Fix validation error when Bundle has no type

hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/search/StaleSearchDeletingSvcImpl.java

@@ -71,10 +71,12 @@ public class StaleSearchDeletingSvcImpl implements IStaleSearchDeletingSvc {
 
 	private void deleteSearch(final Long theSearchPid) {
 		Search searchToDelete = mySearchDao.findOne(theSearchPid);
-		ourLog.info("Deleting search {}/{} - Created[{}] -- Last returned[{}]", searchToDelete.getId(), searchToDelete.getUuid(), searchToDelete.getCreated(), searchToDelete.getSearchLastReturned());
+		if (searchToDelete != null) {
-		mySearchIncludeDao.deleteForSearch(searchToDelete.getId());
+			ourLog.info("Deleting search {}/{} - Created[{}] -- Last returned[{}]", searchToDelete.getId(), searchToDelete.getUuid(), searchToDelete.getCreated(), searchToDelete.getSearchLastReturned());
-		mySearchResultDao.deleteForSearch(searchToDelete.getId());
+			mySearchIncludeDao.deleteForSearch(searchToDelete.getId());
-		mySearchDao.delete(searchToDelete);
+			mySearchResultDao.deleteForSearch(searchToDelete.getId());
+			mySearchDao.delete(searchToDelete);
+		}
 	}
 
 	@Override

hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/util/SubscriptionsRequireManualActivationInterceptorDstu2.java

@@ -42,7 +42,7 @@ import static org.apache.commons.lang3.StringUtils.isNotBlank;
 public class SubscriptionsRequireManualActivationInterceptorDstu2 extends ServerOperationInterceptorAdapter {
 
 	@Autowired
-	@Qualifier("mySubscriptionDaoR4")
+	@Qualifier("mySubscriptionDaoDstu2")
 	private IFhirResourceDao<Subscription> myDao;
 
 	@Override

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

@@ -13,8 +13,8 @@ import java.util.Map;
 import java.util.Set;
 import java.util.regex.Matcher;
 import java.util.regex.Pattern;
-
 import org.apache.commons.lang3.StringUtils;
+
 import org.hl7.fhir.dstu3.conformance.ProfileUtilities;
 import org.hl7.fhir.dstu3.context.IWorkerContext;
 import org.hl7.fhir.dstu3.context.IWorkerContext.ValidationResult;
@@ -105,6 +105,7 @@ import org.w3c.dom.Node;
 
 import com.google.gson.Gson;
 import com.google.gson.JsonObject;
+import com.google.gson.stream.JsonWriter;
 
 import ca.uhn.fhir.util.ObjectUtil;
 
@@ -292,8 +293,6 @@ public class InstanceValidator extends BaseValidator implements IResourceValidat
     source = Source.InstanceValidator;
   }
 
-
-
   @Override
   public boolean isNoInvariantChecks() {
     return noInvariantChecks;
@@ -1358,33 +1357,19 @@ public class InstanceValidator extends BaseValidator implements IResourceValidat
     checkFixedValue(errors, path + ".denominator", focus.getNamedChild("denominator"), fixed.getDenominator(), "denominator", focus);
   }
 
-	private Reference readAsReference(Element item) {
-		Reference r = new Reference();
-		r.setDisplay(item.getNamedChildValue("display"));
-		r.setReference(item.getNamedChildValue("reference"));
-		List<Element> identifier = item.getChildrenByName("identifier");
-		if (identifier.isEmpty() == false) {
-			r.setIdentifier(readAsIdentifier(identifier.get(0)));
-		}
-		return r;
-	}
-	private Identifier readAsIdentifier(Element item) {
-		Identifier r = new Identifier();
-		r.setSystem(item.getNamedChildValue("system"));
-		r.setValue(item.getNamedChildValue("value"));
-		return r;
-	}
-
   private void checkReference(Object appContext, List<ValidationMessage> errors, String path, Element element, StructureDefinition profile, ElementDefinition container, String parentType, NodeStack stack) throws FHIRException, IOException {
-	  Reference reference = readAsReference(element);
+    String ref = null;
+    try {
+      // Do this inside a try because invalid instances might provide more than one reference.
+      ref = element.getNamedChildValue("reference");
+    } catch (Error e) {
       
-	  String ref = reference.getReference();
+    }
-	  if (Utilities.noString(ref)) {
+    if (Utilities.noString(ref)) {
-		  if (Utilities.noString(reference.getIdentifier().getSystem()) && Utilities.noString(reference.getIdentifier().getValue())) {
+      // todo - what should we do in this case?
-			  warning(errors, IssueType.STRUCTURE, element.line(), element.col(), path, !Utilities.noString(element.getNamedChildValue("display")), "A Reference without an actual reference or identifier should have a display");
+      warning(errors, IssueType.STRUCTURE, element.line(), element.col(), path, !Utilities.noString(element.getNamedChildValue("display")), "A Reference without an actual reference should have a display");
-		  }
+      return;
-		  return;
+    }
-	  }
 
