Merge remote-tracking branch 'refs/remotes/jamesagnew/master'

hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/dstu3/FhirResourceDaoCodeSystemDstu3.java

@@ -119,21 +119,12 @@ public class FhirResourceDaoCodeSystemDstu3 extends FhirResourceDaoDstu3<CodeSys
 			system = theSystem.getValue();
 		}
 
-		// CodeValidationResult validateOutcome = myJpaValidationSupport.validateCode(getContext(), system, code, null);
+		ourLog.info("Looking up {} / {}", system, code);
-		//
-		// LookupCodeResult result = new LookupCodeResult();
-		// result.setSearchedForCode(code);
-		// result.setSearchedForSystem(system);
-		// result.setFound(false);
-		// if (validateOutcome.isOk()) {
-		// result.setFound(true);
-		// result.setCodeIsAbstract(validateOutcome.asConceptDefinition().getAbstract());
-		// result.setCodeDisplay(validateOutcome.asConceptDefinition().getDisplay());
-		// }
-		// return result;
 		
 		if (myValidationSupport.isCodeSystemSupported(getContext(), system)) {
 
+			ourLog.info("Code system {} is supported", system);
+
 			CodeValidationResult result = myValidationSupport.validateCode(getContext(), system, code, null);
 			if (result != null) {
 				if (result.isOk()) {

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

@@ -74,7 +74,7 @@ public abstract class BaseJpaDstu3Test extends BaseJpaTest {
 	protected IFhirResourceDao<CarePlan> myCarePlanDao;
 	@Autowired
 	@Qualifier("myCodeSystemDaoDstu3")
-	protected IFhirResourceDao<CodeSystem> myCodeSystemDao;
+	protected IFhirResourceDaoCodeSystem<CodeSystem, Coding, CodeableConcept> myCodeSystemDao;
 	@Autowired
 	@Qualifier("myCompartmentDefinitionDaoDstu3")
 	protected IFhirResourceDao<CompartmentDefinition> myCompartmentDefinitionDao;

hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/dstu3/FhirResourceDaoDstu3TerminologyTest.java

@@ -11,15 +11,11 @@ import java.util.ArrayList;
 import java.util.List;
 import java.util.Set;
 
-import org.hl7.fhir.dstu3.model.AllergyIntolerance;
+import org.hl7.fhir.dstu3.model.*;
 import org.hl7.fhir.dstu3.model.AllergyIntolerance.AllergyIntoleranceCategory;
 import org.hl7.fhir.dstu3.model.AllergyIntolerance.AllergyIntoleranceClinicalStatus;
-import org.hl7.fhir.dstu3.model.AuditEvent;
-import org.hl7.fhir.dstu3.model.CodeSystem;
 import org.hl7.fhir.dstu3.model.CodeSystem.CodeSystemContentMode;
 import org.hl7.fhir.dstu3.model.CodeSystem.ConceptDefinitionComponent;
-import org.hl7.fhir.dstu3.model.Observation;
-import org.hl7.fhir.dstu3.model.ValueSet;
 import org.hl7.fhir.dstu3.model.ValueSet.ConceptSetComponent;
 import org.hl7.fhir.dstu3.model.ValueSet.FilterOperator;
 import org.hl7.fhir.dstu3.model.ValueSet.ValueSetComposeComponent;
@@ -32,6 +28,7 @@ import org.junit.Ignore;
 import org.junit.Test;
 
 import ca.uhn.fhir.jpa.dao.DaoConfig;
+import ca.uhn.fhir.jpa.dao.IFhirResourceDaoCodeSystem.LookupCodeResult;
 import ca.uhn.fhir.jpa.dao.SearchParameterMap;
 import ca.uhn.fhir.jpa.entity.ResourceTable;
 import ca.uhn.fhir.jpa.entity.TermCodeSystemVersion;
@@ -159,6 +156,28 @@ public class FhirResourceDaoDstu3TerminologyTest extends BaseJpaDstu3Test {
 		}
 	}
 
