Fix issue deleting CodeSystem resources (#1316)

* Fix deleting CodeSystem resources

* Test fixes

* Address review comments

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

@@ -35,8 +35,11 @@ public interface ITermCodeSystemVersionDao extends JpaRepository<TermCodeSystemV
 	@Query("DELETE FROM TermCodeSystemVersion csv WHERE csv.myCodeSystem = :cs")
 	void deleteForCodeSystem(@Param("cs") TermCodeSystem theCodeSystem);
 
+	@Query("SELECT cs FROM TermCodeSystemVersion cs WHERE cs.myResourcePid = :resource_id")
+	List<TermCodeSystemVersion> findByCodeSystemPid(@Param("resource_id") Long theCodeSystemResourcePid);
+
 	@Query("SELECT cs FROM TermCodeSystemVersion cs WHERE cs.myResource.myId = :resource_id")
-	List<TermCodeSystemVersion> findByCodeSystemResource(@Param("resource_id") Long theCodeSystemResourcePid);
+	List<TermCodeSystemVersion> findByCodeSystemResourcePid(@Param("resource_id") Long theCodeSystemResourcePid);
 
 	@Query("SELECT cs FROM TermCodeSystemVersion cs WHERE cs.myCodeSystemHavingThisVersionAsCurrentVersionIfAny.myResource.myId = :resource_id")
 	TermCodeSystemVersion findCurrentVersionForCodeSystemResourcePid(@Param("resource_id") Long theCodeSystemResourcePid);

hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/entity/TermCodeSystemVersion.java

@@ -53,6 +53,9 @@ public class TermCodeSystemVersion implements Serializable {
 	@JoinColumn(name = "RES_ID", referencedColumnName = "RES_ID", nullable = false, updatable = false, foreignKey = @ForeignKey(name = "FK_CODESYSVER_RES_ID"))
 	private ResourceTable myResource;
 
+	@Column(name = "RES_ID", insertable = false, updatable = false)
+	private Long myResourcePid;
+
 	@Column(name = "CS_VERSION_ID", nullable = true, updatable = false, length = MAX_VERSION_LENGTH)
 	private String myCodeSystemVersionId;
 	/**

hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/term/BaseHapiTerminologySvcImpl.java

@@ -295,7 +295,8 @@ public abstract class BaseHapiTerminologySvcImpl implements IHapiTerminologySvc,
 		myCodeSystemDao.flush();
 
 		int i = 0;
-		for (TermCodeSystemVersion next : myCodeSystemVersionDao.findByCodeSystemResource(theCodeSystem.getPid())) {
+		List<TermCodeSystemVersion> codeSystemVersions = myCodeSystemVersionDao.findByCodeSystemPid(theCodeSystem.getPid());
+		for (TermCodeSystemVersion next : codeSystemVersions) {
 			deleteCodeSystemVersion(next.getPid());
 		}
 		myCodeSystemVersionDao.deleteForCodeSystem(theCodeSystem);
@@ -1647,7 +1648,7 @@ public abstract class BaseHapiTerminologySvcImpl implements IHapiTerminologySvc,
 		ValidateUtil.isNotBlankOrThrowInvalidRequest(theSystemUri, "No system URI supplied");
 
 		// Grab the existing versions so we can delete them later
-		List<TermCodeSystemVersion> existing = myCodeSystemVersionDao.findByCodeSystemResource(theCodeSystemResourcePid);
+		List<TermCodeSystemVersion> existing = myCodeSystemVersionDao.findByCodeSystemResourcePid(theCodeSystemResourcePid);
 
 		/*
 		 * For now we always delete old versions. At some point it would be nice to allow configuration to keep old versions.

