Sync DSTU2 validator with RI

hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/dstu2/BaseJpaDstu2Test.java

@@ -183,6 +183,7 @@ public abstract class BaseJpaDstu2Test extends BaseJpaTest {
 		myDaoConfig.setHardSearchLimit(1000);
 		myDaoConfig.setHardTagListLimit(1000);
 		myDaoConfig.setIncludeLimit(2000);
+		myDaoConfig.setAllowExternalReferences(new DaoConfig().isAllowExternalReferences());
 	}
 
 	@Before

hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/provider/ResourceProviderDstu2Test.java

@@ -33,6 +33,7 @@ import org.apache.commons.lang3.StringUtils;
 import org.apache.http.client.ClientProtocolException;
 import org.apache.http.client.methods.CloseableHttpResponse;
 import org.apache.http.client.methods.HttpDelete;
+import org.apache.http.client.methods.HttpEntityEnclosingRequestBase;
 import org.apache.http.client.methods.HttpGet;
 import org.apache.http.client.methods.HttpPost;
 import org.apache.http.client.methods.HttpPut;
@@ -41,6 +42,7 @@ import org.apache.http.entity.StringEntity;
 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.model.api.Bundle;
@@ -2186,6 +2188,53 @@ public class ResourceProviderDstu2Test extends BaseResourceProviderDstu2Test {
 		}
 	}
 	
+	/**
+	 * From example from david hay - moved to the hl7org_dstu2 project
+	 */
+	@Test
+	@Ignore
+	public void testValidateDavidsAllergyIntolerance() throws Exception {
+		myDaoConfig.setAllowExternalReferences(true);
+		
+		/*
+		 * Upload structurredef 
+		 */
+		
+		String contents = IOUtils.toString(getClass().getResourceAsStream("/allergyintolerance-sd-david.json"), "UTF-8");
+		HttpEntityEnclosingRequestBase post = new HttpPut(ourServerBase + "/StructureDefinition/ohAllergyIntolerance");
+		post.setEntity(new StringEntity(contents, ContentType.create(Constants.CT_FHIR_JSON, "UTF-8")));
+		CloseableHttpResponse response = ourHttpClient.execute(post);
+		try {
+			String resp = IOUtils.toString(response.getEntity().getContent());
+			ourLog.info(resp);
+			assertEquals(201, response.getStatusLine().getStatusCode());
+		} finally {
+			IOUtils.closeQuietly(response.getEntity().getContent());
+			response.close();
+		}
+		
+		/*
+		 * Validate
+		 */
+		
+		contents = IOUtils.toString(getClass().getResourceAsStream("/allergyintolerance-david.json"), "UTF-8");
+
+		post = new HttpPost(ourServerBase + "/AllergyIntolerance/$validate?_pretty=true");
+		post.setEntity(new StringEntity(contents, ContentType.create(Constants.CT_FHIR_JSON, "UTF-8")));
+
+		response = ourHttpClient.execute(post);
+		try {
+			String resp = IOUtils.toString(response.getEntity().getContent());
+			ourLog.info(resp);
+			assertEquals(200, response.getStatusLine().getStatusCode());
+			assertThat(resp, not(containsString("Resource has no id")));
+		} finally {
+			IOUtils.closeQuietly(response.getEntity().getContent());
+			response.close();
+		}
+	}
+
+
 	@Test
 	public void testValidateResourceHuge() throws IOException {
 
@@ -2318,4 +2367,5 @@ public class ResourceProviderDstu2Test extends BaseResourceProviderDstu2Test {
 
 	}
 
+	
 }

hapi-fhir-jpaserver-base/src/test/resources/allergyintolerance-david.json

@@ -0,0 +1,152 @@
+{
+  "resourceType": "AllergyIntolerance",
+  "id": "84651",
+  "meta": {
+    "versionId": "1",
+    "lastUpdated": "2016-05-19T15:43:49.815-04:00",
+    "profile": [
+      "http://fhir.hl7.org.nz/dstu2/StructureDefinition/ohAllergyIntolerance"
+    ]
+  },
+  "extension": [
+    {
+      "url": "http://fhir.hl7.org.nz/dstu2/StructureDefinition/al-endDate",
+      "valueDateTime": "2016-05-03"
+    },
+    {
+      "url": "http://fhir.hl7.org.nz/dstu2/StructureDefinition/al-informantRole",
+      "valueCodeableConcept": {
+        "coding": [
+          {
+            "system": "http://snomed.info/sct",
+            "version": "http://snomed.info/sct/32506021000036107/version/20150531",
+            "code": "133932002",
+            "display": "Carer"
+          }
+        ]
+      }
+    },
+    {
+      "url": "http://fhir.hl7.org.nz/dstu2/StructureDefinition/al-reasonClosed",
+      "valueCodeableConcept": {
+        "coding": [
+          {
+            "system": "http://orionhealth.com/problem-list/adverse-reaction-reason-closed",
+            "code": "1",
+            "display": "Disproven"
+          }
+        ]
+      }
+    },
+    {
+      "url": "http://fhir.hl7.org.nz/dstu2/StructureDefinition/al-classification",
+      "valueCodeableConcept": {
+        "coding": [
+          {
+            "system": "http://snomed.info/sct",
+            "version": "http://snomed.info/sct/32506021000036107/version/20150531",
+            "code": "419076005",
+            "display": "Allergic reaction"
+          }
+        ]
+      }
+    }
+  ],
+  "language": [
+    "en"
+  ],
+  "identifier": [
+    {
+      "system": "http://orionhealth.com/identifier/problem-list/ORGNISATION_ORION",
+      "value": "2.25.148135789146703435349240718177383549558.8.4.4.0/522911"
+    }
+  ],
+  "patient": {
+    "reference": "Patient/64909"
+  },
+  "substance": {
+    "coding": [
+      {
+        "system": "http://snomed.info/sct",
+        "version": "http://snomed.info/sct/32506021000036107/version/20150531",
+        "code": "84430008",
+        "display": "Cross reacting antibody"
+      }
+    ]
+  },
+  "status": "inactive",
+  "criticality": "CRITH",
+  "category": "environment",
+  "reaction": [
+    {
+      "certainty": "likely",
+      "_certainty": {
+        "extension": [
+          {
+            "url": "http://fhir.hl7.org.nz/dstu2/StructureDefinition/originalValue",
+            "valueCodeableConcept": {
+              "coding": [
+                {
+                  "system": "http://orionhealth.com/problem-list/adverse-reaction-certainty",
+                  "code": "SUSPECTED",
+                  "display": "Suspected"
+                }
+              ]
+            }
+          }
+        ]
+      },
+      "manifestation": [
+        {
+          "extension": [
+            {
+              "url": "http://fhir.hl7.org.nz/dstu2/StructureDefinition/al-manifestationSeverity",
+              "valueCodeableConcept": {
+                "coding": [
+                  {
+                    "system": "http://snomed.info/sct",
+                    "version": "http://snomed.info/sct/900000000000207008/version/20150531",
+                    "code": "442452003",
+                    "display": "Life-Threatening"
+                  }
+                ]
+              }
+            }
+          ],
+          "coding": [
+            {
+              "system": "http://orionhealth.com/problem-list/clinical-manifestation",
+              "code": "FT",
+              "display": "rlo"
+            }
+          ]
+        },
+        {
+          "extension": [
+            {
+              "url": "http://fhir.hl7.org.nz/dstu2/StructureDefinition/al-manifestationSeverity",
+              "valueCodeableConcept": {
+                "coding": [
+                  {
+                    "system": "http://orionhealth.com/problem-list/severity",
+                    "code": "UNKNOWN",
+                    "display": "Unknown"
+                  }
+                ]
+              }
+            }
+          ],
+          "coding": [
+            {
+              "system": "http://snomed.info/sct",
+              "version": "http://snomed.info/sct/32506021000036107/version/20150531",
+              "code": "95332009",
+              "display": "Rash of systemic lupus erythematosus"
+            }
+          ]
+        }
+      ],
+      "severity": "severe"
+    }
+  ]
+}