+	@Test
+	public void testLookupSnomed() {
+		CodeSystem codeSystem = new CodeSystem();
+		codeSystem.setUrl("http://snomed.info/sct");
+		codeSystem.setContent(CodeSystemContentMode.NOTPRESENT);
+		IIdType id = myCodeSystemDao.create(codeSystem, mySrd).getId().toUnqualified();
+
+		ResourceTable table = myResourceTableDao.findOne(id.getIdPartAsLong());
+
+		TermCodeSystemVersion cs = new TermCodeSystemVersion();
+		cs.setResource(table);
+		cs.setResourceVersionId(table.getVersion());
+		TermConcept parentA = new TermConcept(cs, "ParentA").setDisplay("Parent A");
+		cs.getConcepts().add(parentA);
+		myTermSvc.storeNewCodeSystemVersion(table.getId(), "http://snomed.info/sct", cs);
+
+		StringType code = new StringType("ParentA");
+		StringType system = new StringType("http://snomed.info/sct");
+		LookupCodeResult outcome = myCodeSystemDao.lookupCode(code, system, null, mySrd);
+		assertEquals(true, outcome.isFound());
+	}
+
 	@Test
 	public void testCodeSystemWithDefinedCodes() {
 		//@formatter:off

hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/provider/dstu3/ResourceProviderDstu3CodeSystemTest.java

@@ -23,6 +23,7 @@ import org.junit.Before;
 import org.junit.Test;
 import org.springframework.transaction.annotation.Transactional;
 
+import ca.uhn.fhir.jpa.dao.dstu3.FhirResourceDaoDstu3TerminologyTest;
 import ca.uhn.fhir.rest.server.exceptions.InvalidRequestException;
 import ca.uhn.fhir.rest.server.exceptions.ResourceNotFoundException;
 import ca.uhn.fhir.util.TestUtil;
@@ -48,10 +49,52 @@ public class ResourceProviderDstu3CodeSystemTest extends BaseResourceProviderDst
 		myExtensionalVsId = myValueSetDao.create(upload, mySrd).getId().toUnqualifiedVersionless();
 	}
 	
+	@Test
+	public void testLookupOnExternalCode() {
+		ResourceProviderDstu3ValueSetTest.createExternalCs(myCodeSystemDao, myResourceTableDao, myTermSvc, mySrd);
+		
+		Parameters respParam = ourClient
+			.operation()
+			.onType(CodeSystem.class)
+			.named("lookup")
+			.withParameter(Parameters.class, "code", new CodeType("ParentA"))
+			.andParameter("system", new UriType(FhirResourceDaoDstu3TerminologyTest.URL_MY_CODE_SYSTEM))
+			.execute();
+
+		String resp = myFhirCtx.newXmlParser().setPrettyPrint(true).encodeResourceToString(respParam);
+		ourLog.info(resp);
+		
+		assertEquals("name", respParam.getParameter().get(0).getName());
+		assertEquals(("Unknown"), ((StringType)respParam.getParameter().get(0).getValue()).getValue());
+		assertEquals("display", respParam.getParameter().get(1).getName());
+		assertEquals("Parent A", ((StringType)respParam.getParameter().get(1).getValue()).getValue());
+		assertEquals("abstract", respParam.getParameter().get(2).getName());
+		assertEquals(false, ((BooleanType)respParam.getParameter().get(2).getValue()).getValue().booleanValue());
+
+		// With HTTP GET
+		respParam = ourClient
+				.operation()
+				.onType(CodeSystem.class)
+				.named("lookup")
+				.withParameter(Parameters.class, "code", new CodeType("ParentA"))
+				.andParameter("system", new UriType(FhirResourceDaoDstu3TerminologyTest.URL_MY_CODE_SYSTEM))
+				.useHttpGet()
+				.execute();
+
+		resp = myFhirCtx.newXmlParser().setPrettyPrint(true).encodeResourceToString(respParam);
+		ourLog.info(resp);
+		
+		assertEquals("name", respParam.getParameter().get(0).getName());
+		assertEquals(("Unknown"), ((StringType)respParam.getParameter().get(0).getValue()).getValue());
+		assertEquals("display", respParam.getParameter().get(1).getName());
+		assertEquals("Parent A", ((StringType)respParam.getParameter().get(1).getValue()).getValue());
+		assertEquals("abstract", respParam.getParameter().get(2).getName());
+		assertEquals(false, ((BooleanType)respParam.getParameter().get(2).getValue()).getValue().booleanValue());
+
+	}
 	
