Fix web testing UI regression

hapi-fhir-base/src/main/java/ca/uhn/fhir/rest/api/RequestTypeEnum.java

@@ -21,5 +21,5 @@
  */
 
 public enum RequestTypeEnum {
-	CONNECT, DELETE, GET, OPTIONS, PATCH, POST, PUT, TRACE, TRACK
+	CONNECT, DELETE, GET, OPTIONS, PATCH, POST, PUT, TRACE, TRACK, HEAD
 }

hapi-fhir-base/src/main/java/ca/uhn/fhir/rest/server/interceptor/BanUnsupportedHttpMethodsInterceptor.java

@@ -44,6 +44,7 @@ public BanUnsupportedHttpMethodsInterceptor() {
 		myAllowedMethods.add(RequestTypeEnum.DELETE);
 		myAllowedMethods.add(RequestTypeEnum.PUT);
 		myAllowedMethods.add(RequestTypeEnum.POST);
+		myAllowedMethods.add(RequestTypeEnum.HEAD);
 	}
 
 	@Override

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

@@ -194,7 +194,6 @@ public abstract class BaseHapiFhirDao<T extends IBaseResource> implements IDao {
 
 	private FhirContext myContext;
 
-	// @PersistenceContext(name = "FHIR_UT", type = PersistenceContextType.TRANSACTION, unitName = "FHIR_UT")
 	@PersistenceContext(type = PersistenceContextType.TRANSACTION)
 	protected EntityManager myEntityManager;
 
@@ -669,7 +668,7 @@ protected void notifyInterceptors(RestOperationTypeEnum theOperationType, Action
 		}
 	}
 
-	private String parseContentTextIntoWords(IBaseResource theResource) {
+	public String parseContentTextIntoWords(IBaseResource theResource) {
 		StringBuilder retVal = new StringBuilder();
 		@SuppressWarnings("rawtypes")
 		List<IPrimitiveType> childElements = getContext().newTerser().getAllPopulatedChildElementsOfType(theResource, IPrimitiveType.class);
@@ -686,6 +685,17 @@ private String parseContentTextIntoWords(IBaseResource theResource) {
 		return retVal.toString();
 	}
 
+	@Override
+	public void populateFullTextFields(final IBaseResource theResource, ResourceTable theEntity) {
+		if (theEntity.getDeleted() != null) {
+			theEntity.setNarrativeTextParsedIntoWords(null);
+			theEntity.setContentTextParsedIntoWords(null);
+		} else {
+			theEntity.setNarrativeTextParsedIntoWords(parseNarrativeTextIntoWords(theResource));
+			theEntity.setContentTextParsedIntoWords(parseContentTextIntoWords(theResource));
+		}
+	}
+
 	private void populateResourceId(final IBaseResource theResource, BaseHasResource theEntity) {
 		IIdType id = theEntity.getIdDt();
 		if (getContext().getVersion().getVersion().isRi()) {
@@ -931,10 +941,6 @@ public BaseHasResource readEntity(IIdType theValueId) {
 		throw new NotImplementedException("");
 	}
 
-	public void setConfig(DaoConfig theConfig) {
-		myConfig = theConfig;
-	}
-
 	// protected MetaDt toMetaDt(Collection<TagDefinition> tagDefinitions) {
 	// MetaDt retVal = new MetaDt();
 	// for (TagDefinition next : tagDefinitions) {
@@ -953,6 +959,10 @@ public void setConfig(DaoConfig theConfig) {
 	// return retVal;
 	// }
 
+	public void setConfig(DaoConfig theConfig) {
+		myConfig = theConfig;
+	}
+
 	@Autowired
 	public void setContext(FhirContext theContext) {
 		myContext = theContext;
@@ -1273,8 +1283,7 @@ protected ResourceTable updateEntity(final IBaseResource theResource, ResourceTa
 				theEntity.setResourceLinks(links);
 				theEntity.setHasLinks(links.isEmpty() == false);
 				theEntity.setIndexStatus(INDEX_STATUS_INDEXED);
-				theEntity.setNarrativeTextParsedIntoWords(parseNarrativeTextIntoWords(theResource));
-				theEntity.setContentTextParsedIntoWords(parseContentTextIntoWords(theResource));
+				populateFullTextFields(theResource, theEntity);
 