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

@@ -83,7 +83,6 @@ public class FhirInstanceValidatorDstu3Test {
 		myValidConcepts.add(theSystem + "___" + theCode);
 	}
 
-	
 	@Test
 	// @Ignore
 	public void testValidateBuiltInProfiles() throws Exception {
@@ -142,11 +141,11 @@ public class FhirInstanceValidatorDstu3Test {
 		assertEquals(1, fpOutput.size());
 		bool = (BooleanType) fpOutput.get(0);
 		assertTrue(bool.getValue());
-//		
+		//		
-//		fpOutput = fp.evaluate(bundle, "component.where(code = %resource.code).empty()");
+		//		fpOutput = fp.evaluate(bundle, "component.where(code = %resource.code).empty()");
-//		assertEquals(1, fpOutput.size());
+		//		assertEquals(1, fpOutput.size());
-//		bool = (BooleanType) fpOutput.get(0);
+		//		bool = (BooleanType) fpOutput.get(0);
-//		assertTrue(bool.getValue());
+		//		assertTrue(bool.getValue());
 
 		ValidationResult output = myVal.validateWithResult(inputString);
 		List<SingleValidationMessage> errors = logResultsAndReturnNonInformationalOnes(output);
@@ -266,8 +265,7 @@ public class FhirInstanceValidatorDstu3Test {
 
 		int index = 0;
 		for (SingleValidationMessage next : theOutput.getMessages()) {
-			ourLog.info("Result {}: {} - {}:{} {} - {}",
+			ourLog.info("Result {}: {} - {}:{} {} - {}", new Object[] { index, next.getSeverity(), defaultString(next.getLocationLine()), defaultString(next.getLocationCol()), next.getLocationString(), next.getMessage() });
-					new Object[] { index, next.getSeverity(), defaultString(next.getLocationLine()), defaultString(next.getLocationCol()), next.getLocationString(), next.getMessage() });
 			index++;
 
 			retVal.add(next);
@@ -482,12 +480,9 @@ public class FhirInstanceValidatorDstu3Test {
 
 	@Test
 	public void testValidateResourceWithDefaultValuesetBadCode() {
-		String input = "<Observation xmlns=\"http://hl7.org/fhir\">\n" + "   <status value=\"notvalidcode\"/>\n" + "   <code>\n" + "      <text value=\"No code here!\"/>\n" + "   </code>\n"
+		String input = "<Observation xmlns=\"http://hl7.org/fhir\">\n" + "   <status value=\"notvalidcode\"/>\n" + "   <code>\n" + "      <text value=\"No code here!\"/>\n" + "   </code>\n" + "</Observation>";
-				+ "</Observation>";
 		ValidationResult output = myVal.validateWithResult(input);
-		assertEquals(
+		assertEquals("The value provided ('notvalidcode') is not in the value set http://hl7.org/fhir/ValueSet/observation-status (http://hl7.org/fhir/ValueSet/observation-status, and a code is required from this value set", output.getMessages().get(0).getMessage());
-				"The value provided ('notvalidcode') is not in the value set http://hl7.org/fhir/ValueSet/observation-status (http://hl7.org/fhir/ValueSet/observation-status, and a code is required from this value set",
-				output.getMessages().get(0).getMessage());
 	}
 
 	@Test
@@ -565,9 +560,7 @@ public class FhirInstanceValidatorDstu3Test {
 		List<SingleValidationMessage> all = logResultsAndReturnAll(output);
 		assertEquals(1, all.size());
 		assertEquals("Patient.identifier.type", all.get(0).getLocationString());
-		assertEquals(
+		assertEquals("None of the codes provided are in the value set http://hl7.org/fhir/ValueSet/identifier-type (http://hl7.org/fhir/ValueSet/identifier-type, and a code should come from this value set unless it has no suitable code", all.get(0).getMessage());
-				"None of the codes provided are in the value set http://hl7.org/fhir/ValueSet/identifier-type (http://hl7.org/fhir/ValueSet/identifier-type, and a code should come from this value set unless it has no suitable code",
-				all.get(0).getMessage());
 		assertEquals(ResultSeverityEnum.WARNING, all.get(0).getSeverity());
 
 	}

hapi-fhir-structures-hl7org-dstu2/src/main/java/org/hl7/fhir/instance/hapi/validation/FhirInstanceValidator.java

@@ -154,6 +154,8 @@ public class FhirInstanceValidator extends BaseValidatorBridge implements IValid
 
     v.setBestPracticeWarningLevel(myBestPracticeWarningLevel);
     v.setAnyExtensionsAllowed(true);
+    v.setRequireResourceId(false);
+    v.setSuppressLoincSnomedMessages(true);
 
     List<ValidationMessage> messages = new ArrayList<ValidationMessage>();
 

hapi-fhir-structures-hl7org-dstu2/src/main/java/org/hl7/fhir/instance/validation/InstanceValidator.java

@@ -39,11 +39,11 @@ import org.hl7.fhir.instance.model.ValueSet.ConceptDefinitionComponent;
 import org.hl7.fhir.instance.model.ValueSet.ValueSetExpansionContainsComponent;
 import org.hl7.fhir.instance.terminologies.ValueSetExpander.ETooCostly;
 import org.hl7.fhir.instance.terminologies.ValueSetExpander.ValueSetExpansionOutcome;
+import org.hl7.fhir.instance.terminologies.ValueSetExpanderFactory;
+import org.hl7.fhir.instance.terminologies.ValueSetExpansionCache;
 import org.hl7.fhir.instance.utilities.CommaSeparatedStringBuilder;
 import org.hl7.fhir.instance.utilities.Utilities;
 import org.hl7.fhir.instance.utilities.xml.XMLUtil;
-import org.hl7.fhir.instance.terminologies.ValueSetExpanderFactory;
-import org.hl7.fhir.instance.terminologies.ValueSetExpansionCache;
 import org.hl7.fhir.instance.utils.EOperationOutcome;
 import org.hl7.fhir.instance.utils.IWorkerContext;
 import org.hl7.fhir.instance.utils.IWorkerContext.ValidationResult;
@@ -59,7 +59,6 @@ import com.google.gson.JsonNull;
 import com.google.gson.JsonObject;
 import com.google.gson.JsonPrimitive;
 
-
 /* 
  * todo:
  * check urn's don't start oid: or uuid: 
@@ -69,6 +68,7 @@ public class InstanceValidator extends BaseValidator implements IResourceValidat
   private boolean anyExtensionsAllowed;
 
   private BestPracticeWarningLevel bpWarnings;
+  private ValueSetExpanderFactory cache;
   // configuration items
   private CheckDisplayOption checkDisplay;
   private IWorkerContext context;
@@ -84,6 +84,14 @@ public class InstanceValidator extends BaseValidator implements IResourceValidat
     super();
     this.context = theContext;
     source = Source.InstanceValidator;
+    cache = new ValueSetExpansionCache(theContext, null);
+  }
+
+  public InstanceValidator(IWorkerContext theContext, ValueSetExpanderFactory theValueSetExpander) throws Exception {
+    super();
+    this.context = theContext;
+    source = Source.InstanceValidator;
+    this.cache = theValueSetExpander;
   }
 
   private boolean allowUnknownExtension(String url) {
@@ -185,34 +193,70 @@ public class InstanceValidator extends BaseValidator implements IResourceValidat
     }
   }
 