 	@Test
 	public void testLookupOperationByCodeAndSystemBuiltInCode() {
-		//@formatter:off
 		Parameters respParam = ourClient
 			.operation()
 			.onType(CodeSystem.class)
@@ -59,7 +102,6 @@ public class ResourceProviderDstu3CodeSystemTest extends BaseResourceProviderDst
 			.withParameter(Parameters.class, "code", new CodeType("ACSN"))
 			.andParameter("system", new UriType("http://hl7.org/fhir/v2/0203"))
 			.execute();
-		//@formatter:on
 
 		String resp = myFhirCtx.newXmlParser().setPrettyPrint(true).encodeResourceToString(respParam);
 		ourLog.info(resp);

hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/provider/dstu3/ResourceProviderDstu3ValueSetTest.java

@@ -1,6 +1,7 @@
 package ca.uhn.fhir.jpa.provider.dstu3;
 
-import static ca.uhn.fhir.jpa.dao.dstu3.FhirResourceDaoDstu3TerminologyTest.*;
+import static ca.uhn.fhir.jpa.dao.dstu3.FhirResourceDaoDstu3TerminologyTest.URL_MY_CODE_SYSTEM;
+import static ca.uhn.fhir.jpa.dao.dstu3.FhirResourceDaoDstu3TerminologyTest.URL_MY_VALUE_SET;
 import static org.hamcrest.Matchers.containsString;
 import static org.hamcrest.Matchers.containsStringIgnoringCase;
 import static org.hamcrest.Matchers.not;
@@ -18,30 +19,27 @@ import org.apache.http.client.methods.CloseableHttpResponse;
 import org.apache.http.client.methods.HttpPost;
 import org.apache.http.entity.ContentType;
 import org.apache.http.entity.StringEntity;
-import org.hl7.fhir.dstu3.model.BooleanType;
+import org.hl7.fhir.dstu3.model.*;
-import org.hl7.fhir.dstu3.model.CodeSystem;
-import org.hl7.fhir.dstu3.model.CodeType;
-import org.hl7.fhir.dstu3.model.Parameters;
-import org.hl7.fhir.dstu3.model.StringType;
-import org.hl7.fhir.dstu3.model.UriType;
-import org.hl7.fhir.dstu3.model.ValueSet;
-import org.hl7.fhir.dstu3.model.ValueSet.ConceptSetComponent;
-import org.hl7.fhir.dstu3.model.ValueSet.FilterOperator;
 import org.hl7.fhir.dstu3.model.CodeSystem.CodeSystemContentMode;
 import org.hl7.fhir.dstu3.model.CodeSystem.ConceptDefinitionComponent;
+import org.hl7.fhir.dstu3.model.ValueSet.ConceptSetComponent;
+import org.hl7.fhir.dstu3.model.ValueSet.FilterOperator;
 import org.hl7.fhir.instance.model.api.IIdType;
 import org.junit.AfterClass;
 import org.junit.Before;
-import org.junit.Ignore;
 import org.junit.Test;
 import org.springframework.transaction.annotation.Transactional;
 