 			} else {
 
@@ -1397,53 +1406,6 @@ protected ResourceTable updateEntity(IBaseResource theResource, ResourceTable en
 		return updateEntity(theResource, entity, theDeletedTimestampOrNull, true, true, theUpdateTime);
 	}
 
-	protected void validateDeleteConflictsEmptyOrThrowException(List<DeleteConflict> theDeleteConflicts) {
-		if (theDeleteConflicts.isEmpty()) {
-			return;
-		}
-
-		IBaseOperationOutcome oo = OperationOutcomeUtil.newInstance(getContext());
-		for (DeleteConflict next : theDeleteConflicts) {
-			String msg = "Unable to delete " + next.getTargetId().toUnqualifiedVersionless().getValue()
-					+ " because at least one resource has a reference to this resource. First reference found was resource " + next.getTargetId().toUnqualifiedVersionless().getValue() + " in path "
-					+ next.getSourcePath();
-			OperationOutcomeUtil.addIssue(getContext(), oo, OO_SEVERITY_ERROR, msg, null, "processing");
-		}
-
-		throw new ResourceVersionConflictException("Delete failed because of constraint failure", oo);
-	}
-
-	/**
-	 * This method is invoked immediately before storing a new resource, or an update to an existing resource to allow the DAO to ensure that it is valid for persistence. By default, checks for the
-	 * "subsetted" tag and rejects resources which have it. Subclasses should call the superclass implementation to preserve this check.
-	 * 
-	 * @param theResource
-	 *           The resource that is about to be persisted
-	 * @param theEntityToSave
-	 *           TODO
-	 */
-	protected void validateResourceForStorage(T theResource, ResourceTable theEntityToSave) {
-		Object tag = null;
-		if (theResource instanceof IResource) {
-			IResource res = (IResource) theResource;
-			TagList tagList = ResourceMetadataKeyEnum.TAG_LIST.get(res);
-			if (tagList != null) {
-				tag = tagList.getTag(Constants.TAG_SUBSETTED_SYSTEM, Constants.TAG_SUBSETTED_CODE);
-			}
-		} else {
-			IAnyResource res = (IAnyResource) theResource;
-			tag = res.getMeta().getTag(Constants.TAG_SUBSETTED_SYSTEM, Constants.TAG_SUBSETTED_CODE);
-		}
-
-		if (tag != null) {
-			throw new UnprocessableEntityException("Resource contains the 'subsetted' tag, and must not be stored as it may contain a subset of available data");
-		}
-
-		String resName = getContext().getResourceDefinition(theResource).getName();
-		validateChildReferences(theResource, resName);
-
-	}
-
 	private void validateChildReferences(IBase theElement, String thePath) {
 		if (theElement == null) {
 			return;
@@ -1499,6 +1461,53 @@ private void validateChildReferences(IBase theElement, String thePath) {
 		}
 	}
 