-  private void checkCodeableConcept(List<ValidationMessage> errors, String path, WrapperElement element, StructureDefinition profile, ElementDefinition theElementCntext) throws EOperationOutcome, Exception {
+  private void checkCodeableConcept(List<ValidationMessage> errors, String path, WrapperElement element, StructureDefinition profile, ElementDefinition theElementCntext)
+      throws EOperationOutcome, Exception {
     if (theElementCntext != null && theElementCntext.hasBinding()) {
       ElementDefinitionBindingComponent binding = theElementCntext.getBinding();
       if (warning(errors, IssueType.CODEINVALID, element.line(), element.col(), path, binding != null, "Binding for " + path + " missing (cc)")) {
         if (binding.hasValueSet() && binding.getValueSet() instanceof Reference) {
-          ValueSet valueset = resolveBindingReference(binding.getValueSet());
+          ValueSet unexpandedVs = resolveBindingReference(binding.getValueSet());
-          if (warning(errors, IssueType.CODEINVALID, element.line(), element.col(), path, valueset != null, "ValueSet " + describeReference(binding.getValueSet()) + " not found")) {
+          if (warning(errors, IssueType.CODEINVALID, element.line(), element.col(), path, unexpandedVs != null, "ValueSet " + describeReference(binding.getValueSet()) + " not found")) {
-          	CodeableConcept cc = null;
+            ValueSet vs;
             try {
-          		cc = readAsCodeableConcept(element);
+              boolean found = false;
-              if (!cc.hasCoding()) {
+              boolean any = false;
-                if (binding.getStrength() == BindingStrength.REQUIRED)
+              WrapperElement c = element.getFirstChild();
-                  rule(errors, IssueType.CODEINVALID, element.line(), element.col(), path, false, "No code provided, and a code is required from the value set " + describeReference(binding.getValueSet()) + " (" + valueset.getUrl());
+              while (c != null) {
-                else if (binding.getStrength() == BindingStrength.EXTENSIBLE)
+                if (c.getName().equals("coding")) {
-                  warning(errors, IssueType.CODEINVALID, element.line(), element.col(), path, false, "No code provided, and a code should be provided from the value set " + describeReference(binding.getValueSet()) + " (" + valueset.getUrl());
+                  any = true;
+                  String system = c.getNamedChildValue("system");
+                  String code = c.getNamedChildValue("code");
+                  if (system != null && code != null) {
+                    ValueSetExpansionOutcome exp = cache.getExpander().expand(unexpandedVs);
+                    vs = exp != null ? exp.getValueset() : null;
+                    if (vs == null) {
+                      if (binding.getStrength() != BindingStrength.REQUIRED) {
+                        ValidationResult validationResult = context.validateCode(system, code, null);
+                        if (validationResult.isOk()) {
+                          found = true;
                         } else {
-          		ValidationResult vr = context.validateCode(cc, valueset);
+                          warning(errors, IssueType.CODEINVALID, element.line(), element.col(), path, false, "Unable to validate code \"{0}\" in code system \"{1}\"", code, system);
-            	if (!vr.isOk()) {
+                          return;
-                if (binding.getStrength() == BindingStrength.REQUIRED)
+                        }
-                    rule(errors, IssueType.CODEINVALID, element.line(), element.col(), path, false, "None of the codes provided are in the value set " + describeReference(binding.getValueSet()) + " (" + valueset.getUrl()+", and a code from this value set is required");
+                      }
+                    }
+                    if (found == false) {
+                      if (!warning(errors, IssueType.CODEINVALID, element.line(), element.col(), path, vs != null, "Unable to expand value set for " + describeReference(binding.getValueSet()))) {
+                        return;
+                      }
+                    }
+                    found = found || codeInExpansion(vs, system, code);
+                  }
+                }
+                c = c.getNextSibling();
+              }
+              if (!any && binding.getStrength() == BindingStrength.REQUIRED)
+                warning(errors, IssueType.CODEINVALID, element.line(), element.col(), path, found,
+                    "No code provided, and value set " + describeReference(binding.getValueSet()) + " (" + unexpandedVs.getUrl() + ") is required");
+              if (any)
+                if (binding.getStrength() == BindingStrength.PREFERRED)
+                  hint(errors, IssueType.CODEINVALID, element.line(), element.col(), path, found,
+                      "None of the codes are in the example value set " + describeReference(binding.getValueSet()) + " (" + unexpandedVs.getUrl() + ")");
                 else if (binding.getStrength() == BindingStrength.EXTENSIBLE)
-                    warning(errors, IssueType.CODEINVALID, element.line(), element.col(), path, false, "None of the codes provided are in the value set " + describeReference(binding.getValueSet()) + " (" + valueset.getUrl() + ", and a code should come from this value set unless it has no suitable code");
+                  warning(errors, IssueType.CODEINVALID, element.line(), element.col(), path, found,
-                else if (binding.getStrength() == BindingStrength.PREFERRED)
+                      "None of the codes are in the expected value set " + describeReference(binding.getValueSet()) + " (" + unexpandedVs.getUrl() + ")");
-                    hint(errors, IssueType.CODEINVALID, element.line(), element.col(), path, false,  "None of the codes provided are in the value set " + describeReference(binding.getValueSet()) + " (" + valueset.getUrl() + ", and a code is recommended to come from this value set");
+
-                }
-            	}
             } catch (Exception e) {
-          		warning(errors, IssueType.CODEINVALID, element.line(), element.col(), path, false, "Error "+e.getMessage()+" validating CodeableConcept");
+              if (e.getMessage() == null) {
+                warning(errors, IssueType.CODEINVALID, element.line(), element.col(), path, false,
+                    "Exception opening value set " + unexpandedVs.getUrl() + " for " + describeReference(binding.getValueSet()) + ": --Null--");
+                // } else if (!e.getMessage().contains("unable to find value set http://snomed.info/sct")) {
+                // hint(errors, IssueType.CODEINVALID, path, suppressLoincSnomedMessages, "Snomed value set - not validated");
+                // } else if (!e.getMessage().contains("unable to find value set http://loinc.org")) {
+                // hint(errors, IssueType.CODEINVALID, path, suppressLoincSnomedMessages, "Loinc value set - not validated");
+              } else
+                warning(errors, IssueType.CODEINVALID, element.line(), element.col(), path, false,
+                    "Exception opening value set " + unexpandedVs.getUrl() + " for " + describeReference(binding.getValueSet()) + ": " + e.getMessage());
             }
           }
         } else if (binding.hasValueSet()) {
@@ -224,25 +268,6 @@ public class InstanceValidator extends BaseValidator implements IResourceValidat
     }
   }
 
-  private CodeableConcept readAsCodeableConcept(WrapperElement element) {
-	  CodeableConcept cc = new CodeableConcept();
-	  List<WrapperElement> list = new ArrayList<WrapperElement>();
-	  element.getNamedChildren("coding", list);
-	  for (WrapperElement item : list)
-	  	cc.addCoding(readAsCoding(item));
-    cc.setText(element.getNamedChildValue("text"));
-	  return cc;
-	}
-
-	private Coding readAsCoding(WrapperElement item) {
-		Coding c = new Coding();
-		c.setSystem(item.getNamedChildValue("system"));
-		c.setVersion(item.getNamedChildValue("version"));
-		c.setCode(item.getNamedChildValue("code"));
-		c.setDisplay(item.getNamedChildValue("display"));
-  	return c;
-	}
-
   private void checkCoding(List<ValidationMessage> errors, String path, WrapperElement focus, Coding fixed) {
     checkFixedValue(errors, path + ".system", focus.getNamedChild("system"), fixed.getSystemElement(), "system");
     checkFixedValue(errors, path + ".code", focus.getNamedChild("code"), fixed.getCodeElement(), "code");
@@ -250,7 +275,7 @@ public class InstanceValidator extends BaseValidator implements IResourceValidat
     checkFixedValue(errors, path + ".userSelected", focus.getNamedChild("userSelected"), fixed.getUserSelectedElement(), "userSelected");
   }
 