+import ca.uhn.fhir.jpa.dao.IFhirResourceDao;
+import ca.uhn.fhir.jpa.dao.data.IResourceTableDao;
 import ca.uhn.fhir.jpa.entity.ResourceTable;
 import ca.uhn.fhir.jpa.entity.TermCodeSystemVersion;
 import ca.uhn.fhir.jpa.entity.TermConcept;
 import ca.uhn.fhir.jpa.entity.TermConceptParentChildLink.RelationshipTypeEnum;
+import ca.uhn.fhir.jpa.term.IHapiTerminologySvc;
 import ca.uhn.fhir.rest.server.Constants;
 import ca.uhn.fhir.rest.server.exceptions.InvalidRequestException;
+import ca.uhn.fhir.rest.server.servlet.ServletRequestDetails;
 import ca.uhn.fhir.util.TestUtil;
 
 public class ResourceProviderDstu3ValueSetTest extends BaseResourceProviderDstu3Test {
@@ -87,12 +85,20 @@ public class ResourceProviderDstu3ValueSetTest extends BaseResourceProviderDstu3
 	}
 
 	private CodeSystem createExternalCs() {
+		IFhirResourceDao<CodeSystem> codeSystemDao = myCodeSystemDao;
+		IResourceTableDao resourceTableDao = myResourceTableDao;
+		IHapiTerminologySvc termSvc = myTermSvc;
+		
+		return createExternalCs(codeSystemDao, resourceTableDao, termSvc, mySrd);
+	}
+
+	public static CodeSystem createExternalCs(IFhirResourceDao<CodeSystem> theCodeSystemDao, IResourceTableDao theResourceTableDao, IHapiTerminologySvc theTermSvc, ServletRequestDetails theRequestDetails) {
 		CodeSystem codeSystem = new CodeSystem();
 		codeSystem.setUrl(URL_MY_CODE_SYSTEM);
 		codeSystem.setContent(CodeSystemContentMode.NOTPRESENT);
-		IIdType id = myCodeSystemDao.create(codeSystem, mySrd).getId().toUnqualified();
+		IIdType id = theCodeSystemDao.create(codeSystem, theRequestDetails).getId().toUnqualified();
 
-		ResourceTable table = myResourceTableDao.findOne(id.getIdPartAsLong());
+		ResourceTable table = theResourceTableDao.findOne(id.getIdPartAsLong());
 
 		TermCodeSystemVersion cs = new TermCodeSystemVersion();
 		cs.setResource(table);
@@ -116,7 +122,7 @@ public class ResourceProviderDstu3ValueSetTest extends BaseResourceProviderDstu3
 		TermConcept parentB = new TermConcept(cs, "ParentB").setDisplay("Parent B");
 		cs.getConcepts().add(parentB);
 
-		myTermSvc.storeNewCodeSystemVersion(table.getId(), URL_MY_CODE_SYSTEM, cs);
+		theTermSvc.storeNewCodeSystemVersion(table.getId(), URL_MY_CODE_SYSTEM, cs);
 		return codeSystem;
 	}
 	

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

@@ -0,0 +1,8 @@
+package ca.uhn.fhirtest.config;
+
+import org.springframework.context.annotation.Configuration;
+
+@Configuration
+public class DbServerConfig {
+
+}

hapi-fhir-jpaserver-uhnfhirtest/src/main/java/ca/uhn/fhirtest/config/TdlDstu2Config.java

@@ -68,7 +68,6 @@ public class TdlDstu2Config extends BaseJavaConfigDstu2 {
 	}
 
 	@Bean(name = "myPersistenceDataSourceDstu1", destroyMethod = "close")
-	@DependsOn("dbServer")
 	public DataSource dataSource() {
 		BasicDataSource retVal = new BasicDataSource();
 //		retVal.setDriver(new org.apache.derby.jdbc.ClientDriver());

hapi-fhir-jpaserver-uhnfhirtest/src/main/java/ca/uhn/fhirtest/config/TdlDstu3Config.java

@@ -65,7 +65,6 @@ public class TdlDstu3Config extends BaseJavaConfigDstu3 {
 	}
 	
 	@Bean(name = "myPersistenceDataSourceDstu3", destroyMethod = "close")
-	@DependsOn("dbServer")
 	public DataSource dataSource() {
 		BasicDataSource retVal = new BasicDataSource();
 //		retVal.setDriver(new org.apache.derby.jdbc.ClientDriver());

hapi-fhir-jpaserver-uhnfhirtest/src/main/java/ca/uhn/fhirtest/config/TestDstu2Config.java

