Get coded valuesets working once again for DSTU2 resoruces

hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/FhirResourceDaoQuestionnaireResponseDstu2.java

@@ -23,6 +23,8 @@ package ca.uhn.fhir.jpa.dao;
 import org.hl7.fhir.instance.model.api.IBaseOperationOutcome;
 import org.hl7.fhir.instance.model.api.IBaseResource;
 import org.hl7.fhir.instance.model.api.IIdType;
+import org.springframework.beans.factory.annotation.Autowired;
+import org.springframework.transaction.PlatformTransactionManager;
 
 import ca.uhn.fhir.context.FhirContext;
 import ca.uhn.fhir.model.api.IResource;
@@ -69,10 +71,9 @@ public class FhirResourceDaoQuestionnaireResponseDstu2 extends FhirResourceDaoDs
 
 		@Override
 		public <T extends IBaseResource> T load(Class<T> theType, IIdType theId) throws ResourceNotFoundException {
+
 			/*
-			 * The QuestionnaireResponse validator uses RI structures, so for now we need
+			 * The QuestionnaireResponse validator uses RI structures, so for now we need to convert between that and HAPI structures. This is a bit hackish, but hopefully it will go away at some point.
-			 * to convert between that and HAPI structures. This is a bit hackish, but
-			 * hopefully it will go away at some point.
 			 */
 			if ("ValueSet".equals(theType.getSimpleName())) {
 				IFhirResourceDao<ValueSet> dao = getDao(ValueSet.class);

hapi-fhir-structures-dstu2/src/main/java/ca/uhn/fhir/rest/server/provider/dstu2/ServerConformanceProvider.java

@@ -51,11 +51,13 @@ import ca.uhn.fhir.model.dstu2.resource.OperationDefinition;
 import ca.uhn.fhir.model.dstu2.resource.OperationDefinition.Parameter;
 import ca.uhn.fhir.model.dstu2.valueset.ConditionalDeleteStatusEnum;
 import ca.uhn.fhir.model.dstu2.valueset.ConformanceResourceStatusEnum;
+import ca.uhn.fhir.model.dstu2.valueset.ConformanceStatementKindEnum;
 import ca.uhn.fhir.model.dstu2.valueset.OperationParameterUseEnum;
 import ca.uhn.fhir.model.dstu2.valueset.ResourceTypeEnum;
 import ca.uhn.fhir.model.dstu2.valueset.RestfulConformanceModeEnum;
 import ca.uhn.fhir.model.dstu2.valueset.SystemRestfulInteractionEnum;
 import ca.uhn.fhir.model.dstu2.valueset.TypeRestfulInteractionEnum;
+import ca.uhn.fhir.model.dstu2.valueset.UnknownContentCodeEnum;
 import ca.uhn.fhir.model.primitive.DateTimeDt;
 import ca.uhn.fhir.model.primitive.IdDt;
 import ca.uhn.fhir.rest.annotation.IdParam;
@@ -162,11 +164,11 @@ public class ServerConformanceProvider implements IServerConformanceProvider<Con
 		retVal.setPublisher(myPublisher);
 		retVal.setDate(DateTimeDt.withCurrentTime());
 		retVal.setFhirVersion("0.5.0"); // TODO: pull from model
-		retVal.setAcceptUnknown("extensions"); // TODO: make this configurable - this is a fairly big effort since the parser
+		retVal.setAcceptUnknown(UnknownContentCodeEnum.UNKNOWN_EXTENSIONS); // TODO: make this configurable - this is a fairly big effort since the parser
 		// needs to be modified to actually allow it
 
 		retVal.getImplementation().setDescription(myRestfulServer.getImplementationDescription());
-		retVal.setKind("instance");
+		retVal.setKind(ConformanceStatementKindEnum.INSTANCE);
 		retVal.getSoftware().setName(myRestfulServer.getServerName());
 		retVal.getSoftware().setVersion(myRestfulServer.getServerVersion());
 		retVal.addFormat(Constants.CT_FHIR_XML);

hapi-fhir-structures-dstu2/src/test/java/ca/uhn/fhir/rest/client/BundleTypeDstu2Test.java