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

@@ -7,6 +7,7 @@ import ca.uhn.fhir.jpa.dao.*;
 import ca.uhn.fhir.jpa.dao.data.*;
 import ca.uhn.fhir.jpa.dao.dstu2.FhirResourceDaoDstu2SearchNoFtTest;
 import ca.uhn.fhir.jpa.dao.r4.BaseJpaR4Test;
+import ca.uhn.fhir.jpa.entity.TermConcept;
 import ca.uhn.fhir.jpa.model.entity.ModelConfig;
 import ca.uhn.fhir.jpa.model.entity.ResourceIndexedSearchParamString;
 import ca.uhn.fhir.jpa.model.entity.ResourceTable;
@@ -105,6 +106,8 @@ public abstract class BaseJpaDstu3Test extends BaseJpaTest {
 	@Qualifier("myConceptMapDaoDstu3")
 	protected IFhirResourceDaoConceptMap<ConceptMap> myConceptMapDao;
 	@Autowired
+	protected ITermConceptDao myConceptDao;
+	@Autowired
 	@Qualifier("myConditionDaoDstu3")
 	protected IFhirResourceDao<Condition> myConditionDao;
 	@Autowired

hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/dstu3/FhirResourceDaoDstu3CodeSystemTest.java

@@ -1,12 +1,16 @@
 package ca.uhn.fhir.jpa.dao.dstu3;
 
-import static org.junit.Assert.assertNotEquals;
+import static org.hamcrest.Matchers.greaterThan;
+import static org.junit.Assert.*;
 
 import java.nio.charset.StandardCharsets;
 
 import ca.uhn.fhir.jpa.term.BaseHapiTerminologySvcImpl;
 import org.apache.commons.io.IOUtils;
 import org.hl7.fhir.dstu3.model.CodeSystem;
+import org.hl7.fhir.dstu3.model.Enumerations;
+import org.hl7.fhir.dstu3.model.IdType;
+import org.hl7.fhir.instance.model.api.IIdType;
 import org.junit.AfterClass;
 import org.junit.Test;
 
@@ -39,5 +43,41 @@ public class FhirResourceDaoDstu3CodeSystemTest extends BaseJpaDstu3Test {
 		
 	}
 
+	@Test
+	public void testDeleteCodeSystemComplete() {
+		BaseHapiTerminologySvcImpl.setForceSaveDeferredAlwaysForUnitTest(false);
+
+		// Create the code system
+		CodeSystem cs = new CodeSystem();
+		cs.setUrl("http://foo");
+		cs.setContent(CodeSystem.CodeSystemContentMode.COMPLETE);
+		cs.setStatus(Enumerations.PublicationStatus.ACTIVE);
+		cs.addConcept().setCode("A");
+		IIdType id = myCodeSystemDao.create(cs, mySrd).getId().toUnqualifiedVersionless();
+		runInTransaction(()->{
+			assertEquals(1, myConceptDao.count());
+		});
+
+		// Update the code system
+		cs = new CodeSystem();
+		cs.setId(id);
+		cs.setUrl("http://foo");
+		cs.setContent(CodeSystem.CodeSystemContentMode.COMPLETE);
+		cs.setStatus(Enumerations.PublicationStatus.ACTIVE);
+		cs.addConcept().setCode("A");
+		cs.addConcept().setCode("B");
+		myCodeSystemDao.update(cs, mySrd);
+		runInTransaction(()->{
+			assertEquals(2, myConceptDao.count());
+		});
+
+		// Delete the code system
+		myCodeSystemDao.delete(id);
+		runInTransaction(()->{
+			assertEquals(0L, myConceptDao.count());
+		});
+
+	}
+
 
 }

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

@@ -2,6 +2,7 @@ package ca.uhn.fhir.jpa.provider.dstu3;
 
 import ca.uhn.fhir.context.FhirContext;
 import ca.uhn.fhir.jpa.dao.dstu3.FhirResourceDaoDstu3TerminologyTest;
+import ca.uhn.fhir.jpa.term.BaseHapiTerminologySvcImpl;
 import ca.uhn.fhir.rest.server.exceptions.InvalidRequestException;
 import ca.uhn.fhir.rest.server.exceptions.ResourceNotFoundException;
 import ca.uhn.fhir.util.TestUtil;
@@ -86,6 +87,53 @@ public class ResourceProviderDstu3CodeSystemTest extends BaseResourceProviderDst
 