@@ -70,7 +70,6 @@ public class TestDstu2Config extends BaseJavaConfigDstu2 {
 	}
 
 	@Bean(name = "myPersistenceDataSourceDstu1", destroyMethod = "close")
-	@DependsOn("dbServer")
 	public DataSource dataSource() {
 		BasicDataSource retVal = new BasicDataSource();
 		retVal.setDriver(new org.postgresql.Driver());

hapi-fhir-jpaserver-uhnfhirtest/src/main/java/ca/uhn/fhirtest/config/TestDstu3Config.java

@@ -74,7 +74,6 @@ public class TestDstu3Config extends BaseJavaConfigDstu3 {
 	}
 
 	@Bean(name = "myPersistenceDataSourceDstu3", destroyMethod = "close")
-	@DependsOn("dbServer")
 	public DataSource dataSource() {
 		BasicDataSource retVal = new BasicDataSource();
 		retVal.setDriver(new org.postgresql.Driver());

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

@@ -10,6 +10,7 @@ import org.apache.commons.io.Charsets;
 import org.apache.commons.lang3.Validate;
 import org.hl7.fhir.dstu3.model.*;
 import org.hl7.fhir.dstu3.model.Bundle.BundleEntryComponent;
+import org.hl7.fhir.dstu3.model.CodeSystem.CodeSystemContentMode;
 import org.hl7.fhir.dstu3.model.CodeSystem.ConceptDefinitionComponent;
 import org.hl7.fhir.dstu3.model.OperationOutcome.IssueSeverity;
 import org.hl7.fhir.dstu3.model.ValueSet.ConceptReferenceComponent;
@@ -142,7 +143,7 @@ public class DefaultProfileValidationSupport implements IValidationSupport {
 	@Override
 	public boolean isCodeSystemSupported(FhirContext theContext, String theSystem) {
 		CodeSystem cs = fetchCodeSystem(theContext, theSystem);
-		return cs != null;
+		return cs != null && cs.getContent() != CodeSystemContentMode.NOTPRESENT;
 	}
 
 	private void loadCodeSystems(FhirContext theContext, Map<String, CodeSystem> theCodeSystems, Map<String, ValueSet> theValueSets, String theClasspath) {

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

@@ -17,6 +17,8 @@ import ca.uhn.fhir.context.FhirContext;
 
 public class ValidationSupportChain implements IValidationSupport {
 
+	private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(ValidationSupportChain.class);
+
 	private List<IValidationSupport> myChain;
 
 	/**
@@ -97,9 +99,16 @@ public class ValidationSupportChain implements IValidationSupport {
 
 	@Override
 	public CodeValidationResult validateCode(FhirContext theCtx, String theCodeSystem, String theCode, String theDisplay) {
+		
+		ourLog.info("Validating code {} in chain with {} items", theCode, myChain.size());
+		
 		for (IValidationSupport next : myChain) {
 			if (next.isCodeSystemSupported(theCtx, theCodeSystem)) {
-				return next.validateCode(theCtx, theCodeSystem, theCode, theDisplay);
+				CodeValidationResult result = next.validateCode(theCtx, theCodeSystem, theCode, theDisplay);
+				ourLog.info("Chain item {} returned outcome {}", next, result.isOk());
+				return result;
+			} else {
+				ourLog.info("Chain item {} does not support code system {}", next, theCodeSystem);
 			}
 		}
 		return myChain.get(0).validateCode(theCtx, theCodeSystem, theCode, theDisplay);

src/changes/changes.xml

@@ -213,6 +213,10 @@
 				Server AuthorizationInterceptor always rejects history operation 
 				at the type level even if rules should allow it.
 			</action>
+			<action type="fix">
+				JPA server terminology service was not correctly validating or expanding codes 
+				in SNOMED CT or LOINC code systems. Thanks to David Hay for reporting!
+			</action>
 		</release>
 		<release version="2.1" date="2016-11-11">
 			<action type="add">