+	protected void validateDeleteConflictsEmptyOrThrowException(List<DeleteConflict> theDeleteConflicts) {
+		if (theDeleteConflicts.isEmpty()) {
+			return;
+		}
+
+		IBaseOperationOutcome oo = OperationOutcomeUtil.newInstance(getContext());
+		for (DeleteConflict next : theDeleteConflicts) {
+			String msg = "Unable to delete " + next.getTargetId().toUnqualifiedVersionless().getValue()
+					+ " because at least one resource has a reference to this resource. First reference found was resource " + next.getTargetId().toUnqualifiedVersionless().getValue() + " in path "
+					+ next.getSourcePath();
+			OperationOutcomeUtil.addIssue(getContext(), oo, OO_SEVERITY_ERROR, msg, null, "processing");
+		}
+
+		throw new ResourceVersionConflictException("Delete failed because of constraint failure", oo);
+	}
+
+	/**
+	 * This method is invoked immediately before storing a new resource, or an update to an existing resource to allow the DAO to ensure that it is valid for persistence. By default, checks for the
+	 * "subsetted" tag and rejects resources which have it. Subclasses should call the superclass implementation to preserve this check.
+	 * 
+	 * @param theResource
+	 *           The resource that is about to be persisted
+	 * @param theEntityToSave
+	 *           TODO
+	 */
+	protected void validateResourceForStorage(T theResource, ResourceTable theEntityToSave) {
+		Object tag = null;
+		if (theResource instanceof IResource) {
+			IResource res = (IResource) theResource;
+			TagList tagList = ResourceMetadataKeyEnum.TAG_LIST.get(res);
+			if (tagList != null) {
+				tag = tagList.getTag(Constants.TAG_SUBSETTED_SYSTEM, Constants.TAG_SUBSETTED_CODE);
+			}
+		} else {
+			IAnyResource res = (IAnyResource) theResource;
+			tag = res.getMeta().getTag(Constants.TAG_SUBSETTED_SYSTEM, Constants.TAG_SUBSETTED_CODE);
+		}
+
+		if (tag != null) {
+			throw new UnprocessableEntityException("Resource contains the 'subsetted' tag, and must not be stored as it may contain a subset of available data");
+		}
+
+		String resName = getContext().getResourceDefinition(theResource).getName();
+		validateChildReferences(theResource, resName);
+
+	}
+
 	protected static boolean isValidPid(IIdType theId) {
 		if (theId == null || theId.getIdPart() == null) {
 			return false;

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

@@ -7,6 +7,7 @@
 
 import ca.uhn.fhir.context.FhirContext;
 import ca.uhn.fhir.jpa.entity.BaseHasResource;
+import ca.uhn.fhir.jpa.entity.ResourceTable;
 import ca.uhn.fhir.jpa.search.PersistedJpaBundleProvider;
 import ca.uhn.fhir.model.api.IResource;
 import ca.uhn.fhir.model.api.ResourceMetadataKeyEnum.ResourceMetadataKeySupportingAnyResource;
@@ -70,4 +71,6 @@ public void put(IResource theResource, Long theObject) {
 	IBaseResource toResource(BaseHasResource theEntity, boolean theForHistoryOperation);
 
 	<R extends IBaseResource> R toResource(Class<R> theResourceType, BaseHasResource theEntity, boolean theForHistoryOperation);
+
+	void populateFullTextFields(IBaseResource theResource, ResourceTable theEntity);
 }

hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/dstu3/JpaValidationSupportDstu3.java

@@ -98,6 +98,9 @@ public <T extends IBaseResource> T fetchResource(FhirContext theContext, Class<T
 				search = myValueSetDao.search(ValueSet.SP_URL, new UriParam(theUri));
 			}
 		} else if ("StructureDefinition".equals(resourceName)) {
+			if (theUri.startsWith("http://hl7.org/fhir/StructureDefinition/")) {
+				return null;
+			}
 			search = myStructureDefinitionDao.search(StructureDefinition.SP_URL, new UriParam(theUri));
 		} else if ("Questionnaire".equals(resourceName)) {
 			search = myQuestionnaireDao.search(IAnyResource.SP_RES_ID, new StringParam(id.getIdPart()));

hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/entity/ResourceTable.java

@@ -77,7 +77,7 @@
 	@Index(name = "IDX_RES_DATE", columnList="RES_UPDATED"), 
 	@Index(name = "IDX_RES_LANG", columnList="RES_TYPE,RES_LANGUAGE"), 
 	@Index(name = "IDX_RES_PROFILE", columnList="RES_PROFILE"),
-	@Index(name = "IDX_INDEXSTATUS", columnList="SP_INDEX_STATUS") 
+	@Index(name = "IDX_INDEXSTATUS", columnList="SP_INDEX_STATUS")
 })
 @AnalyzerDefs({
 	@AnalyzerDef(name = "autocompleteEdgeAnalyzer",

hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/dstu3/BaseJpaDstu3Test.java