     Element we = localResolve(ref, stack, errors, path);
     String refType;
@@ -2816,6 +2801,8 @@ public class InstanceValidator extends BaseValidator implements IResourceValidat
     List<Element> entries = new ArrayList<Element>();
     bundle.getNamedChildren("entry", entries);
     String type = bundle.getNamedChildValue("type");
+    type = StringUtils.defaultString(type);
+
     if (entries.size() == 0) {
       rule(errors, IssueType.INVALID, stack.getLiteralPath(), !(type.equals("document") || type.equals("message")), "Documents or Messages must contain at least one entry");
     } else {

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

@@ -667,9 +667,9 @@ public class InstanceValidator extends BaseValidator implements IResourceValidat
       try {
         if (context.fetchResourceWithException(ValueSet.class, system) != null) {
           rule(errors, IssueType.CODEINVALID, element.line(), element.col(), path, false, "Invalid System URI: "+system+" - cannot use a value set URI as a system");
-          return false;
+          // Lloyd: This error used to prohibit checking for downstream issues, but there are some cases where that checking needs to occur.  Please talk to me before changing the code back. 
-        } else
+        }
-          return true;
+        return true;
       }
       catch (Exception e) {
         return true;
@@ -1445,7 +1445,7 @@ public class InstanceValidator extends BaseValidator implements IResourceValidat
         refType = "bundle";
       }
     }
-    ReferenceValidationPolicy pol = refType.equals("contained") ? ReferenceValidationPolicy.CHECK_VALID : fetcher == null ? ReferenceValidationPolicy.IGNORE : fetcher.validationPolicy(hostContext.appContext, path, ref);
+    ReferenceValidationPolicy pol = refType.equals("contained") || refType.equals("bundle") ? ReferenceValidationPolicy.CHECK_VALID : fetcher == null ? ReferenceValidationPolicy.IGNORE : fetcher.validationPolicy(hostContext.appContext, path, ref);
 
     if (pol.checkExists()) {
       if (we == null) {
@@ -2783,6 +2783,8 @@ public class InstanceValidator extends BaseValidator implements IResourceValidat
     List<Element> entries = new ArrayList<Element>();
     bundle.getNamedChildren("entry", entries);
     String type = bundle.getNamedChildValue("type");
+    type = StringUtils.defaultString(type);
+
     if (entries.size() == 0) {
       rule(errors, IssueType.INVALID, stack.getLiteralPath(), !(type.equals("document") || type.equals("message")), "Documents or Messages must contain at least one entry");
     } else {

hapi-fhir-validation/src/test/java/ca/uhn/fhir/r4/validation/FhirInstanceValidatorR4Test.java

@@ -1,4 +1,4 @@
-package ca.uhn.fhir.validation;
+package ca.uhn.fhir.r4.validation;
 
 import static org.hamcrest.Matchers.containsString;
 import static org.hamcrest.Matchers.empty;
@@ -17,7 +17,12 @@ import java.io.InputStream;
 import java.util.*;
 import java.util.zip.GZIPInputStream;
 
+import ca.uhn.fhir.validation.FhirValidator;
+import ca.uhn.fhir.validation.ResultSeverityEnum;
+import ca.uhn.fhir.validation.SingleValidationMessage;
+import ca.uhn.fhir.validation.ValidationResult;
 import org.apache.commons.io.IOUtils;
+import org.hl7.fhir.dstu3.hapi.validation.FhirInstanceValidatorDstu3Test;
 import org.hl7.fhir.instance.model.api.IBaseResource;
 import org.hl7.fhir.r4.hapi.ctx.*;
 import org.hl7.fhir.r4.hapi.ctx.IValidationSupport.CodeValidationResult;
@@ -533,6 +538,16 @@ public class FhirInstanceValidatorR4Test {
 		assertEquals(output.toString(), 0, output.getMessages().size());
 	}
 
+	@Test
+	public void testValidateBundleWithNoType() throws Exception {
+		String vsContents = IOUtils.toString(FhirInstanceValidatorR4Test.class.getResourceAsStream("/r4/bundle-with-no-type.json"), "UTF-8");
+
+		ValidationResult output = myVal.validateWithResult(vsContents);
+		logResultsAndReturnNonInformationalOnes(output);
+		assertThat(output.getMessages().toString(), containsString("Element 'Bundle.type': minimum required = 1"));
+	}
+
+
 	@Test
 	public void testValidateRawXmlResourceWithEmptyPrimitive() {
 		// @formatter:off

hapi-fhir-validation/src/test/java/org/hl7/fhir/dstu3/hapi/validation/FhirInstanceValidatorDstu3Test.java