-  private void checkCoding(List<ValidationMessage> errors, String path, WrapperElement element, StructureDefinition profile, ElementDefinition theElementCntext, boolean inCodeableConcept) throws EOperationOutcome, Exception {
+  private void checkCoding(List<ValidationMessage> errors, String path, WrapperElement element, StructureDefinition profile, ElementDefinition context) throws EOperationOutcome, Exception {
     String code = element.getNamedChildValue("code");
     String system = element.getNamedChildValue("system");
     String display = element.getNamedChildValue("display");
@@ -258,31 +283,37 @@ public class InstanceValidator extends BaseValidator implements IResourceValidat
 
     if (system != null && code != null) {
       if (checkCode(errors, element, path, code, system, display))
-        if (theElementCntext != null && theElementCntext.getBinding() != null) {
+        if (context != null && context.getBinding() != null) {
-          ElementDefinitionBindingComponent binding = theElementCntext.getBinding();
+          ElementDefinitionBindingComponent binding = context.getBinding();
           if (warning(errors, IssueType.CODEINVALID, element.line(), element.col(), path, binding != null, "Binding for " + path + " missing")) {
             if (binding.hasValueSet() && binding.getValueSet() instanceof Reference) {
-              ValueSet valueset = resolveBindingReference(binding.getValueSet());
+              ValueSet vs = resolveBindingReference(binding.getValueSet());
-              if (warning(errors, IssueType.CODEINVALID, element.line(), element.col(), path, valueset != null, "ValueSet " + describeReference(binding.getValueSet()) + " not found")) {
+              if (warning(errors, IssueType.CODEINVALID, element.line(), element.col(), path, vs != null, "ValueSet " + describeReference(binding.getValueSet()) + " not found")) {
-              	Coding c = null;
                 try {
-              		c = readAsCoding(element);
+                  vs = cache.getExpander().expand(vs).getValueset();
-              		ValidationResult vr = context.validateCode(c, valueset);
+                  if (warning(errors, IssueType.CODEINVALID, element.line(), element.col(), path, vs != null, "Unable to expand value set for " + describeReference(binding.getValueSet()))) {
-                	if (!vr.isOk()) {
                     if (binding.getStrength() == BindingStrength.REQUIRED)
-                      warning(errors, IssueType.CODEINVALID, element.line(), element.col(), path, false, "The value provided is not in the value set " + describeReference(binding.getValueSet()) + " (" + valueset.getUrl() + ", and a code is required from this value set");
+                      rule(errors, IssueType.CODEINVALID, element.line(), element.col(), path, codeInExpansion(vs, system, code),
+                          "Code {" + system + "}" + code + " is not in value set " + describeReference(binding.getValueSet()) + " (" + vs.getUrl() + ")");
                     else if (binding.getStrength() == BindingStrength.EXTENSIBLE)
-                      warning(errors, IssueType.CODEINVALID, element.line(), element.col(), path, false, "The value provided is not in the value set " + describeReference(binding.getValueSet()) + " (" + valueset.getUrl() + ", and a code should come from this value set unless it has no suitable code");
+                      warning(errors, IssueType.CODEINVALID, element.line(), element.col(), path, codeInExpansion(vs, system, code),
-                    else if (binding.getStrength() == BindingStrength.PREFERRED)
+                          "Code {" + system + "}" + code + " is not in value set " + describeReference(binding.getValueSet()) + " (" + vs.getUrl() + ")");
-                    	hint(errors, IssueType.CODEINVALID, element.line(), element.col(), path, false,  "The value provided is not in the value set " + describeReference(binding.getValueSet()) + " (" + valueset.getUrl() + ", and a code is recommended to come from this value set");
+                    else
+                      hint(errors, IssueType.CODEINVALID, element.line(), element.col(), path, codeInExpansion(vs, system, code),
+                          "Code {" + system + "}" + code + " is not in value set " + describeReference(binding.getValueSet()) + " (" + vs.getUrl() + ")");
                   }
                 } catch (Exception e) {
-              		warning(errors, IssueType.CODEINVALID, element.line(), element.col(), path, false, "Error "+e.getMessage()+" validating CodeableConcept");
+                  if (e.getMessage() == null)
+                    warning(errors, IssueType.CODEINVALID, element.line(), element.col(), path, false,
+                        "Exception opening value set " + vs.getUrl() + " for " + describeReference(binding.getValueSet()) + ": --Null--");
+                  else
+                    warning(errors, IssueType.CODEINVALID, element.line(), element.col(), path, false,
+                        "Exception opening value set " + vs.getUrl() + " for " + describeReference(binding.getValueSet()) + ": " + e.getMessage());
                 }
               }
             } else if (binding.hasValueSet()) {
               hint(errors, IssueType.CODEINVALID, element.line(), element.col(), path, false, "Binding by URI reference cannot be checked");
-            } else if (!inCodeableConcept) {
+            } else {
               hint(errors, IssueType.CODEINVALID, element.line(), element.col(), path, false, "Binding for path " + path + " has no source, so can't be checked");
             }
           }
@@ -312,7 +343,7 @@ public class InstanceValidator extends BaseValidator implements IResourceValidat
           if (warning(errors, IssueType.INVALID, element.line(), element.col(), p, pr != null, "StructureDefinition reference \"{0}\" could not be resolved", ref)) {
             if (rule(errors, IssueType.STRUCTURE, element.line(), element.col(), p, pr.hasSnapshot(),
                 "StructureDefinition has no snapshot - validation is against the snapshot, so it must be provided")) {
-              validateElement(errors, pr, pr.getSnapshot().getElement().get(0), null, null, element, element.getName(), stack, false);
+              validateElement(errors, pr, pr.getSnapshot().getElement().get(0), null, null, element, element.getName(), stack);
             }
           }
           i++;
@@ -619,28 +650,41 @@ public class InstanceValidator extends BaseValidator implements IResourceValidat
   }
 
   // note that we don't check the type here; it could be string, uri or code.
-  private void checkPrimitiveBinding(List<ValidationMessage> errors, String path, String type, ElementDefinition elementContext, WrapperElement element) throws Exception {
+  private void checkPrimitiveBinding(List<ValidationMessage> errors, String path, String type, ElementDefinition context, WrapperElement element) throws Exception {
     if (!element.hasAttribute("value"))
       return;
 
     String value = element.getAttribute("value");
-    String system = null;
+
-    String display = null;
     // System.out.println("check "+value+" in "+path);
 
