FIx validation for resources using v2 tables

hapi-fhir-base/src/main/resources/ca/uhn/fhir/narrative/Medication.html

@@ -11,7 +11,14 @@ a browser.
 <!--*/-->
 
 <div>
+	<th:block th:switch="${fhirVersion}">
+		<th:block th:case="'DSTU1'">
 			<div class="hapiHeaderText" th:if="${not resource.nameElement.empty}" th:narrative="${resource.name}"></div>	
+		</th:block>
+		<th:block th:case="*">
+			<div class="hapiHeaderText" th:if="${not resource.code.empty}" th:narrative="${resource.code}"></div>	
+		</th:block>
+	</th:block>
 </div>
 
 <!--/*-->

hapi-fhir-jpaserver-base/src/main/resources/fhir-spring-subscription-config-dstu2.xml

@@ -13,7 +13,7 @@
 	<context:annotation-config />
 
 	<websocket:handlers>
-		<websocket:mapping path="/baseDstu2/websocket" handler="mySubscriptionWebsocketHandler" />
+		<websocket:mapping path="/websocket/dstu2" handler="mySubscriptionWebsocketHandler" />
 	</websocket:handlers>
 
 	<!-- 

hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/provider/SubscriptionsDstu2Test.java

@@ -183,7 +183,7 @@ public class SubscriptionsDstu2Test extends BaseResourceProviderDstu2Test {
 		SimpleEchoSocket socket = new SimpleEchoSocket(subsId);
 		try {
 			client.start();
-			URI echoUri = new URI("ws://localhost:" + ourPort + "/baseDstu2/websocket");
+			URI echoUri = new URI("ws://localhost:" + ourPort + "/websocket/dstu2");
 			ClientUpgradeRequest request = new ClientUpgradeRequest();
 			client.connect(socket, echoUri, request);
 			ourLog.info("Connecting to : {}", echoUri);

hapi-fhir-jpaserver-uhnfhirtest/src/main/java/ca/uhn/fhirtest/DerbyNetworkServer.java

@@ -1,5 +1,9 @@
 package ca.uhn.fhirtest;
 
+import java.io.IOException;
+import java.io.PrintWriter;
+import java.io.Writer;
+
 import org.apache.derby.drda.NetworkServerControl;
 import org.springframework.beans.factory.DisposableBean;
 import org.springframework.beans.factory.InitializingBean;
@@ -22,7 +26,30 @@ public class DerbyNetworkServer implements InitializingBean, DisposableBean {
 	@Override
 	public void afterPropertiesSet() throws Exception {
 		server = new NetworkServerControl();
-		server.start (null);
+		Writer w = new Writer() {
+
+			@Override
+			public void write(char[] theCbuf, int theOff, int theLen) throws IOException {
+				ourLog.info("[DERBY] " + new String(theCbuf, theOff, theLen));
+			}
+
+			@Override
+			public void flush() throws IOException {
+				// nothing
+			}
+
+			@Override
+			public void close() throws IOException {
+				// nothing
+			}};
+		server.start (new PrintWriter(w));
+	}
+
+	
+	public static void main(String[] args) throws Exception {
+		DerbyNetworkServer s = new DerbyNetworkServer();
+		s.afterPropertiesSet();
+		s.destroy();
 	}
 	
 }

hapi-fhir-jpaserver-uhnfhirtest/src/main/java/ca/uhn/fhirtest/TestRestfulServer.java

@@ -8,6 +8,7 @@ import javax.servlet.ServletException;
 import javax.servlet.http.HttpServletRequest;
 
 import org.apache.commons.lang3.StringUtils;
+import org.springframework.context.ApplicationContext;
 import org.springframework.context.support.ClassPathXmlApplicationContext;
 import org.springframework.web.context.ContextLoaderListener;
 import org.springframework.web.context.WebApplicationContext;
@@ -35,7 +36,7 @@ public class TestRestfulServer extends RestfulServer {
 
 	private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(TestRestfulServer.class);
 