 	}
 
+	@Test
+	public void testDeleteCodeSystemComplete2() {
+		BaseHapiTerminologySvcImpl.setForceSaveDeferredAlwaysForUnitTest(false);
+
+		String input = "{\n" +
+			"    \"resourceType\": \"CodeSystem\",\n" +
+			"    \"id\": \"CDRTestCodeSystem\",\n" +
+			"    \"url\": \"http://fkcfhir.org/fhir/cs/CDRTestCodeSystem\",\n" +
+			"    \"identifier\": {\n" +
+			"        \"value\": \"CDRTestCodeSystem\"\n" +
+			"    },\n" +
+			"    \"name\": \"CDRTestCodeSystem\",\n" +
+			"    \"status\": \"retired\",\n" +
+			"    \"publisher\": \"FMCNA\",\n" +
+			"    \"description\": \"Smile CDR Test Code System \",\n" +
+			"    \"hierarchyMeaning\": \"grouped-by\",\n" +
+			"    \"content\": \"complete\",\n" +
+			"    \"concept\": [\n" +
+			"        {\n" +
+			"            \"code\": \"IHD\",\n" +
+			"            \"display\": \"IHD\"\n" +
+			"        },\n" +
+			"        {\n" +
+			"            \"code\": \"HHD\",\n" +
+			"            \"display\": \"HHD\"\n" +
+			"        }\n" +
+			"    ]\n" +
+			"}";
+
+		// Create the code system
+		CodeSystem cs = (CodeSystem) myFhirCtx.newJsonParser().parseResource(input);
+		ourClient.update().resource(cs).execute();
+		runInTransaction(()->{
+			assertEquals(26, myConceptDao.count());
+		});
+
+		// Delete the code system
+		ourClient.delete().resource(cs).execute();
+		runInTransaction(()->{
+			assertEquals(24L, myConceptDao.count());
+		});
+
+	}
+
+
+
+
 	@Test
 	public void testLookupOperationByCodeAndSystemBuiltInCode() {
 		Parameters respParam = ourClient

hapi-fhir-structures-dstu3/src/test/java/ca/uhn/fhir/rest/server/InterceptorDstu3Test.java

@@ -298,7 +298,7 @@ public class InterceptorDstu3Test {
 		@Create()
 		public MethodOutcome create(@ResourceParam Patient theResource) {
 			ourLastPatient = theResource;
-			return new MethodOutcome();
+			return new MethodOutcome().setCreated(true);
 		}
 
 		@Operation(name="$postOperation")

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

@@ -7,7 +7,7 @@ import ca.uhn.fhir.model.dstu2.resource.ValueSet;
 import ca.uhn.fhir.tinder.model.*;
 import ca.uhn.fhir.tinder.util.XMLUtils;
 import org.apache.commons.lang3.StringUtils;
-import org.apache.commons.lang3.text.WordUtils;
+import org.apache.commons.text.WordUtils;
 import org.apache.maven.plugin.MojoExecutionException;
 import org.apache.maven.plugin.MojoFailureException;
 import org.w3c.dom.Document;

src/changes/changes.xml

@@ -89,6 +89,11 @@
 				The informational message returned in an OperationOutcome when a delete failed due to cascades not being enabled
 				contained an incorrect example. This has been corrected.
 			</action>
+            <action type="fix">
+                In some cases, deleting a CodeSystem resource would fail because the underlying
+                codes were not correctly deleted from the terminology service tables. This is
+                fixed.
+            </action>            
 			<action type="change">
 				Two foreign keys have been dropped from the HFJ_SEARCH_RESULT table used by the FHIR search query cache. These
 				constraints did not add value and caused unneccessary contention when used under high load.