     // firstly, resolve the value set
-    ElementDefinitionBindingComponent binding = elementContext.getBinding();
+    ElementDefinitionBindingComponent binding = context.getBinding();
     if (binding.hasValueSet() && binding.getValueSet() instanceof Reference) {
       ValueSet vs = resolveBindingReference(binding.getValueSet());
       if (warning(errors, IssueType.CODEINVALID, element.line(), element.col(), path, vs != null, "ValueSet {0} not found", describeReference(binding.getValueSet()))) {
-      	ValidationResult vr = context.validateCode(system, value, display, vs);
+        try {
-      	if (!vr.isOk()) {
+          ValueSetExpansionOutcome expansionOutcome = cache.getExpander().expand(vs);
+          vs = expansionOutcome != null ? expansionOutcome.getValueset() : null;
+          if (warning(errors, IssueType.CODEINVALID, element.line(), element.col(), path, vs != null, "Unable to expand value set for {0}", describeReference(binding.getValueSet()))) {
+            boolean ok = codeInExpansion(vs, null, value);
             if (binding.getStrength() == BindingStrength.REQUIRED)
-      			warning(errors, IssueType.CODEINVALID, element.line(), element.col(), path, false, "The value provided is not in the value set " + describeReference(binding.getValueSet()) + " (" + vs.getUrl() + ", and a code is required from this value set");
+              rule(errors, IssueType.CODEINVALID, element.line(), element.col(), path, ok, "Coded value {0} is not in value set {1} ({2})", value, describeReference(binding.getValueSet()),
+                  vs.getUrl());
             else if (binding.getStrength() == BindingStrength.EXTENSIBLE)
-      			warning(errors, IssueType.CODEINVALID, element.line(), element.col(), path, false, "The value provided is not in the value set " + describeReference(binding.getValueSet()) + " (" + vs.getUrl() + ", and a code should come from this value set unless it has no suitable code");
+              warning(errors, IssueType.CODEINVALID, element.line(), element.col(), path, ok, "Coded value {0} is not in value set {1} ({2})", value, describeReference(binding.getValueSet()),
-      		else if (binding.getStrength() == BindingStrength.PREFERRED)
+                  vs.getUrl());
-      			hint(errors, IssueType.CODEINVALID, element.line(), element.col(), path, false,  "The value provided is not in the value set " + describeReference(binding.getValueSet()) + " (" + vs.getUrl() + ", and a code is recommended to come from this value set");
+            else
+              hint(errors, IssueType.CODEINVALID, element.line(), element.col(), path, ok, "Coded value {0} is not in value set {1} ({2})", value, describeReference(binding.getValueSet()),
+                  vs.getUrl());
+          }
+        } catch (ETooCostly e) {
+          if (e.getMessage() == null)
+            warning(errors, IssueType.CODEINVALID, element.line(), element.col(), path, false,
+                "Exception opening value set " + vs.getUrl() + " for " + describeReference(binding.getValueSet()) + ": --Null--");
+          else
+            warning(errors, IssueType.CODEINVALID, element.line(), element.col(), path, false,
+                "Exception opening value set " + vs.getUrl() + " for " + describeReference(binding.getValueSet()) + ": " + e.getMessage());
         }
       }
     } else
@@ -883,7 +927,7 @@ public class InstanceValidator extends BaseValidator implements IResourceValidat
     return context;
   }
 
-  private ElementDefinition getCriteriaForDiscriminator(String path, ElementDefinition ed, String discriminator, StructureDefinition profile) throws Exception {
+  private ElementDefinition getCriteriaForDiscriminator(String path, ElementDefinition ed, String discriminator, StructureDefinition profile, List<ValidationMessage> errors) throws Exception {
     List<ElementDefinition> childDefinitions = ProfileUtilities.getChildMap(profile, ed);
     List<ElementDefinition> snapshot = null;
     if (childDefinitions.isEmpty()) {
@@ -892,14 +936,18 @@ public class InstanceValidator extends BaseValidator implements IResourceValidat
         throw new Exception("Error in profile for " + path + " no children, no type");
       if (ed.getType().size() > 1)
         throw new Exception("Error in profile for " + path + " multiple types defined in slice discriminator");
-      StructureDefinition type;
+      
+      String url;
       if (ed.getType().get(0).hasProfile()) {
-        // need to do some special processing for reference here...
+        url = ed.getType().get(0).getProfile().get(0).getValue();
-        if (ed.getType().get(0).getCode().equals("Reference"))
+      } else {
-          discriminator = discriminator.substring(discriminator.indexOf(".")+1);
+        url = "http://hl7.org/fhir/StructureDefinition/" + ed.getType().get(0).getCode();
-        type = context.fetchResource(StructureDefinition.class, ed.getType().get(0).getProfile().get(0).getValue());
+      }
-      } else
+      StructureDefinition type = context.fetchResource(StructureDefinition.class, url);
-        type = context.fetchResource(StructureDefinition.class, "http://hl7.org/fhir/StructureDefinition/" + ed.getType().get(0).getCode());
+      if (type == null) {
+        super.fail(errors, IssueType.INCOMPLETE, path, false, "Failed to retrieve StructureDefinition with URL: " + url);
+        return null;
+      }
       snapshot = type.getSnapshot().getElement();
       ed = snapshot.get(0);
     } else {
@@ -950,8 +998,7 @@ public class InstanceValidator extends BaseValidator implements IResourceValidat
   }
 
   private Element getValueForDiscriminator(WrapperElement element, String discriminator, ElementDefinition criteria) {
-    // throw new Error("validation of slices not done yet");
+    throw new Error("validation of slices not done yet");
-    return null;
   }
 
   private ValueSet getValueSet(String system) throws Exception {
@@ -968,25 +1015,13 @@ public class InstanceValidator extends BaseValidator implements IResourceValidat
 
   private boolean isAbsolute(String uri) {
     return Utilities.noString(uri) || uri.startsWith("http:") || uri.startsWith("https:") || uri.startsWith("urn:uuid:") || uri.startsWith("urn:oid:") || uri.startsWith("urn:ietf:")
-        || uri.startsWith("urn:iso:") || isValidFHIRUrn(uri);
+        || uri.startsWith("urn:iso:");
-  }
-
-  private boolean isValidFHIRUrn(String uri) {
-    return (uri.equals("urn:x-fhir:uk:id:nhs-number"));
   }
 
   public boolean isAnyExtensionsAllowed() {
     return anyExtensionsAllowed;
   }
 
-  private boolean isParametersEntry(String path) {
-    String[] parts = path.split("\\/");
-    if (path.startsWith("/f:"))
-      return parts.length == 4 && parts[parts.length-3].equals("f:Parameters") && parts[parts.length-2].startsWith("f:parameter") && parts[parts.length-1].startsWith("f:resource");
-    else
-      return parts.length == 4 && parts[parts.length-3].equals("Parameters") && parts[parts.length-2].startsWith("parameter") && parts[parts.length-1].startsWith("resource");
-  }
-  
   private boolean isBundleEntry(String path) {
     String[] parts = path.split("\\/");
     if (path.startsWith("/f:"))
@@ -995,6 +1030,14 @@ public class InstanceValidator extends BaseValidator implements IResourceValidat
       return parts.length > 2 && parts[parts.length - 1].equals("resource") && ((parts.length > 2 && parts[parts.length - 3].equals("entry")) || parts[parts.length - 2].equals("entry"));
   }
 
