JPA server was not correctly validating and expanding SCT codes

hapifhir · Jan 19, 2017 · d1542e9 · d1542e9
1 parent 64e3435
commit d1542e9
Show file tree

Hide file tree

Showing 9 changed files with 39 additions and 11 deletions.
diff --git a/hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/dstu3/BaseJpaDstu3Test.java b/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;

diff --git a/...ver-base/src/test/java/ca/uhn/fhir/jpa/dao/dstu3/FhirResourceDaoDstu3TerminologyTest.java b/...ver-base/src/test/java/ca/uhn/fhir/jpa/dao/dstu3/FhirResourceDaoDstu3TerminologyTest.java
@@ -11,15 +11,11 @@
 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.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 void testCodeSystemCreateDuplicateFails() {
 		}
 	}
 
+	@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

diff --git a/hapi-fhir-jpaserver-uhnfhirtest/src/main/java/ca/uhn/fhirtest/config/DbServerConfig.java b/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 {
+
+}
diff --git a/hapi-fhir-jpaserver-uhnfhirtest/src/main/java/ca/uhn/fhirtest/config/TdlDstu2Config.java b/hapi-fhir-jpaserver-uhnfhirtest/src/main/java/ca/uhn/fhirtest/config/TdlDstu2Config.java
@@ -68,7 +68,6 @@ public DaoConfig daoConfig() {
 	}
 
 	@Bean(name = "myPersistenceDataSourceDstu1", destroyMethod = "close")
-	@DependsOn("dbServer")
 	public DataSource dataSource() {
 		BasicDataSource retVal = new BasicDataSource();
 //		retVal.setDriver(new org.apache.derby.jdbc.ClientDriver());

diff --git a/hapi-fhir-jpaserver-uhnfhirtest/src/main/java/ca/uhn/fhirtest/config/TdlDstu3Config.java b/hapi-fhir-jpaserver-uhnfhirtest/src/main/java/ca/uhn/fhirtest/config/TdlDstu3Config.java
@@ -65,7 +65,6 @@ public IServerInterceptor securityInterceptor() {
 	}
 
 	@Bean(name = "myPersistenceDataSourceDstu3", destroyMethod = "close")
-	@DependsOn("dbServer")
 	public DataSource dataSource() {
 		BasicDataSource retVal = new BasicDataSource();
 //		retVal.setDriver(new org.apache.derby.jdbc.ClientDriver());

diff --git a/hapi-fhir-jpaserver-uhnfhirtest/src/main/java/ca/uhn/fhirtest/config/TestDstu2Config.java b/hapi-fhir-jpaserver-uhnfhirtest/src/main/java/ca/uhn/fhirtest/config/TestDstu2Config.java
@@ -70,7 +70,6 @@ public DaoConfig daoConfig() {
 	}
 
 	@Bean(name = "myPersistenceDataSourceDstu1", destroyMethod = "close")
-	@DependsOn("dbServer")
 	public DataSource dataSource() {
 		BasicDataSource retVal = new BasicDataSource();
 		retVal.setDriver(new org.postgresql.Driver());

diff --git a/hapi-fhir-jpaserver-uhnfhirtest/src/main/java/ca/uhn/fhirtest/config/TestDstu3Config.java b/hapi-fhir-jpaserver-uhnfhirtest/src/main/java/ca/uhn/fhirtest/config/TestDstu3Config.java
@@ -74,7 +74,6 @@ public IServerInterceptor securityInterceptor() {
 	}
 
 	@Bean(name = "myPersistenceDataSourceDstu3", destroyMethod = "close")
-	@DependsOn("dbServer")
 	public DataSource dataSource() {
 		BasicDataSource retVal = new BasicDataSource();
 		retVal.setDriver(new org.postgresql.Driver());

diff --git a/...tu3/src/main/java/org/hl7/fhir/dstu3/hapi/validation/DefaultProfileValidationSupport.java b/...tu3/src/main/java/org/hl7/fhir/dstu3/hapi/validation/DefaultProfileValidationSupport.java
@@ -10,6 +10,7 @@
 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 void flush() {
 	@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) {

diff --git a/src/changes/changes.xml b/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">