@@ -27,6 +27,8 @@ import ca.uhn.fhir.context.FhirContext;
 import ca.uhn.fhir.model.api.Bundle;
 import ca.uhn.fhir.model.dstu2.resource.Patient;
 import ca.uhn.fhir.model.valueset.BundleTypeEnum;
+import ca.uhn.fhir.rest.client.interceptor.BearerTokenAuthInterceptor;
+import ca.uhn.fhir.rest.client.interceptor.LoggingInterceptor;
 import ca.uhn.fhir.rest.server.Constants;
 
 public class BundleTypeDstu2Test {
@@ -74,4 +76,18 @@ public class BundleTypeDstu2Test {
 
 		assertThat(body, Matchers.containsString("<type value=\"" + BundleTypeEnum.TRANSACTION.getCode()));
 	}
+	
+	
+	public static void main(String[] args) {
+		
+		FhirContext ctx = FhirContext.forDstu2();
+		IGenericClient client = ctx.newRestfulGenericClient("http://54.165.58.158:8081/FHIRServer/fhir");
+		client.registerInterceptor(new BearerTokenAuthInterceptor("AN3uCTC5B"));
+		client.registerInterceptor(new LoggingInterceptor(true));
+		Bundle result = client.search().forResource(Patient.class).where(Patient.NAME.matches().value("Alice")).execute();
+		
+		System.out.println(result.getEntries().size());
+		
+	}
+	
 }

hapi-fhir-structures-dstu2/src/test/java/ca/uhn/fhir/rest/client/ClientServerValidationTestDstu2.java

@@ -35,14 +35,15 @@ import ca.uhn.fhir.rest.client.exceptions.FhirClientConnectionException;
 import ca.uhn.fhir.rest.client.exceptions.FhirClientInappropriateForServerException;
 import ca.uhn.fhir.rest.client.interceptor.BasicAuthInterceptor;
 import ca.uhn.fhir.rest.server.Constants;
+import ca.uhn.fhir.rest.server.exceptions.AuthenticationException;
 
 public class ClientServerValidationTestDstu2 {
 
 	private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(ClientServerValidationTestDstu2.class);
 	private FhirContext myCtx;
+	private boolean myFirstResponse;
 	private HttpClient myHttpClient;
 	private HttpResponse myHttpResponse;
-	private boolean myFirstResponse;
 
 	@Before
 	public void before() {
@@ -54,6 +55,119 @@ public class ClientServerValidationTestDstu2 {
 		myFirstResponse = true;
 	}
 
