Validation fixes

hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/dstu3/FhirResourceDaoDstu3.java

@@ -41,6 +41,7 @@ import org.springframework.beans.factory.annotation.Qualifier;
 import ca.uhn.fhir.context.RuntimeResourceDefinition;
 import ca.uhn.fhir.context.RuntimeSearchParam;
 import ca.uhn.fhir.jpa.dao.BaseHapiFhirResourceDao;
+import ca.uhn.fhir.jpa.dao.IFhirResourceDao;
 import ca.uhn.fhir.jpa.entity.ResourceTable;
 import ca.uhn.fhir.jpa.util.DeleteConflict;
 import ca.uhn.fhir.model.api.Bundle;
@@ -129,9 +130,20 @@ public class FhirResourceDaoDstu3<T extends IAnyResource> extends BaseHapiFhirRe
 
 		validator.registerValidatorModule(new IdChecker(theMode));
 
+		IBaseResource resourceToValidateById = null;
+		if (theId != null && theId.hasResourceType() && theId.hasIdPart()) {
+			Class<? extends IBaseResource> type = getContext().getResourceDefinition(theId.getResourceType()).getImplementingClass();
+			IFhirResourceDao<? extends IBaseResource> dao = getDao(type);
+			resourceToValidateById = dao.read(theId, theRequestDetails);
+		}
+		
 		ValidationResult result;
 		if (theResource == null) {
-			throw new InvalidRequestException("No resource supplied for $validate operation (resource is required unless mode is \"delete\")");
+			if (resourceToValidateById != null) {
+				result = validator.validateWithResult(resourceToValidateById);
+			} else {
+				throw new InvalidRequestException("No resource supplied for $validate operation (resource is required unless mode is \"delete\")");
+			}
 		} else if (isNotBlank(theRawResource)) {
 			result = validator.validateWithResult(theRawResource);
 		} else {

hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/dstu3/FhirResourceDaoDstu3SearchNoFtTest.java

@@ -610,12 +610,12 @@ public class FhirResourceDaoDstu3SearchNoFtTest extends BaseJpaDstu3Test {
 	public void testSearchCompositeParamDate() {
 		Observation o1 = new Observation();
 		o1.getCode().addCoding().setSystem("foo").setCode("testSearchCompositeParamDateN01");
-		o1.setValue(new Period().setStartElement(new DateTimeType("2001-01-01T11:11:11")).setEndElement(new DateTimeType("2001-01-01T12:11:11")));
+		o1.setValue(new Period().setStartElement(new DateTimeType("2001-01-01T11:11:11Z")).setEndElement(new DateTimeType("2001-01-01T12:11:11Z")));
 		IIdType id1 = myObservationDao.create(o1, mySrd).getId().toUnqualifiedVersionless();
 
 		Observation o2 = new Observation();
 		o2.getCode().addCoding().setSystem("foo").setCode("testSearchCompositeParamDateN01");
-		o2.setValue(new Period().setStartElement(new DateTimeType("2001-01-02T11:11:11")).setEndElement(new DateTimeType("2001-01-02T12:11:11")));
+		o2.setValue(new Period().setStartElement(new DateTimeType("2001-01-02T11:11:11Z")).setEndElement(new DateTimeType("2001-01-02T12:11:11Z")));
 		IIdType id2 = myObservationDao.create(o2, mySrd).getId().toUnqualifiedVersionless();
 