-	private ClassPathXmlApplicationContext myAppCtx;
+	private ApplicationContext myAppCtx;
 
 	@SuppressWarnings("unchecked")
 	@Override
@@ -44,6 +45,7 @@ public class TestRestfulServer extends RestfulServer {
 
 		// Get the spring context from the web container (it's declared in web.xml)
 		WebApplicationContext parentAppCtx = ContextLoaderListener.getCurrentWebApplicationContext();
+		myAppCtx = (parentAppCtx);
 
 		// These two parmeters are also declared in web.xml
 		String implDesc = getInitParameter("ImplementationDescription");
@@ -64,9 +66,6 @@ public class TestRestfulServer extends RestfulServer {
 		String baseUrlProperty;
 		switch (fhirVersionParam.trim().toUpperCase()) {
 		case "DSTU1": {
-			myAppCtx = new ClassPathXmlApplicationContext(new String[] { 
-					"hapi-fhir-server-database-config-dstu1.xml", 
-					"hapi-fhir-server-resourceproviders-dstu1.xml"}, parentAppCtx);
 			setFhirContext(FhirContext.forDstu1());
 			beans = myAppCtx.getBean("myResourceProvidersDstu1", List.class);
 			systemProviderDstu1 = myAppCtx.getBean("mySystemProviderDstu1", JpaSystemProviderDstu1.class);
@@ -79,11 +78,6 @@ public class TestRestfulServer extends RestfulServer {
 			break;
 		}
 		case "DSTU2": {
-			myAppCtx = new ClassPathXmlApplicationContext(new String[] {
-					"hapi-fhir-server-database-config-dstu2.xml", 
-					"hapi-fhir-server-resourceproviders-dstu2.xml", 
-					"fhir-spring-subscription-config-dstu2.xml"
-					}, parentAppCtx);
 			setFhirContext(FhirContext.forDstu2());
 			beans = myAppCtx.getBean("myResourceProvidersDstu2", List.class);
 			systemProviderDstu2 = myAppCtx.getBean("mySystemProviderDstu2", JpaSystemProviderDstu2.class);

hapi-fhir-jpaserver-uhnfhirtest/src/main/webapp/WEB-INF/web.xml

@@ -12,6 +12,11 @@
 			/WEB-INF/hapi-fhir-server-config.xml
 			/WEB-INF/hapi-fhir-tester-application-context.xml
 			/WEB-INF/hapi-fhir-tester-config.xml
+			classpath:/hapi-fhir-server-database-config-dstu1.xml 
+			classpath:/hapi-fhir-server-database-config-dstu2.xml 
+			classpath:hapi-fhir-server-resourceproviders-dstu1.xml
+			classpath:hapi-fhir-server-resourceproviders-dstu2.xml
+			classpath:fhir-spring-subscription-config-dstu2.xml
 		</param-value>
 	</context-param>
 
@@ -25,6 +30,7 @@
 			<param-value>
 				/WEB-INF/hapi-fhir-tester-application-context.xml
 				/WEB-INF/hapi-fhir-tester-config.xml
+				classpath:fhir-spring-subscription-config-dstu2.xml
 			</param-value>
 		</init-param>
 		<load-on-startup>2</load-on-startup>

hapi-fhir-structures-dstu2/src/test/java/ca/uhn/fhir/narrative/DefaultThymeleafNarrativeGeneratorTestDstu2.java

@@ -1,5 +1,6 @@
 package ca.uhn.fhir.narrative;
 
+import static org.hamcrest.Matchers.containsString;
 import static org.junit.Assert.assertEquals;
 import static org.junit.Assert.assertThat;
 import static org.junit.Assert.assertTrue;
@@ -92,7 +93,6 @@ public class DefaultThymeleafNarrativeGeneratorTestDstu2 {
 
 	}
 
-
 	@Test
 	public void testGenerateDiagnosticReport() throws DataFormatException {
 		DiagnosticReport value = new DiagnosticReport();
@@ -216,4 +216,20 @@ public class DefaultThymeleafNarrativeGeneratorTestDstu2 {
 