@@ -220,6 +220,8 @@ public abstract class BaseJpaDstu3Test extends BaseJpaTest {
 	@Autowired
 	@Qualifier("myValueSetDaoDstu3")
 	protected IFhirResourceDaoValueSet<ValueSet, Coding, CodeableConcept> myValueSetDao;
+	@Autowired
+	protected PlatformTransactionManager myTransactionMgr;
 	@After()
 	public void afterGrabCaches() {
 		ourValueSetDao = myValueSetDao;

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

@@ -30,6 +30,9 @@
 import org.junit.AfterClass;
 import org.junit.Ignore;
 import org.junit.Test;
+import org.springframework.transaction.TransactionStatus;
+import org.springframework.transaction.support.TransactionCallback;
+import org.springframework.transaction.support.TransactionTemplate;
 
 import ca.uhn.fhir.jpa.dao.BaseHapiFhirDao;
 import ca.uhn.fhir.jpa.dao.SearchParameterMap;
@@ -49,6 +52,36 @@
 public class FhirResourceDaoDstu3SearchNoFtTest extends BaseJpaDstu3Test {
 	private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(FhirResourceDaoDstu3SearchNoFtTest.class);
 
+	@Test
+	public void testSearchWithRevIncludes() {
+		final String methodName = "testSearchWithRevIncludes";
+		TransactionTemplate txTemplate = new TransactionTemplate(myTransactionMgr);
+		txTemplate.setPropagationBehavior(TransactionTemplate.PROPAGATION_REQUIRES_NEW);
+		IIdType pid = txTemplate.execute(new TransactionCallback<IIdType>() {
+
+			@Override
+			public IIdType doInTransaction(TransactionStatus theStatus) {
+				org.hl7.fhir.dstu3.model.Patient p = new org.hl7.fhir.dstu3.model.Patient();
+				p.addName().addFamily(methodName);
+				IIdType pid = myPatientDao.create(p).getId().toUnqualifiedVersionless();
+
+				org.hl7.fhir.dstu3.model.Condition c = new org.hl7.fhir.dstu3.model.Condition();
+				c.getSubject().setReferenceElement(pid);
+				myConditionDao.create(c);
+
+				return pid;
+			}
+		});
+
+		SearchParameterMap map = new SearchParameterMap();
+		map.add(Patient.SP_RES_ID, new StringParam(pid.getIdPart()));
+		map.addRevInclude(Condition.INCLUDE_PATIENT);
+		IBundleProvider results = myPatientDao.search(map);
+		List<IBaseResource> foundResources = results.getResources(0, results.size());
+		assertEquals(Patient.class, foundResources.get(0).getClass());
+		assertEquals(Condition.class, foundResources.get(1).getClass());
+	}
+
 	@Test
 	public void testCodeSearch() {
 		Subscription subs = new Subscription();
@@ -276,7 +309,7 @@ public void testSearchAll() {
 
 	@Test
 	public void testHasParameter() {
-		IIdType pid0, pid1;
+		IIdType pid0;
 		{
 			Patient patient = new Patient();
 			patient.addIdentifier().setSystem("urn:system").setValue("001");
@@ -287,7 +320,7 @@ public void testHasParameter() {
 			Patient patient = new Patient();
 			patient.addIdentifier().setSystem("urn:system").setValue("001");
 			patient.addName().addFamily("Tester").addGiven("Joe");
-			pid1 = myPatientDao.create(patient, mySrd).getId().toUnqualifiedVersionless();
+			myPatientDao.create(patient, mySrd).getId().toUnqualifiedVersionless();
 		}
 		{
 			Observation obs = new Observation();
@@ -907,6 +940,7 @@ public void testSearchLastUpdatedParam() throws InterruptedException {
 		}
 	}
 