@@ -336,6 +336,15 @@ public class FhirInstanceValidatorDstu3Test {
 		assertTrue(output.isSuccessful());
 	}
 
+	@Test
+	public void testValidateBundleWithNoType() throws Exception {
+		String vsContents = IOUtils.toString(FhirInstanceValidatorDstu3Test.class.getResourceAsStream("/dstu3/bundle-with-no-type.json"), "UTF-8");
+
+		ValidationResult output = myVal.validateWithResult(vsContents);
+		logResultsAndReturnNonInformationalOnes(output);
+		assertThat(output.getMessages().toString(), containsString("Element 'Bundle.type': minimum required = 1"));
+	}
+
 	/**
 	 * See #739
 	 */

hapi-fhir-validation/src/test/resources/dstu3/bundle-with-no-type.json

@@ -0,0 +1,73 @@
+{
+  "resourceType": "Bundle",
+  "entry": [
+    {
+      "fullUrl": "http://localhost:5555/phr/baseDstu3/Person/PERSON1",
+      "resource": {
+        "resourceType": "Person",
+        "id": "PERSON1",
+        "meta": {
+          "versionId": "1",
+          "lastUpdated": "2017-08-17T16:19:40.109+03:00"
+        },
+        "identifier": [
+          {
+            "value": "081181-9984"
+          }
+        ],
+        "name": [
+          {
+            "text": "Anna Testi",
+            "family": "Testi",
+            "given": [
+              "Anna"
+            ]
+          },
+          {
+            "family": "asdfas"
+          }
+        ],
+        "telecom": [
+          {
+            "use": "home"
+          },
+          {
+            "system": "phone",
+            "value": "(044) 1234567",
+            "use": "work"
+          }
+        ],
+        "gender": "female",
+        "birthDate": "1981-11-08",
+        "address": [
+          {
+            "line": [
+              "Osuuspankkitie 2"
+            ],
+            "city": "Helsinki",
+            "postalCode": "00120",
+            "country": "Suomi"
+          },
+          {
+            "city": "Blo-49847020"
+          }
+        ],
+        "active": true,
+        "link": [
+          {
+            "target": {
+              "reference": "Patient/PATIENT1",
+              "display": "Anna Testi"
+            }
+          }
+        ]
+      },
+      "request": {
+        "method": "PUT",
+        "url": "Person/PERSON1",
+        "ifMatch": "1"
+      }
+    }
+  ]
+}
+

hapi-fhir-validation/src/test/resources/r4/bundle-with-no-type.json

@@ -0,0 +1,73 @@
+{
+  "resourceType": "Bundle",
+  "entry": [
+    {
+      "fullUrl": "http://localhost:5555/phr/baseDstu3/Person/PERSON1",
+      "resource": {
+        "resourceType": "Person",
+        "id": "PERSON1",
+        "meta": {
+          "versionId": "1",
+          "lastUpdated": "2017-08-17T16:19:40.109+03:00"
+        },
+        "identifier": [
+          {
+            "value": "081181-9984"
+          }
+        ],
+        "name": [
+          {
+            "text": "Anna Testi",
+            "family": "Testi",
+            "given": [
+              "Anna"
+            ]
+          },
+          {
+            "family": "asdfas"
+          }
+        ],
+        "telecom": [
+          {
+            "use": "home"
+          },
+          {
+            "system": "phone",
+            "value": "(044) 1234567",
+            "use": "work"
+          }
+        ],
+        "gender": "female",
+        "birthDate": "1981-11-08",
+        "address": [
+          {
+            "line": [
+              "Osuuspankkitie 2"
+            ],
+            "city": "Helsinki",
+            "postalCode": "00120",
+            "country": "Suomi"
+          },
+          {
+            "city": "Blo-49847020"
+          }
+        ],
+        "active": true,
+        "link": [
+          {
+            "target": {
+              "reference": "Patient/PATIENT1",
+              "display": "Anna Testi"
+            }
+          }
+        ]
+      },
+      "request": {
+        "method": "PUT",
+        "url": "Person/PERSON1",
+        "ifMatch": "1"
+      }
+    }
+  ]
+}
+

src/changes/changes.xml

@@ -55,6 +55,10 @@
 				the ID of the search, meaning that if a search returns results from the Query
 				cache, it will reuse the ID of the previously returned Bundle
 			</action>
+			<action type="fix">
+				Fix a NullPointerException when validating a Bundle (in DSTU3/R4) with no
+				<![CDATA[<code>Bundle.type</code>]]> value
+			</action>
 		</release>
 		<release version="3.0.0" date="2017-09-27">
 			<action type="add">