 		{
@@ -627,21 +627,21 @@ public class FhirResourceDaoDstu3SearchNoFtTest extends BaseJpaDstu3Test {
 		}
 		{
 			TokenParam v0 = new TokenParam("foo", "testSearchCompositeParamDateN01");
-			DateParam v1 = new DateParam(">2001-01-01T10:12:12");
+			DateParam v1 = new DateParam(">2001-01-01T10:12:12Z");
 			CompositeParam<TokenParam, DateParam> val = new CompositeParam<TokenParam, DateParam>(v0, v1);
 			IBundleProvider result = myObservationDao.search(Observation.SP_CODE_VALUE_DATE, val);
 			assertThat(toUnqualifiedVersionlessIds(result), containsInAnyOrder(id1, id2));
 		}
 		{
 			TokenParam v0 = new TokenParam("foo", "testSearchCompositeParamDateN01");
-			DateParam v1 = new DateParam("gt2001-01-01T11:12:12");
+			DateParam v1 = new DateParam("gt2001-01-01T11:12:12Z");
 			CompositeParam<TokenParam, DateParam> val = new CompositeParam<TokenParam, DateParam>(v0, v1);
 			IBundleProvider result = myObservationDao.search(Observation.SP_CODE_VALUE_DATE, val);
 			assertThat(toUnqualifiedVersionlessIds(result), containsInAnyOrder(id1, id2));
 		}
 		{
 			TokenParam v0 = new TokenParam("foo", "testSearchCompositeParamDateN01");
-			DateParam v1 = new DateParam("gt2001-01-01T15:12:12");
+			DateParam v1 = new DateParam("gt2001-01-01T15:12:12Z");
 			CompositeParam<TokenParam, DateParam> val = new CompositeParam<TokenParam, DateParam>(v0, v1);
 			IBundleProvider result = myObservationDao.search(Observation.SP_CODE_VALUE_DATE, val);
 			assertThat(toUnqualifiedVersionlessIds(result), containsInAnyOrder(id2));

hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/provider/ResourceProviderDstu1Test.java

@@ -10,6 +10,8 @@ import static org.junit.Assert.fail;
 import java.util.ArrayList;
 import java.util.Date;
 import java.util.List;
+import java.util.Locale;
+import java.util.TimeZone;
 import java.util.concurrent.TimeUnit;
 
 import org.apache.commons.io.IOUtils;
@@ -135,7 +137,7 @@ public class ResourceProviderDstu1Test  extends BaseJpaTest {
 	}
 
 	@Test
-	public void testCreateWithClientSuppliedId() {
+	public void testCreateWithClientSuppliedId() throws Exception {
 		deleteToken("Patient", Patient.SP_IDENTIFIER, "urn:system", "testCreateWithId01");
 
 		Patient p1 = new Patient();

hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/provider/dstu3/ResourceProviderDstu3Test.java

@@ -2706,6 +2706,30 @@ public class ResourceProviderDstu3Test extends BaseResourceProviderDstu3Test {
 		}
 	}
 
+	@Test
+	public void testValidateResourceInstanceOnServer() throws IOException {
+
+		Patient patient = new Patient();
+		patient.addName().addGiven("James");
+		patient.setBirthDateElement(new DateType("2011-02-02"));
+		patient.addContact().setGender(AdministrativeGender.MALE);
+		patient.addCommunication().setPreferred(true); // missing language
+
+		IIdType id = myPatientDao.create(patient, mySrd).getId().toUnqualifiedVersionless();
+		
+		HttpGet get = new HttpGet(ourServerBase + "/Patient/" + id.getIdPart() + "/$validate");
+		CloseableHttpResponse response = ourHttpClient.execute(get);
+		try {
+			String resp = IOUtils.toString(response.getEntity().getContent());
+			ourLog.info(resp);
+			assertEquals(412, response.getStatusLine().getStatusCode());
+			assertThat(resp, containsString("SHALL at least contain a contact's details or a reference to an organization"));
+		} finally {
+			IOUtils.closeQuietly(response.getEntity().getContent());
+			response.close();
+		}
+	}
+
 	// Y
 	@Test
 	public void testValidateResourceHuge() throws IOException {

hapi-fhir-structures-dstu3/src/main/java/org/hl7/fhir/dstu3/validation/InstanceValidator.java

@@ -813,6 +813,9 @@ public class InstanceValidator extends BaseValidator implements IResourceValidat
   }
 
   private void checkPrimitive(List<ValidationMessage> errors, String path, String type, ElementDefinition context, Element e, StructureDefinition profile) {
+    if (isBlank(e.primitiveValue())) {
+      return;
+    }
     if (type.equals("boolean")) {
       rule(errors, IssueType.INVALID, e.line(), e.col(), path, "true".equals(e.primitiveValue()) || "false".equals(e.primitiveValue()), "boolean values must be 'true' or 'false'");
     }
@@ -821,7 +824,7 @@ public class InstanceValidator extends BaseValidator implements IResourceValidat
       rule(errors, IssueType.INVALID, e.line(), e.col(), path, !e.primitiveValue().startsWith("uuid:"), "URI values cannot start with uuid:");
       rule(errors, IssueType.INVALID, e.line(), e.col(), path, e.primitiveValue().equals(e.primitiveValue().trim()), "URI values cannot have leading or trailing whitespace");
     }
-    if (!type.equalsIgnoreCase("string") && e.hasPrimitiveValue()) {
+    if (!type.equalsIgnoreCase("string")) {
       if (rule(errors, IssueType.INVALID, e.line(), e.col(), path, e.primitiveValue() == null || e.primitiveValue().length() > 0, "@value cannot be empty")) {
         warning(errors, IssueType.INVALID, e.line(), e.col(), path, e.primitiveValue() == null || e.primitiveValue().trim().equals(e.primitiveValue()), "value should not start or finish with whitespace");
       }
@@ -842,13 +845,13 @@ public class InstanceValidator extends BaseValidator implements IResourceValidat
       rule(errors, IssueType.INVALID, e.line(), e.col(), path, yearIsValid(e.primitiveValue()), "The value '" + e.primitiveValue() + "' does not have a valid year");
     }
 