+	@SuppressWarnings("deprecation")
 	@Test
 	public void testSearchLastUpdatedParamWithComparator() throws InterruptedException {
 		IIdType id0;
@@ -2339,7 +2373,7 @@ public void testSearchWithUriParam() throws Exception {
 
 		ValueSet vs2 = new ValueSet();
 		vs2.setUrl("http://hl7.org/foo/bar");
-		IIdType id2 = myValueSetDao.create(vs2, mySrd).getId().toUnqualifiedVersionless();
+		myValueSetDao.create(vs2, mySrd).getId().toUnqualifiedVersionless();
 
 		IBundleProvider result;
 		result = myValueSetDao.search(ValueSet.SP_URL, new UriParam("http://hl7.org/fhir/ValueSet/basic-resource-type"));

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

@@ -5,31 +5,25 @@
 import static org.junit.Assert.fail;
 
 import java.io.IOException;
+import java.nio.charset.StandardCharsets;
 
 import org.apache.commons.io.IOUtils;
-import org.hl7.fhir.dstu3.model.Bundle;
+import org.hl7.fhir.dstu3.model.*;
 import org.hl7.fhir.dstu3.model.Bundle.BundleEntryComponent;
-import org.hl7.fhir.dstu3.model.IdType;
-import org.hl7.fhir.dstu3.model.Observation;
 import org.hl7.fhir.dstu3.model.Observation.ObservationStatus;
-import org.hl7.fhir.dstu3.model.OperationOutcome;
-import org.hl7.fhir.dstu3.model.Organization;
-import org.hl7.fhir.dstu3.model.Patient;
-import org.hl7.fhir.dstu3.model.StructureDefinition;
-import org.hl7.fhir.dstu3.model.ValueSet;
 import org.hl7.fhir.instance.model.api.IBaseResource;
 import org.hl7.fhir.instance.model.api.IIdType;
 import org.junit.AfterClass;
 import org.junit.Ignore;
 import org.junit.Test;
 
+import ca.uhn.fhir.jpa.util.StopWatch;
 import ca.uhn.fhir.rest.api.MethodOutcome;
 import ca.uhn.fhir.rest.api.ValidationModeEnum;
 import ca.uhn.fhir.rest.server.EncodingEnum;
 import ca.uhn.fhir.rest.server.exceptions.InvalidRequestException;
 import ca.uhn.fhir.rest.server.exceptions.PreconditionFailedException;
 import ca.uhn.fhir.rest.server.exceptions.ResourceVersionConflictException;
-import ca.uhn.fhir.rest.server.servlet.ServletRequestDetails;
 import ca.uhn.fhir.util.TestUtil;
 
 public class FhirResourceDaoDstu3ValidateTest extends BaseJpaDstu3Test {
@@ -40,6 +34,31 @@ public static void afterClassClearContext() {
 		TestUtil.clearAllStaticFieldsForUnitTest();
 	}
 
+	@Test
+	public void testValidateStructureDefinition() throws Exception {
+		String input = IOUtils.toString(getClass().getResourceAsStream("/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);
+		} catch (PreconditionFailedException e) {
+			ourLog.info(myFhirCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(e.getOperationOutcome()));
+		}
+		ourLog.info("Done validation");
+
+		StopWatch sw = new StopWatch();
+		ourLog.info("Starting validation");
+		try {
+			myStructureDefinitionDao.validate(sd, null, null, null, ValidationModeEnum.UPDATE, null, mySrd);
+		} catch (PreconditionFailedException e) {
+			// ok
+		}
+		ourLog.info("Done validation in {}ms", sw.getMillis());
+
+	}
+
 
 	@Test
 	@Ignore