+  private boolean isParametersEntry(String path) {
+    String[] parts = path.split("\\/");
+    if (path.startsWith("/f:"))
+      return parts.length == 4 && parts[parts.length-3].equals("f:Parameters") && parts[parts.length-2].startsWith("f:parameter") && parts[parts.length-1].startsWith("f:resource");
+    else
+      return parts.length == 4 && parts[parts.length-3].equals("Parameters") && parts[parts.length-2].startsWith("parameter") && parts[parts.length-1].startsWith("resource");
+  }
+  
   private boolean isPrimitiveType(String type) {
     return type.equalsIgnoreCase("boolean") || type.equalsIgnoreCase("integer") || type.equalsIgnoreCase("string") || type.equalsIgnoreCase("decimal") || type.equalsIgnoreCase("uri")
         || type.equalsIgnoreCase("base64Binary") || type.equalsIgnoreCase("instant") || type.equalsIgnoreCase("date") || type.equalsIgnoreCase("uuid") || type.equalsIgnoreCase("id")
@@ -1096,9 +1139,9 @@ public class InstanceValidator extends BaseValidator implements IResourceValidat
     } else {
       // split into base, type, and id
       String u = null;
-      if (fullUrl != null && fullUrl.endsWith(type+"/"+id))
+      if (fullUrl != null && fullUrl.endsWith(type + "/" + id))
         // fullUrl = complex
-        u = fullUrl.substring((type+"/"+id).length())+ref;
+        u = fullUrl.substring((type + "/" + id).length()) + ref;
       String[] parts = ref.split("\\/");
       if (parts.length >= 2) {
         String t = parts[0];
@@ -1179,15 +1222,19 @@ public class InstanceValidator extends BaseValidator implements IResourceValidat
    *          - the definition of how slicing is determined
    * @param ed
    *          - the slice for which to test membership
+   * @param errors 
    * @return
    * @throws Exception
    */
-  private boolean sliceMatches(WrapperElement element, String path, ElementDefinition slice, ElementDefinition ed, StructureDefinition profile) throws Exception {
+  private boolean sliceMatches(WrapperElement element, String path, ElementDefinition slice, ElementDefinition ed, StructureDefinition profile, List<ValidationMessage> errors) throws Exception {
     if (!slice.getSlicing().hasDiscriminator())
       return false; // cannot validate in this case
     for (StringType s : slice.getSlicing().getDiscriminator()) {
       String discriminator = s.getValue();
-      ElementDefinition criteria = getCriteriaForDiscriminator(path, ed, discriminator, profile);
+      ElementDefinition criteria = getCriteriaForDiscriminator(path, ed, discriminator, profile, errors);
+      if (criteria == null) {
+        return false;
+      }
       if (discriminator.equals("url") && criteria.getPath().equals("Extension.url")) {
         if (!element.getAttribute("url").equals(((UriType) criteria.getFixed()).asStringValue()))
           return false;
@@ -1207,7 +1254,7 @@ public class InstanceValidator extends BaseValidator implements IResourceValidat
     // profile is valid, and matches the resource name
     if (rule(errors, IssueType.STRUCTURE, element.line(), element.col(), stack.getLiteralPath(), profile.hasSnapshot(),
         "StructureDefinition has no snapshot - validation is against the snapshot, so it must be provided")) {
-      validateElement(errors, profile, profile.getSnapshot().getElement().get(0), null, null, element, element.getName(), stack, false);
+      validateElement(errors, profile, profile.getSnapshot().getElement().get(0), null, null, element, element.getName(), stack);
 
       checkDeclaredProfiles(errors, element, stack);
 
@@ -1638,7 +1685,7 @@ public class InstanceValidator extends BaseValidator implements IResourceValidat
   // firstBase = ebase == null ? base : ebase;
 
   private void validateElement(List<ValidationMessage> errors, StructureDefinition profile, ElementDefinition definition, StructureDefinition cprofile, ElementDefinition context,
-      WrapperElement element, String actualType, NodeStack stack, boolean inCodeableConcept) throws Exception {
+      WrapperElement element, String actualType, NodeStack stack) throws Exception {
     // irrespective of what element it is, it cannot be empty
     if (element.isXml()) {
       rule(errors, IssueType.INVALID, element.line(), element.col(), stack.getLiteralPath(), FormatUtilities.FHIR_NS.equals(element.getNamespace()),
@@ -1679,7 +1726,7 @@ public class InstanceValidator extends BaseValidator implements IResourceValidat
             match = nameMatches(ei.name, tail(ed.getPath()));
           } else {
             if (nameMatches(ei.name, tail(ed.getPath())))
-              match = sliceMatches(ei.element, ei.path, slice, ed, profile);
+              match = sliceMatches(ei.element, ei.path, slice, ed, profile, errors);
           }
           if (match) {
             if (rule(errors, IssueType.INVALID, ei.line(), ei.col(), ei.path, ei.definition == null, "Element matches more than one slice"))
@@ -1760,7 +1807,6 @@ public class InstanceValidator extends BaseValidator implements IResourceValidat
         String localStackLiterapPath = localStack.getLiteralPath();
         String eiPath = ei.path;
         assert(eiPath.equals(localStackLiterapPath)) : "ei.path: " + ei.path + "  -  localStack.getLiterapPath: " + localStackLiterapPath;
-        boolean thisIsCodeableConcept = false;
 
         if (type != null) {
           if (isPrimitiveType(type))
@@ -1769,11 +1815,10 @@ public class InstanceValidator extends BaseValidator implements IResourceValidat
             if (type.equals("Identifier"))
               checkIdentifier(errors, ei.path, ei.element, ei.definition);
             else if (type.equals("Coding"))
-              checkCoding(errors, ei.path, ei.element, profile, ei.definition, inCodeableConcept);
+              checkCoding(errors, ei.path, ei.element, profile, ei.definition);
-            else if (type.equals("CodeableConcept")) {
+            else if (type.equals("CodeableConcept"))
               checkCodeableConcept(errors, ei.path, ei.element, profile, ei.definition);
-              thisIsCodeableConcept = true;
+            else if (type.equals("Reference"))
-            } else if (type.equals("Reference"))
               checkReference(errors, ei.path, ei.element, profile, ei.definition, actualType, localStack);
 
             if (type.equals("Extension"))
@@ -1784,13 +1829,13 @@ public class InstanceValidator extends BaseValidator implements IResourceValidat
             else {
               StructureDefinition p = getProfileForType(type);
               if (rule(errors, IssueType.STRUCTURE, ei.line(), ei.col(), ei.path, p != null, "Unknown type " + type)) {
-                validateElement(errors, p, p.getSnapshot().getElement().get(0), profile, ei.definition, ei.element, type, localStack, thisIsCodeableConcept);
+                validateElement(errors, p, p.getSnapshot().getElement().get(0), profile, ei.definition, ei.element, type, localStack);
               }
             }
           }
         } else {
           if (rule(errors, IssueType.STRUCTURE, ei.line(), ei.col(), stack.getLiteralPath(), ei.definition != null, "Unrecognised Content " + ei.name))
-            validateElement(errors, profile, ei.definition, null, null, ei.element, type, localStack, false);
+            validateElement(errors, profile, ei.definition, null, null, ei.element, type, localStack);
         }
       }
     }
@@ -1830,15 +1875,6 @@ public class InstanceValidator extends BaseValidator implements IResourceValidat
         ok = rule(errors, IssueType.INVALID, element.line(), element.col(), stack.addToLiteralPath(resourceName), profile != null, "No profile found for resource type '" + resourceName + "'");
       } else {
         String type = profile.hasConstrainedType() ? profile.getConstrainedType() : profile.getName();
-        // special case: we have a bundle, and the profile is not for a bundle. We'll try the first entry instead 
-        if (!type.equals(resourceName) && resourceName.equals("Bundle")) {
-          WrapperElement first = getFirstEntry(element);
-          if (first != null && first.getResourceType().equals(type)) {
-            element = first;
-            resourceName = element.getResourceType();
-            needsId = false;
-          }
-        }
         ok = rule(errors, IssueType.INVALID, -1, -1, stack.addToLiteralPath(resourceName), type.equals(resourceName),
             "Specified profile type was '" + profile.getConstrainedType() + "', but resource type was '" + resourceName + "'");
       }
@@ -1852,18 +1888,6 @@ public class InstanceValidator extends BaseValidator implements IResourceValidat
     }
   }
 