-    if (type.equals("code") && e.primitiveValue() != null) {
+    if (type.equals("code")) {
       // Technically, a code is restricted to string which has at least one character and no leading or trailing whitespace, and where there is no whitespace
       // other than single spaces in the contents
       rule(errors, IssueType.INVALID, e.line(), e.col(), path, passesCodeWhitespaceRules(e.primitiveValue()), "The code '" + e.primitiveValue() + "' is not valid (whitespace rules)");
     }
 
-    if (context.hasBinding() && e.primitiveValue() != null) {
+    if (context.hasBinding()) {
       checkPrimitiveBinding(errors, path, type, context, e, profile);
     }
 

hapi-fhir-structures-dstu3/src/test/java/ca/uhn/fhir/rest/server/ValidateDstu3Test.java

@@ -8,6 +8,7 @@ import java.util.concurrent.TimeUnit;
 
 import org.apache.commons.io.IOUtils;
 import org.apache.http.HttpResponse;
+import org.apache.http.client.methods.HttpGet;
 import org.apache.http.client.methods.HttpPost;
 import org.apache.http.entity.ContentType;
 import org.apache.http.entity.StringEntity;
@@ -30,6 +31,7 @@ import org.junit.BeforeClass;
 import org.junit.Test;
 
 import ca.uhn.fhir.context.FhirContext;
+import ca.uhn.fhir.rest.annotation.IdParam;
 import ca.uhn.fhir.rest.annotation.ResourceParam;
 import ca.uhn.fhir.rest.annotation.Validate;
 import ca.uhn.fhir.rest.api.MethodOutcome;
@@ -48,6 +50,7 @@ public class ValidateDstu3Test {
 	private static int ourPort;
 	private static Server ourServer;
 	public static Patient ourLastPatient;
+	private static IdType ourLastId;
 
 	@Before()
 	public void before() {
@@ -58,7 +61,6 @@ public class ValidateDstu3Test {
 		ourLastProfile = null;
 	}
 
-
 	@Test
 	public void testValidate() throws Exception {
 
@@ -218,6 +220,25 @@ public class ValidateDstu3Test {
 		assertThat(resp, stringContainsInOrder("<OperationOutcome", "FOOBAR"));
 	}
 
+	@Test
+	public void testValidateWithGet() throws Exception {
+		ourOutcomeToReturn = new OperationOutcome();
+		ourOutcomeToReturn.addIssue().setDiagnostics("FOOBAR");
+
+		HttpGet httpGet = new HttpGet("http://localhost:" + ourPort + "/Patient/123/$validate");
+
+		HttpResponse status = ourClient.execute(httpGet);
+		String resp = IOUtils.toString(status.getEntity().getContent());
+		IOUtils.closeQuietly(status.getEntity().getContent());
+
+		assertEquals(200, status.getStatusLine().getStatusCode());
+
+		assertThat(resp, stringContainsInOrder("<OperationOutcome", "FOOBAR"));
+		assertEquals(null, ourLastPatient);
+		assertEquals("Patient", ourLastId.getResourceType());
+		assertEquals("123", ourLastId.getIdPart());
+	}
+
 	@AfterClass
 	public static void afterClassClearContext() throws Exception {
 		ourServer.stop();
@@ -271,15 +292,16 @@ public class ValidateDstu3Test {
 		}
 