 	}
 
+	@Test
+	public void testGenerateMedication() {
+		Medication med = new Medication();
+		med.getCode().setText("ciproflaxin");
+
+		NarrativeDt narrative = new NarrativeDt();
+		myGen.generateNarrative(med, narrative);
+
+		String string = narrative.getDiv().toString();
+		assertThat(string, containsString("ciproflaxin"));
+
+		String title = myGen.generateTitle(med);
+		assertEquals("ciproflaxin", title);
+
+	}
+
 }

hapi-fhir-structures-hl7org-dstu2/src/main/java/ca/uhn/fhir/validation/DefaultProfileValidationSupport.java

@@ -1,5 +1,7 @@
 package ca.uhn.fhir.validation;
 
+import static org.apache.commons.lang3.StringUtils.isNotBlank;
+
 import java.io.InputStream;
 import java.io.InputStreamReader;
 import java.io.UnsupportedEncodingException;
@@ -21,9 +23,10 @@ import ca.uhn.fhir.rest.server.exceptions.InternalErrorException;
 public class DefaultProfileValidationSupport implements IValidationSupport {
 
   private Map<String, ValueSet> myDefaultValueSets;
+  private Map<String, ValueSet> myCodeSystems;
 
   @Override
-	public boolean isCodeSystemSupported(String theSystem) {
+  public boolean isCodeSystemSupported(FhirContext theContext, String theSystem) {
     return false;
   }
 
@@ -70,17 +73,51 @@ public class DefaultProfileValidationSupport implements IValidationSupport {
   }
 
   @Override
-  public CodeValidationResult validateCode(String theCodeSystem, String theCode, String theDisplay) {
+  public CodeValidationResult validateCode(FhirContext theContext, String theCodeSystem, String theCode, String theDisplay) {
     return new CodeValidationResult(IssueSeverity.INFORMATION, "Unknown code: " + theCodeSystem + " / " + theCode);
   }
 
   @Override
-  public ValueSet fetchCodeSystem(String theSystem) {
+  public ValueSet fetchCodeSystem(FhirContext theContext, String theSystem) {
-    return null;
+    Map<String, ValueSet> codeSystems = myCodeSystems;
+    if (codeSystems == null) {
+      codeSystems = new HashMap<String, ValueSet>();
+
+      loadCodeSystems(theContext, codeSystems, "/org/hl7/fhir/instance/model/valueset/valuesets.xml");
+      loadCodeSystems(theContext, codeSystems, "/org/hl7/fhir/instance/model/valueset/v2-tables.xml");
+      loadCodeSystems(theContext, codeSystems, "/org/hl7/fhir/instance/model/valueset/v3-codesystems.xml");
+
+      myCodeSystems = codeSystems;
+    }
+
+    return codeSystems.get(theSystem);
+  }
+
+  private void loadCodeSystems(FhirContext theContext, Map<String, ValueSet> codeSystems, String file) {
+    InputStream valuesetText = DefaultProfileValidationSupport.class.getResourceAsStream(file);
+    if (valuesetText != null) {
+      InputStreamReader reader;
+      try {
+        reader = new InputStreamReader(valuesetText, "UTF-8");
+      } catch (UnsupportedEncodingException e) {
+        // Shouldn't happen!
+        throw new InternalErrorException("UTF-8 encoding not supported on this platform", e);
+      }
+
+      FhirContext ctx = FhirInstanceValidator.getHl7OrgDstu2Ctx(theContext);
+      Bundle bundle = ctx.newXmlParser().parseResource(Bundle.class, reader);
+      for (BundleEntryComponent next : bundle.getEntry()) {
+        ValueSet nextValueSet = (ValueSet) next.getResource();
+        String system = nextValueSet.getCodeSystem().getSystem();
+        if (isNotBlank(system)) {
+          codeSystems.put(system, nextValueSet);
+        }
+      }
+    }
   }
 