-  private WrapperElement getFirstEntry(WrapperElement bundle) {
-    List<WrapperElement> list = new ArrayList<WrapperElement>();
-    bundle.getNamedChildren("entry", list);
-    if (list.isEmpty())
-      return null;
-    WrapperElement resource = list.get(0).getNamedChild("resource");
-    if (resource == null)
-      return null;
-    else
-      return resource.getFirstChild();
-  }
-
   private void validateSections(List<ValidationMessage> errors, List<WrapperElement> entries, WrapperElement focus, NodeStack stack, String fullUrl, String id) {
     List<WrapperElement> sections = new ArrayList<WrapperElement>();
     focus.getNamedChildren("entry", sections);
@@ -1877,8 +1901,7 @@ public class InstanceValidator extends BaseValidator implements IResourceValidat
   }
 
   private boolean valueMatchesCriteria(Element value, ElementDefinition criteria) {
-    // throw new Error("validation of slices not done yet");
+    throw new Error("validation of slices not done yet");
-    return false;
   }
 
   private boolean yearIsValid(String v) {
@@ -2079,6 +2102,7 @@ public class InstanceValidator extends BaseValidator implements IResourceValidat
     public int line() {
       return line;
     }
+
   }
 
   public class ElementInfo {
@@ -2148,7 +2172,9 @@ public class InstanceValidator extends BaseValidator implements IResourceValidat
     private void createChildren() {
       // System.out.println(" ..: "+path);
       // we're going to make this look like the XML
-      if (element != null) {
+      if (element == null)
+        throw new Error("not done yet");
+
       if (element instanceof JsonPrimitive) {
         // we may have an element_ too
         if (_element != null && _element instanceof JsonObject)
@@ -2164,10 +2190,6 @@ public class InstanceValidator extends BaseValidator implements IResourceValidat
       } else
         throw new Error("unexpected condition: " + element.getClass().getName());
     }
-      if (_element != null) {
-
-      }
-    }
 
     @Override
     public String getAttribute(String name) {

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

@@ -9,12 +9,14 @@ import static org.mockito.Matchers.any;
 import static org.mockito.Mockito.mock;
 import static org.mockito.Mockito.when;
 
+import java.io.IOException;
 import java.util.ArrayList;
 import java.util.HashMap;
 import java.util.List;
 import java.util.Map;
 
 import org.apache.commons.io.IOUtils;
+import org.apache.commons.lang3.builder.EqualsBuilder;
 import org.hl7.fhir.instance.hapi.validation.DefaultProfileValidationSupport;
 import org.hl7.fhir.instance.hapi.validation.FhirInstanceValidator;
 import org.hl7.fhir.instance.hapi.validation.IValidationSupport;
@@ -24,11 +26,13 @@ import org.hl7.fhir.instance.model.Observation;
 import org.hl7.fhir.instance.model.Observation.ObservationStatus;
 import org.hl7.fhir.instance.model.Patient;
 import org.hl7.fhir.instance.model.StringType;
+import org.hl7.fhir.instance.model.StructureDefinition;
 import org.hl7.fhir.instance.model.ValueSet;
 import org.hl7.fhir.instance.model.ValueSet.ConceptDefinitionComponent;
 import org.hl7.fhir.instance.model.ValueSet.ConceptSetComponent;
 import org.hl7.fhir.instance.model.ValueSet.ValueSetExpansionComponent;
 import org.hl7.fhir.instance.model.api.IBaseResource;
+import org.hl7.fhir.instance.validation.InstanceValidator;
 import org.junit.AfterClass;
 import org.junit.Before;
 import org.junit.Rule;
@@ -45,7 +49,27 @@ public class FhirInstanceValidatorTest {
 
   private static FhirContext ourCtx = FhirContext.forDstu2Hl7Org();
   private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(FhirInstanceValidatorTest.class);
-  private static DefaultProfileValidationSupport ourDefaultValidationSupport = new DefaultProfileValidationSupport();
+  private static DefaultProfileValidationSupport ourDefaultValidationSupport = new DefaultProfileValidationSupport() {
+    @Override
+    public <T extends IBaseResource> T fetchResource(FhirContext theContext, Class<T> theClass, String theUri) {
+      if (theUri.equals("http://fhir.hl7.org.nz/dstu2/StructureDefinition/ohAllergyIntolerance")) {
+        String contents;
+        try {
+          contents = IOUtils.toString(getClass().getResourceAsStream("/allergyintolerance-sd-david.json"), "UTF-8");
+        } catch (IOException e) {
+          throw new Error(e);
+        }
+        StructureDefinition sd = ourCtx.newJsonParser().parseResource(StructureDefinition.class, contents);
+        return (T) sd;
+      }
+      T retVal = super.fetchResource(theContext, theClass, theUri);
+      if (retVal == null) {
+        ourLog.warn("Can not fetch: {}", theUri);
+      }
+      return retVal;
+    }
+    
+  };
   private FhirInstanceValidator myInstanceVal;
   private IValidationSupport myMockSupport;
 
@@ -102,9 +126,10 @@ public class FhirInstanceValidatorTest {
         .thenAnswer(new Answer<IBaseResource>() {
           @Override
           public IBaseResource answer(InvocationOnMock theInvocation) throws Throwable {
-            IBaseResource retVal = ourDefaultValidationSupport.fetchResource(
+            FhirContext fhirContext = (FhirContext) theInvocation.getArguments()[0];
-                (FhirContext) theInvocation.getArguments()[0], (Class<IBaseResource>) theInvocation.getArguments()[1],
+            Class<IBaseResource> type = (Class<IBaseResource>) theInvocation.getArguments()[1];
-                (String) theInvocation.getArguments()[2]);
+            String uri = (String) theInvocation.getArguments()[2];
+            IBaseResource retVal = ourDefaultValidationSupport.fetchResource(fhirContext, type, uri);
             ourLog.info("fetchResource({}, {}) : {}",
                 new Object[] { theInvocation.getArguments()[1], theInvocation.getArguments()[2], retVal });
             return retVal;
@@ -188,6 +213,20 @@ public class FhirInstanceValidatorTest {
     assertEquals(output.toString(), 0, output.getMessages().size());
   }
 
+  /**
+   * Received by email from David Hay
+   */
+  @Test
+  public void testValidateAllergyIntoleranceFromDavid() throws Exception {
+
+    String input = IOUtils.toString(getClass().getResourceAsStream("/allergyintolerance-david.json"), "UTF-8");
+    
+    // Just make sure this doesn't crash
+    ValidationResult output = myVal.validateWithResult(input);
+    ourLog.info(output.toString());
+
+  }
+
   @Test
   public void testValidateRawJsonResourceBadAttributes() {
     // @formatter:off
@@ -327,7 +366,7 @@ public class FhirInstanceValidatorTest {
         + "   <code>\n" + "      <text value=\"No code here!\"/>\n" + "   </code>\n" + "</Observation>";
     ValidationResult output = myVal.validateWithResult(input);
     assertEquals(
-        "The value provided is not in the value set http://hl7.org/fhir/ValueSet/observation-status (http://hl7.org/fhir/ValueSet/observation-status, and a code is required from this value set",
+        "Coded value notvalidcode is not in value set http://hl7.org/fhir/ValueSet/observation-status (http://hl7.org/fhir/ValueSet/observation-status)",
         output.getMessages().get(0).getMessage());
   }
 