 		@Validate()
-		public MethodOutcome validatePatient(@ResourceParam Patient thePatient, @Validate.Mode ValidationModeEnum theMode, @Validate.Profile String theProfile) {
+		public MethodOutcome validatePatient(@ResourceParam Patient thePatient, @IdParam IdType theId, @Validate.Mode ValidationModeEnum theMode, @Validate.Profile String theProfile) {
 
 			ourLastPatient = thePatient;
+			ourLastId = theId;
 			IdType id;
 			if (thePatient != null) {
-			id = new IdType(thePatient.getIdentifier().get(0).getValue());
+				id = new IdType(thePatient.getIdentifier().get(0).getValue());
-			if (thePatient.getIdElement().isEmpty() == false) {
+				if (thePatient.getIdElement().isEmpty() == false) {
-				id = thePatient.getIdElement();
+					id = thePatient.getIdElement();
-			}
+				}
 			} else {
 				id = new IdType("1");
 			}

hapi-fhir-structures-dstu3/src/test/java/ca/uhn/fhir/validation/FhirInstanceValidatorDstu3Test.java

@@ -422,6 +422,60 @@ public class FhirInstanceValidatorDstu3Test {
 		assertEquals(output.toString(), 0, output.getMessages().size());
 	}
 
+	@Test
+	public void testValidateRawXmlResourceWithEmptyPrimitive() {
+		// @formatter:off
+		String input = "<Patient xmlns=\"http://hl7.org/fhir\"><name><given/></name></Patient>";
+		// @formatter:on
+
+		ValidationResult output = myVal.validateWithResult(input);
+		assertEquals(output.toString(), 1, output.getMessages().size());
+		assertThat(output.getMessages().get(0).getMessage(), containsString("Element must have some content"));
+	}
+
+	@Test
+	public void testValidateRawXmlResourceWithPrimitiveContainingOnlyAnExtension() {
+		// @formatter:off
+		String input = "<ActivityDefinition xmlns=\"http://hl7.org/fhir\">\n" + 
+				"                        <id value=\"referralToMentalHealthCare\"/>\n" + 
+				"                        <status value=\"draft\"/>\n" + 
+				"                        <description value=\"refer to primary care mental-health integrated care program for evaluation and treatment of mental health conditions now\"/>\n" + 
+				"                        <relatedResource>\n" + 
+				"                                <type value=\"citation\"/>\n" + 
+				"                                <document>\n" + 
+				"                                        <url value=\"blah blah blah\"/>\n" + 
+				"                                        <title value=\"citation title\"/>\n" + 
+				"                                </document>\n" + 
+				"                                <resource>\n" + 
+				"                                        <reference value=\"DocumentReference/123\"/> <!-- DocumentReference -->\n" + 
+				"                                        <display value=\"citation title\"/>\n" + 
+				"                                </resource>\n" + 
+				"                        </relatedResource>\n" + 
+				"                        <category value=\"referral\"/>\n" + 
+				"                        <code>\n" + 
+				"                                <coding>\n" + 
+				"                                        <!-- Error: Connection to http://localhost:960 refused -->\n" + 
+				"                                        <!--<system value=\"http://snomed.info/sct\"/>-->\n" + 
+				"                                        <code value=\"306206005\"/>\n" + 
+				"                                </coding>\n" + 
+				"                        </code>\n" + 
+				"                        <!-- Specifying this this way results in a null reference exception in the validator -->\n" + 
+				"                        <timingTiming>\n" + 
+				"                                <event>\n" + 
+				"                                        <extension url=\"http://fhir.org/cql-expression\">\n" + 
+				"                                                <valueString value=\"Now()\"/>\n" + 
+				"                                        </extension>\n" + 
+				"                                </event>\n" + 
+				"                        </timingTiming>\n" + 
+				"                        <participantType value=\"practitioner\"/>\n" + 
+				"                </ActivityDefinition>";
+		// @formatter:on
+
+		ValidationResult output = myVal.validateWithResult(input);
+		List<SingleValidationMessage> res = logResultsAndReturnNonInformationalOnes(output);
+		assertEquals(output.toString(), 0, res.size());
+	}
+
 	@Test
 	public void testValidateRawXmlResourceBadAttributes() {
 		//@formatter:off

src/changes/changes.xml

@@ -404,6 +404,10 @@
 				end of the resource instead of in the correct
 				order
 			</action>
+			<action type="fix">
+				Fix STU3 JPA resource providers to allow validate operation 
+				at instance level
+			</action>
 		</release>
 		<release version="1.5" date="2016-04-20">
 			<action type="fix" issue="339">