   @Override
-  public ValueSetExpansionComponent expandValueSet(ConceptSetComponent theInclude) {
+  public ValueSetExpansionComponent expandValueSet(FhirContext theContext, ConceptSetComponent theInclude) {
     return null;
   }
 

hapi-fhir-structures-hl7org-dstu2/src/main/java/ca/uhn/fhir/validation/FhirInstanceValidator.java

@@ -269,7 +269,7 @@ public class FhirInstanceValidator extends BaseValidatorBridge implements IValid
 
     @Override
     public ValueSetExpansionComponent expandVS(ConceptSetComponent theInc) {
-      return myValidationSupport.expandValueSet(theInc);
+      return myValidationSupport.expandValueSet(myCtx, theInc);
     }
 
     @Override
@@ -282,7 +282,7 @@ public class FhirInstanceValidator extends BaseValidatorBridge implements IValid
       if (myValidationSupport == null) {
         return null;
       } else {
-        return myValidationSupport.fetchCodeSystem(theSystem);
+        return myValidationSupport.fetchCodeSystem(myCtx, theSystem);
       }
     }
 
@@ -335,13 +335,13 @@ public class FhirInstanceValidator extends BaseValidatorBridge implements IValid
       if (myValidationSupport == null) {
         return false;
       } else {
-        return myValidationSupport.isCodeSystemSupported(theSystem);
+        return myValidationSupport.isCodeSystemSupported(myCtx, theSystem);
       }
     }
 
     @Override
     public ValidationResult validateCode(String theSystem, String theCode, String theDisplay) {
-      CodeValidationResult result = myValidationSupport.validateCode(theSystem, theCode, theDisplay);
+      CodeValidationResult result = myValidationSupport.validateCode(myCtx, theSystem, theCode, theDisplay);
       if (result == null) {
         return null;
       }

hapi-fhir-structures-hl7org-dstu2/src/main/java/ca/uhn/fhir/validation/IValidationSupport.java

@@ -18,7 +18,7 @@ public interface IValidationSupport {
    *          The portion to include
    * @return The expansion
    */
-  ValueSetExpansionComponent expandValueSet(ConceptSetComponent theInclude);
+  ValueSetExpansionComponent expandValueSet(FhirContext theContext, ConceptSetComponent theInclude);
 
   /**
    * Fetch a code system by ID
@@ -27,7 +27,7 @@ public interface IValidationSupport {
    *          The code system
    * @return The valueset (must not be null, but can be an empty ValueSet)
    */
-  ValueSet fetchCodeSystem(String theSystem);
+  ValueSet fetchCodeSystem(FhirContext theContext, String theSystem);
 
   /**
    * Loads a resource needed by the validation (a StructureDefinition, or a
@@ -53,7 +53,7 @@ public interface IValidationSupport {
    * @return Returns <code>true</code> if codes in the given code system can be
    *         validated
    */
-  boolean isCodeSystemSupported(String theSystem);
+  boolean isCodeSystemSupported(FhirContext theContext, String theSystem);
 
   /**
    * Validates that the given code exists and if possible returns a display
@@ -68,7 +68,7 @@ public interface IValidationSupport {
    *          The display name, if it should also be validated
    * @return Returns a validation result object
    */
-  CodeValidationResult validateCode(String theCodeSystem, String theCode, String theDisplay);
+  CodeValidationResult validateCode(FhirContext theContext, String theCodeSystem, String theCode, String theDisplay);
 
   public class CodeValidationResult {
     private ConceptDefinitionComponent definition;

hapi-fhir-structures-hl7org-dstu2/src/main/java/ca/uhn/fhir/validation/ValidationSupportChain.java

@@ -24,19 +24,19 @@ public class ValidationSupportChain implements IValidationSupport {
   }
 