@@ -342,16 +381,16 @@ public class FhirInstanceValidatorTest {
 
     ValidationResult output = myVal.validateWithResult(patient);
     List<SingleValidationMessage> all = logResultsAndReturnAll(output);
-    assertEquals(1, all.size());
+    assertEquals(2, all.size());
     assertEquals("/f:Patient/f:identifier/f:type", all.get(0).getLocationString());
-    assertEquals("None of the codes provided are in the value set http://hl7.org/fhir/ValueSet/identifier-type (http://hl7.org/fhir/ValueSet/identifier-type, and a code should come from this value set unless it has no suitable code", all.get(0).getMessage());
+    assertEquals("None of the codes are in the expected value set http://hl7.org/fhir/ValueSet/identifier-type (http://hl7.org/fhir/ValueSet/identifier-type)", all.get(0).getMessage());
     assertEquals(ResultSeverityEnum.WARNING, all.get(0).getSeverity());
 
     patient = new Patient();
     patient.addIdentifier().setSystem("http://system").setValue("12345").getType().addCoding().setSystem("http://hl7.org/fhir/v2/0203").setCode("MR");
 
     output = myVal.validateWithResult(patient);
-    all = logResultsAndReturnAll(output);
+    all = logResultsAndReturnNonInformationalOnes(output);
     assertEquals(0, all.size());
   }
 
@@ -367,8 +406,8 @@ public class FhirInstanceValidatorTest {
 
     ValidationResult output = myVal.validateWithResult(input);
     List<SingleValidationMessage> errors = logResultsAndReturnNonInformationalOnes(output);
-    assertEquals(errors.toString(), 0, errors.size());
+    assertEquals(errors.toString(), 1, errors.size());
-
+    assertEquals("Unable to validate code \"12345\" in code system \"http://loinc.org\"", errors.get(0).getMessage());
   }
 
   @Test
@@ -402,8 +441,8 @@ public class FhirInstanceValidatorTest {
 
     ValidationResult output = myVal.validateWithResult(input);
     List<SingleValidationMessage> errors = logResultsAndReturnNonInformationalOnes(output);
-    assertEquals(errors.toString(), 0, errors.size());
+    assertEquals(errors.toString(), 1, errors.size());
-    
+    assertEquals("Unable to validate code \"1234\" in code system \"http://loinc.org\"", errors.get(0).getMessage());   
     
   }
 
@@ -418,7 +457,7 @@ public class FhirInstanceValidatorTest {
     input.getCode().addCoding().setSystem("http://acme.org").setCode("12345");
 
     ValidationResult output = myVal.validateWithResult(input);
-    List<SingleValidationMessage> errors = logResultsAndReturnAll(output);
+    List<SingleValidationMessage> errors = logResultsAndReturnNonInformationalOnes(output);
     assertEquals(errors.toString(), 0, errors.size());
   }
 

hapi-fhir-structures-hl7org-dstu2/src/test/resources/allergyintolerance-david.json

@@ -0,0 +1,152 @@
+{
+  "resourceType": "AllergyIntolerance",
+  "id": "84651",
+  "meta": {
+    "versionId": "1",
+    "lastUpdated": "2016-05-19T15:43:49.815-04:00",
+    "profile": [
+      "http://fhir.hl7.org.nz/dstu2/StructureDefinition/ohAllergyIntolerance"
+    ]
+  },
+  "extension": [
+    {
+      "url": "http://fhir.hl7.org.nz/dstu2/StructureDefinition/al-endDate",
+      "valueDateTime": "2016-05-03"
+    },
+    {
+      "url": "http://fhir.hl7.org.nz/dstu2/StructureDefinition/al-informantRole",
+      "valueCodeableConcept": {
+        "coding": [
+          {
+            "system": "http://snomed.info/sct",
+            "version": "http://snomed.info/sct/32506021000036107/version/20150531",
+            "code": "133932002",
+            "display": "Carer"
+          }
+        ]
+      }
+    },
+    {
+      "url": "http://fhir.hl7.org.nz/dstu2/StructureDefinition/al-reasonClosed",
+      "valueCodeableConcept": {
+        "coding": [
+          {
+            "system": "http://orionhealth.com/problem-list/adverse-reaction-reason-closed",
+            "code": "1",
+            "display": "Disproven"
+          }
+        ]
+      }
+    },
+    {
+      "url": "http://fhir.hl7.org.nz/dstu2/StructureDefinition/al-classification",
+      "valueCodeableConcept": {
+        "coding": [
+          {
+            "system": "http://snomed.info/sct",
+            "version": "http://snomed.info/sct/32506021000036107/version/20150531",
+            "code": "419076005",
+            "display": "Allergic reaction"
+          }
+        ]
+      }
+    }
+  ],
+  "language": [
+    "en"
+  ],
+  "identifier": [
+    {
+      "system": "http://orionhealth.com/identifier/problem-list/ORGNISATION_ORION",
+      "value": "2.25.148135789146703435349240718177383549558.8.4.4.0/522911"
+    }
+  ],
+  "patient": {
+    "reference": "Patient/64909"
+  },
+  "substance": {
+    "coding": [
+      {
+        "system": "http://snomed.info/sct",
+        "version": "http://snomed.info/sct/32506021000036107/version/20150531",
+        "code": "84430008",
+        "display": "Cross reacting antibody"
+      }
+    ]
+  },
+  "status": "inactive",
+  "criticality": "CRITH",
+  "category": "environment",
+  "reaction": [
+    {
+      "certainty": "likely",
+      "_certainty": {
+        "extension": [
+          {
+            "url": "http://fhir.hl7.org.nz/dstu2/StructureDefinition/originalValue",
+            "valueCodeableConcept": {
+              "coding": [
+                {
+                  "system": "http://orionhealth.com/problem-list/adverse-reaction-certainty",
+                  "code": "SUSPECTED",
+                  "display": "Suspected"
+                }
+              ]
+            }
+          }
+        ]
+      },
+      "manifestation": [
+        {
+          "extension": [
+            {
+              "url": "http://fhir.hl7.org.nz/dstu2/StructureDefinition/al-manifestationSeverity",
+              "valueCodeableConcept": {
+                "coding": [
+                  {
+                    "system": "http://snomed.info/sct",
+                    "version": "http://snomed.info/sct/900000000000207008/version/20150531",
+                    "code": "442452003",
+                    "display": "Life-Threatening"
+                  }
+                ]
+              }
+            }
+          ],
+          "coding": [
+            {
+              "system": "http://orionhealth.com/problem-list/clinical-manifestation",
+              "code": "FT",
+              "display": "rlo"
+            }
+          ]
+        },
+        {
+          "extension": [
+            {
+              "url": "http://fhir.hl7.org.nz/dstu2/StructureDefinition/al-manifestationSeverity",
+              "valueCodeableConcept": {
+                "coding": [
+                  {
+                    "system": "http://orionhealth.com/problem-list/severity",
+                    "code": "UNKNOWN",
+                    "display": "Unknown"
+                  }
+                ]
+              }
+            }
+          ],
+          "coding": [
+            {
+              "system": "http://snomed.info/sct",
+              "version": "http://snomed.info/sct/32506021000036107/version/20150531",
+              "code": "95332009",
+              "display": "Rash of systemic lupus erythematosus"
+            }
+          ]
+        }
+      ],
+      "severity": "severe"
+    }
+  ]
+}

src/changes/changes.xml

@@ -234,6 +234,9 @@
 				had any extensions. Thanks to GitHub user @Virdulys for submitting and
 				providing a test case!
 			</action>
+			<action type="add">
+				Update DSTU2 InstanceValidator to latest version from upstream 
+			</action>
 		</release>
 		<release version="1.5" date="2016-04-20">
 			<action type="fix" issue="339">

src/site/resources/CNAME

@@ -0,0 +1 @@
+hapifhir.io