+	@Test
+	public void testClientUsesInterceptors() throws Exception {
+		Conformance conf = new Conformance();
+		conf.setFhirVersion("0.5.0");
+		final String confResource = myCtx.newXmlParser().encodeResourceToString(conf);
+
+		ArgumentCaptor<HttpUriRequest> capt = ArgumentCaptor.forClass(HttpUriRequest.class);
+
+		when(myHttpResponse.getStatusLine()).thenReturn(new BasicStatusLine(new ProtocolVersion("HTTP", 1, 1), 200, "OK"));
+		when(myHttpResponse.getEntity().getContentType()).thenReturn(new BasicHeader("content-type", Constants.CT_FHIR_XML + "; charset=UTF-8"));
+		when(myHttpResponse.getEntity().getContent()).thenAnswer(new Answer<InputStream>() {
+			@Override
+			public InputStream answer(InvocationOnMock theInvocation) throws Throwable {
+				if (myFirstResponse) {
+					myFirstResponse = false;
+					return new ReaderInputStream(new StringReader(confResource), Charset.forName("UTF-8"));
+				} else {
+					Patient resource = new Patient();
+					resource.addName().addFamily().setValue("FAM");
+					return new ReaderInputStream(new StringReader(myCtx.newXmlParser().encodeResourceToString(resource)), Charset.forName("UTF-8"));
+				}
+			}
+		});
+
+		when(myHttpClient.execute(capt.capture())).thenReturn(myHttpResponse);
+
+		myCtx.getRestfulClientFactory().setServerValidationMode(ServerValidationModeEnum.ONCE);
+		IGenericClient client = myCtx.newRestfulGenericClient("http://foo");
+		client.registerInterceptor(new BasicAuthInterceptor("USER", "PASS"));
+		Patient pt = (Patient) client.read(new UriDt("http://foo/Patient/123"));
+		assertEquals("FAM", pt.getNameFirstRep().getFamilyAsSingleString());
+
+		assertEquals(2, capt.getAllValues().size());
+
+		Header auth = capt.getAllValues().get(0).getFirstHeader("Authorization");
+		assertNotNull(auth);
+		assertEquals("Basic VVNFUjpQQVNT", auth.getValue());
+		auth = capt.getAllValues().get(1).getFirstHeader("Authorization");
+		assertNotNull(auth);
+		assertEquals("Basic VVNFUjpQQVNT", auth.getValue());
+	}
+
+	@Test
+	public void testForceConformanceCheck() throws Exception {
+		Conformance conf = new Conformance();
+		conf.setFhirVersion("0.5.0");
+		final String confResource = myCtx.newXmlParser().encodeResourceToString(conf);
+
+		ArgumentCaptor<HttpUriRequest> capt = ArgumentCaptor.forClass(HttpUriRequest.class);
+
+		when(myHttpResponse.getStatusLine()).thenReturn(new BasicStatusLine(new ProtocolVersion("HTTP", 1, 1), 200, "OK"));
+		when(myHttpResponse.getEntity().getContentType()).thenReturn(new BasicHeader("content-type", Constants.CT_FHIR_XML + "; charset=UTF-8"));
+		when(myHttpResponse.getEntity().getContent()).thenAnswer(new Answer<InputStream>() {
+			@Override
+			public InputStream answer(InvocationOnMock theInvocation) throws Throwable {
+				if (myFirstResponse) {
+					myFirstResponse = false;
+					return new ReaderInputStream(new StringReader(confResource), Charset.forName("UTF-8"));
+				} else {
+					Patient resource = new Patient();
+					resource.addName().addFamily().setValue("FAM");
+					return new ReaderInputStream(new StringReader(myCtx.newXmlParser().encodeResourceToString(resource)), Charset.forName("UTF-8"));
+				}
+			}
+		});
+
+		when(myHttpClient.execute(capt.capture())).thenReturn(myHttpResponse);
+
+		myCtx.getRestfulClientFactory().setServerValidationMode(ServerValidationModeEnum.ONCE);
+
+		IGenericClient client = myCtx.newRestfulGenericClient("http://foo");
+		client.registerInterceptor(new BasicAuthInterceptor("USER", "PASS"));
+
+		client.forceConformanceCheck();
+
+		assertEquals(1, capt.getAllValues().size());
+
+		Patient pt = (Patient) client.read(new UriDt("http://foo/Patient/123"));
+		assertEquals("FAM", pt.getNameFirstRep().getFamilyAsSingleString());
+
+		assertEquals(2, capt.getAllValues().size());
+
+		Header auth = capt.getAllValues().get(0).getFirstHeader("Authorization");
+		assertNotNull(auth);
+		assertEquals("Basic VVNFUjpQQVNT", auth.getValue());
+		auth = capt.getAllValues().get(1).getFirstHeader("Authorization");
+		assertNotNull(auth);
+		assertEquals("Basic VVNFUjpQQVNT", auth.getValue());
+	}
+
+	@Test
+	public void testServerReturnsAnHttp401() throws Exception {
+		ArgumentCaptor<HttpUriRequest> capt = ArgumentCaptor.forClass(HttpUriRequest.class);
+
+		when(myHttpResponse.getStatusLine()).thenReturn(new BasicStatusLine(new ProtocolVersion("HTTP", 1, 1), 401, "Unauthorized"));
+		when(myHttpResponse.getEntity().getContentType()).thenReturn(new BasicHeader("content-type", Constants.CT_TEXT));
+		when(myHttpResponse.getEntity().getContent()).thenAnswer(new Answer<InputStream>() {
+			@Override
+			public InputStream answer(InvocationOnMock theInvocation) throws Throwable {
+				return new ReaderInputStream(new StringReader("Unauthorized"), Charset.forName("UTF-8"));
+			}
+		});
+		when(myHttpClient.execute(capt.capture())).thenReturn(myHttpResponse);
+
+		IGenericClient client = myCtx.newRestfulGenericClient("http://foo");
+		try {
+			client.read().resource(Patient.class).withId("123").execute();
+			fail();
+		} catch (AuthenticationException e) {
+			// good
+		}
+	}
+
 	@Test
 	public void testServerReturnsAppropriateVersionForDstu2_040() throws Exception {
 		Conformance conf = new Conformance();
@@ -157,94 +271,4 @@ public class ClientServerValidationTestDstu2 {
 		}
 	}
 