   @Override
-  public ValueSetExpansionComponent expandValueSet(ConceptSetComponent theInclude) {
+  public ValueSetExpansionComponent expandValueSet(FhirContext theCtx, ConceptSetComponent theInclude) {
     for (IValidationSupport next : myChain) {
-      if (next.isCodeSystemSupported(theInclude.getSystem())) {
+      if (next.isCodeSystemSupported(theCtx, theInclude.getSystem())) {
-        return next.expandValueSet(theInclude);
+        return next.expandValueSet(theCtx, theInclude);
       }
     }
-    return myChain.get(0).expandValueSet(theInclude);
+    return myChain.get(0).expandValueSet(theCtx, theInclude);
   }
 
   @Override
-  public ValueSet fetchCodeSystem(String theSystem) {
+  public ValueSet fetchCodeSystem(FhirContext theCtx, String theSystem) {
     for (IValidationSupport next : myChain) {
-      ValueSet retVal = next.fetchCodeSystem(theSystem);
+      ValueSet retVal = next.fetchCodeSystem(theCtx, theSystem);
       if (retVal != null) {
         return retVal;
       }
@@ -56,9 +56,9 @@ public class ValidationSupportChain implements IValidationSupport {
   }
 
   @Override
-  public boolean isCodeSystemSupported(String theSystem) {
+  public boolean isCodeSystemSupported(FhirContext theCtx, String theSystem) {
     for (IValidationSupport next : myChain) {
-      if (next.isCodeSystemSupported(theSystem)) {
+      if (next.isCodeSystemSupported(theCtx, theSystem)) {
         return true;
       }
     }
@@ -66,13 +66,13 @@ public class ValidationSupportChain implements IValidationSupport {
   }
 
   @Override
-  public CodeValidationResult validateCode(String theCodeSystem, String theCode, String theDisplay) {
+  public CodeValidationResult validateCode(FhirContext theCtx, String theCodeSystem, String theCode, String theDisplay) {
     for (IValidationSupport next : myChain) {
-      if (next.isCodeSystemSupported(theCodeSystem)) {
+      if (next.isCodeSystemSupported(theCtx, theCodeSystem)) {
-        return next.validateCode(theCodeSystem, theCode, theDisplay);
+        return next.validateCode(theCtx, theCodeSystem, theCode, theDisplay);
       }
     }
-    return myChain.get(0).validateCode(theCodeSystem, theCode, theDisplay);
+    return myChain.get(0).validateCode(theCtx, theCodeSystem, theCode, theDisplay);
   }
 
 }

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

@@ -16,6 +16,7 @@ import org.apache.commons.io.IOUtils;
 import org.hl7.fhir.instance.model.CodeType;
 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.ValueSet;
 import org.hl7.fhir.instance.model.ValueSet.ConceptDefinitionComponent;
@@ -61,19 +62,19 @@ public class FhirInstanceValidatorTest {
     myValidConcepts = new ArrayList<String>();
 
