xml"));
+		String input = IOUtils.toString(FhirResourceDaoR4ValidateTest.class.getResourceAsStream("/questionnaire_r4.xml"));
 		try {
-		MethodOutcome results = myQuestionnaireDao.validate(null, null, input, EncodingEnum.XML, ValidationModeEnum.UPDATE, null, mySrd);
+			MethodOutcome results = myQuestionnaireDao.validate(null, null, input, EncodingEnum.XML, ValidationModeEnum.UPDATE, null, mySrd);
-		OperationOutcome oo = (OperationOutcome) results.getOperationOutcome();
+			OperationOutcome oo = (OperationOutcome) results.getOperationOutcome();
-		ourLog.info(myFhirCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(oo));
+			ourLog.info(myFhirCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(oo));
 		} catch (PreconditionFailedException e) {
 			// this is a failure of the test
 			ourLog.info(myFhirCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(e.getOperationOutcome()));
@@ -356,4 +402,9 @@ public class FhirResourceDaoR4ValidateTest extends BaseJpaR4Test {
 		}
 	}
 
+	@AfterClass
+	public static void afterClassClearContext() {
+		TestUtil.clearAllStaticFieldsForUnitTest();
+	}
+
 }

hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/provider/r4/ResourceProviderR4Test.java

@@ -391,6 +391,26 @@ public class ResourceProviderR4Test extends BaseResourceProviderR4Test {
 
 	}
 
+	@Test
+	public void testCreateWithClientAssignedId() throws IOException {
+		
+		Patient p = new Patient();
+		p.setActive(true);
+		p.setId("AAA");
+		String encoded = myFhirCtx.newJsonParser().encodeResourceToString(p);
+		
+		HttpPut httpPut = new HttpPut(ourServerBase + "/Patient/AAA");
+		httpPut.setEntity(new StringEntity(encoded, ContentType.parse("application/json+fhir")));
+		try (CloseableHttpResponse status = ourHttpClient.execute(httpPut)) {
+			String responseContent = IOUtils.toString(status.getEntity().getContent(), StandardCharsets.UTF_8);
+			ourLog.info(status.getStatusLine().toString());
+			ourLog.info(responseContent);
+
+			assertEquals(201, status.getStatusLine().getStatusCode());
+			assertThat(responseContent, containsString("true"));
+		}
+
+	}
 
 
 	@Before

hapi-fhir-validation/src/main/java/org/hl7/fhir/r4/validation/InstanceValidator.java

@@ -2371,13 +2371,17 @@ public class InstanceValidator extends BaseValidator implements IResourceValidat
         return null;
       } else {
         long t = System.nanoTime();
-        if (!Utilities.isAbsoluteUrl(reference))
+			ValueSet fr = context.fetchResource(ValueSet.class, reference);
-          reference = resolve(uri, reference);
+			if (fr == null) {
-        ValueSet fr = context.fetchResource(ValueSet.class, reference);
+				if (!Utilities.isAbsoluteUrl(reference)) {
-        txTime = txTime + (System.nanoTime() - t);
+					reference = resolve(uri, reference);
+					fr = context.fetchResource(ValueSet.class, reference);
+				}
+			}
+			txTime = txTime + (System.nanoTime() - t);
         return fr;
       }
-    } else 
+    } else
       return null;
   }