-	@Test
-	public void testClientUsesInterceptors() throws Exception {
-		Conformance conf = new Conformance();
-		conf.setFhirVersion("0.5.0");
-		final String confResource = myCtx.newXmlParser().encodeResourceToString(conf);
-
-		ArgumentCaptor<HttpUriRequest> capt = ArgumentCaptor.forClass(HttpUriRequest.class);
-
-		when(myHttpResponse.getStatusLine()).thenReturn(new BasicStatusLine(new ProtocolVersion("HTTP", 1, 1), 200, "OK"));
-		when(myHttpResponse.getEntity().getContentType()).thenReturn(new BasicHeader("content-type", Constants.CT_FHIR_XML + "; charset=UTF-8"));
-		when(myHttpResponse.getEntity().getContent()).thenAnswer(new Answer<InputStream>() {
-			@Override
-			public InputStream answer(InvocationOnMock theInvocation) throws Throwable {
-				if (myFirstResponse) {
-					myFirstResponse = false;
-					return new ReaderInputStream(new StringReader(confResource), Charset.forName("UTF-8"));
-				} else {
-					Patient resource = new Patient();
-					resource.addName().addFamily().setValue("FAM");
-					return new ReaderInputStream(new StringReader(myCtx.newXmlParser().encodeResourceToString(resource)), Charset.forName("UTF-8"));
-				}
-			}
-		});
-
-		when(myHttpClient.execute(capt.capture())).thenReturn(myHttpResponse);
-
-		myCtx.getRestfulClientFactory().setServerValidationMode(ServerValidationModeEnum.ONCE);
-		IGenericClient client = myCtx.newRestfulGenericClient("http://foo");
-		client.registerInterceptor(new BasicAuthInterceptor("USER", "PASS"));
-		Patient pt = (Patient) client.read(new UriDt("http://foo/Patient/123"));
-		assertEquals("FAM", pt.getNameFirstRep().getFamilyAsSingleString());
-		
-		assertEquals(2, capt.getAllValues().size());
-		
-		Header auth = capt.getAllValues().get(0).getFirstHeader("Authorization");
-		assertNotNull(auth);
-		assertEquals("Basic VVNFUjpQQVNT", auth.getValue());
-		auth = capt.getAllValues().get(1).getFirstHeader("Authorization");
-		assertNotNull(auth);
-		assertEquals("Basic VVNFUjpQQVNT", auth.getValue());
-	}
-
-	@Test
-	public void testForceConformanceCheck() throws Exception {
-		Conformance conf = new Conformance();
-		conf.setFhirVersion("0.5.0");
-		final String confResource = myCtx.newXmlParser().encodeResourceToString(conf);
-
-		ArgumentCaptor<HttpUriRequest> capt = ArgumentCaptor.forClass(HttpUriRequest.class);
-
-		when(myHttpResponse.getStatusLine()).thenReturn(new BasicStatusLine(new ProtocolVersion("HTTP", 1, 1), 200, "OK"));
-		when(myHttpResponse.getEntity().getContentType()).thenReturn(new BasicHeader("content-type", Constants.CT_FHIR_XML + "; charset=UTF-8"));
-		when(myHttpResponse.getEntity().getContent()).thenAnswer(new Answer<InputStream>() {
-			@Override
-			public InputStream answer(InvocationOnMock theInvocation) throws Throwable {
-				if (myFirstResponse) {
-					myFirstResponse = false;
-					return new ReaderInputStream(new StringReader(confResource), Charset.forName("UTF-8"));
-				} else {
-					Patient resource = new Patient();
-					resource.addName().addFamily().setValue("FAM");
-					return new ReaderInputStream(new StringReader(myCtx.newXmlParser().encodeResourceToString(resource)), Charset.forName("UTF-8"));
-				}
-			}
-		});
-
-		when(myHttpClient.execute(capt.capture())).thenReturn(myHttpResponse);
-
-		myCtx.getRestfulClientFactory().setServerValidationMode(ServerValidationModeEnum.ONCE);
-		
-		IGenericClient client = myCtx.newRestfulGenericClient("http://foo");
-		client.registerInterceptor(new BasicAuthInterceptor("USER", "PASS"));
-		
-		client.forceConformanceCheck();
-
-		assertEquals(1, capt.getAllValues().size());
-
-		Patient pt = (Patient) client.read(new UriDt("http://foo/Patient/123"));
-		assertEquals("FAM", pt.getNameFirstRep().getFamilyAsSingleString());
-		
-		assertEquals(2, capt.getAllValues().size());
-		
-		Header auth = capt.getAllValues().get(0).getFirstHeader("Authorization");
-		assertNotNull(auth);
-		assertEquals("Basic VVNFUjpQQVNT", auth.getValue());
-		auth = capt.getAllValues().get(1).getFirstHeader("Authorization");
-		assertNotNull(auth);
-		assertEquals("Basic VVNFUjpQQVNT", auth.getValue());
-	}
-
 }

hapi-tinder-plugin/src/main/java/ca/uhn/fhir/tinder/TinderStructuresMojo.java

@@ -228,7 +228,7 @@ public class TinderStructuresMojo extends AbstractMojo {
 		String dtOutputDir = "target/generated-sources/tinder/ca/uhn/fhir/model/dev/composite";
 