     myMockSupport = mock(IValidationSupport.class);
-    when(myMockSupport.expandValueSet(any(ConceptSetComponent.class))).thenAnswer(new Answer<ValueSetExpansionComponent>() {
+    when(myMockSupport.expandValueSet(any(FhirContext.class), any(ConceptSetComponent.class))).thenAnswer(new Answer<ValueSetExpansionComponent>() {
       @Override
       public ValueSetExpansionComponent answer(InvocationOnMock theInvocation) throws Throwable {
         ConceptSetComponent arg = (ConceptSetComponent)theInvocation.getArguments()[0];
         ValueSetExpansionComponent retVal = mySupportedCodeSystemsForExpansion.get(arg.getSystem());
         if (retVal == null) {
-          retVal = myDefaultValidationSupport.expandValueSet(arg);
+          retVal = myDefaultValidationSupport.expandValueSet(any(FhirContext.class), arg);
         }
         ourLog.info("expandValueSet({}) : {}", new Object[] { theInvocation.getArguments()[0], retVal });
         return retVal;
       }
     });
-    when(myMockSupport.isCodeSystemSupported(any(String.class))).thenAnswer(new Answer<Boolean>() {
+    when(myMockSupport.isCodeSystemSupported(any(FhirContext.class), any(String.class))).thenAnswer(new Answer<Boolean>() {
       @Override
       public Boolean answer(InvocationOnMock theInvocation) throws Throwable {
         boolean retVal = mySupportedCodeSystemsForExpansion.containsKey(theInvocation.getArguments()[0]);
@@ -93,27 +94,28 @@ public class FhirInstanceValidatorTest {
             return retVal;
           }
         });
-    when(myMockSupport.validateCode(any(String.class), any(String.class), any(String.class)))
+    when(myMockSupport.validateCode(any(FhirContext.class), any(String.class), any(String.class), any(String.class)))
         .thenAnswer(new Answer<CodeValidationResult>() {
           @Override
           public CodeValidationResult answer(InvocationOnMock theInvocation) throws Throwable {
-            String system = (String) theInvocation.getArguments()[0];
+            FhirContext ctx = (FhirContext) theInvocation.getArguments()[0];
-            String code = (String) theInvocation.getArguments()[1];
+            String system = (String) theInvocation.getArguments()[1];
+            String code = (String) theInvocation.getArguments()[2];
             CodeValidationResult retVal;
             if (myValidConcepts.contains(system + "___" + code)) {
               retVal = new CodeValidationResult(new ConceptDefinitionComponent(new CodeType(code)));
             } else {
-              retVal = myDefaultValidationSupport.validateCode(system, code, (String) theInvocation.getArguments()[2]);
+              retVal = myDefaultValidationSupport.validateCode(ctx, system, code, (String) theInvocation.getArguments()[2]);
             }
             ourLog.info("validateCode({}, {}, {}) : {}",
                 new Object[] { system, code, (String) theInvocation.getArguments()[2], retVal });
             return retVal;
           }
         });
-    when(myMockSupport.fetchCodeSystem(any(String.class))).thenAnswer(new Answer<ValueSet>() {
+    when(myMockSupport.fetchCodeSystem(any(FhirContext.class), any(String.class))).thenAnswer(new Answer<ValueSet>() {
       @Override
       public ValueSet answer(InvocationOnMock theInvocation) throws Throwable {
-        ValueSet retVal = myDefaultValidationSupport.fetchCodeSystem((String) theInvocation.getArguments()[0]);
+        ValueSet retVal = myDefaultValidationSupport.fetchCodeSystem((FhirContext) theInvocation.getArguments()[0],(String) theInvocation.getArguments()[1]);
         ourLog.info("fetchCodeSystem({}) : {}", new Object[] { (String) theInvocation.getArguments()[0], retVal });
         return retVal;
       }
@@ -306,6 +308,29 @@ public class FhirInstanceValidatorTest {
         output.getMessages().get(0).getMessage());
   }
 
+  
+  @Test
+  public void testValidateResourceWithValuesetExpansion() {
+    
+    Patient patient = new Patient();
+    patient.addIdentifier().setSystem("http://system").setValue("12345").getType().addCoding().setSystem("foo").setCode("bar");
+
+    ValidationResult output = myVal.validateWithResult(patient);
+    List<SingleValidationMessage> all = logResultsAndReturnAll(output);
+    assertEquals(1, all.size());
+    assertEquals("/f:Patient/f:identifier/f:type", all.get(0).getLocationString());
+    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);
+    assertEquals(0, all.size());
+  }
+
+  
   @Test
   public void testValidateResourceWithExampleBindingCodeValidationFailing() {
     Observation input = new Observation();

src/changes/changes.xml

@@ -84,6 +84,13 @@
 				a more appropriate 400/404 in the JPA server (vread on invalid version,
 				delete with no ID, etc.)
 			</action>
+			<action type="fix">
+				Fix narrative generation for DSTU2 Medication resource
+			</action>
+			<action type="fix">
+				Profile validator now works for valuesets which use
+				v2 tables
+			</action>
 		</release>
 		<release version="1.2" date="2015-09-18">
 			<action type="add">