 		ResourceGeneratorUsingSpreadsheet rp = new ResourceGeneratorUsingSpreadsheet("dstu2", ".");
-		rp.setBaseResourceNames(Arrays.asList( "observation"  
+		rp.setBaseResourceNames(Arrays.asList( "bundle"  
 //				//, "contract" 
 //				"valueset", "organization", "location" 
 //				, "observation", "conformance"

hapi-tinder-plugin/src/main/java/ca/uhn/fhir/tinder/ValueSetGenerator.java

@@ -31,6 +31,8 @@ import ca.uhn.fhir.model.dstu.resource.ValueSet.ComposeInclude;
 import ca.uhn.fhir.model.dstu.resource.ValueSet.Define;
 import ca.uhn.fhir.model.dstu.resource.ValueSet.DefineConcept;
 import ca.uhn.fhir.model.dstu2.resource.Bundle.Entry;
+import ca.uhn.fhir.model.dstu2.resource.ValueSet.CodeSystem;
+import ca.uhn.fhir.model.dstu2.resource.ValueSet.CodeSystemConcept;
 import ca.uhn.fhir.model.dstu2.resource.ValueSet.ComposeIncludeConcept;
 import ca.uhn.fhir.model.primitive.CodeDt;
 import ca.uhn.fhir.parser.IParser;
@@ -187,7 +189,7 @@ public class ValueSetGenerator {
 	}
 
 	private ValueSetTm parseValueSet(ca.uhn.fhir.model.dstu2.resource.ValueSet nextVs) {
-		myConceptCount += nextVs.getDefine().getConcept().size();
+		myConceptCount += nextVs.getCodeSystem().getConcept().size();
 		ourLog.info("Parsing ValueSetTm #{} - {} - {} concepts total", myValueSetCount++, nextVs.getName(), myConceptCount);
 		// output.addConcept(next.getCode().getValue(),
 		// next.getDisplay().getValue(), next.getDefinition());
@@ -200,9 +202,9 @@ public class ValueSetGenerator {
 		vs.setClassName(toClassName(nextVs.getName()));
 
 		{
-			ca.uhn.fhir.model.dstu2.resource.ValueSet.Define define = nextVs.getDefine();
+			CodeSystem define = nextVs.getCodeSystem();
 			String system = define.getSystemElement().getValueAsString();
-			for (ca.uhn.fhir.model.dstu2.resource.ValueSet.DefineConcept nextConcept : define.getConcept()) {
+			for (CodeSystemConcept nextConcept : define.getConcept()) {
 				String nextCodeValue = nextConcept.getCode();
 				String nextCodeDisplay = StringUtils.defaultString(nextConcept.getDisplay());
 				String nextCodeDefinition = StringUtils.defaultString(nextConcept.getDefinition());

hapi-tinder-plugin/src/main/java/ca/uhn/fhir/tinder/parser/BaseStructureParser.java

@@ -81,20 +81,20 @@ public abstract class BaseStructureParser {
 		myResources.add(theResource);
 	}
 
-	private void bindValueSets(BaseElement theResource, ValueSetGenerator theVsp) {
+	private void bindValueSets(BaseElement theElement, ValueSetGenerator theVsp) {
-		if (isNotBlank(theResource.getBinding())) {
+		if (isNotBlank(theElement.getBinding())) {
-			String bindingClass = theVsp.getClassForValueSetIdAndMarkAsNeeded(theResource.getBinding());
+			String bindingClass = theVsp.getClassForValueSetIdAndMarkAsNeeded(theElement.getBinding());
 			if (bindingClass != null) {
 				ourLog.debug("Adding binding ValueSet class: {}", bindingClass);
-				theResource.setBindingClass(bindingClass);
+				theElement.setBindingClass(bindingClass);
 				addImport(bindingClass);
 				myLocallyDefinedClassNames.put(bindingClass, "valueset");
 			} else {
-				ourLog.debug("No binding found for: {}", theResource.getBinding());
+				ourLog.debug("No binding found for: {}", theElement.getBinding());
 				ourLog.debug(" * Valid: {}", new TreeSet<String>(theVsp.getValueSets().keySet()));
 			}
 		}
-		for (BaseElement next : theResource.getChildren()) {
+		for (BaseElement next : theElement.getChildren()) {
 			bindValueSets(next, theVsp);
 		}
 	}