Fix issue deleting CodeSystem resources (#1316)
* Fix deleting CodeSystem resources * Test fixes * Address review comments
This commit is contained in:
James Agnew
GitHub
parent
004f42cdcc
commit
6f44d7c360
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@ -35,8 +35,11 @@ public interface ITermCodeSystemVersionDao extends JpaRepository<TermCodeSystemV
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@Query("DELETE FROM TermCodeSystemVersion csv WHERE csv.myCodeSystem = :cs")
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void deleteForCodeSystem(@Param("cs") TermCodeSystem theCodeSystem);
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@Query("SELECT cs FROM TermCodeSystemVersion cs WHERE cs.myResourcePid = :resource_id")
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List<TermCodeSystemVersion> findByCodeSystemPid(@Param("resource_id") Long theCodeSystemResourcePid);
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@Query("SELECT cs FROM TermCodeSystemVersion cs WHERE cs.myResource.myId = :resource_id")
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List<TermCodeSystemVersion> findByCodeSystemResource(@Param("resource_id") Long theCodeSystemResourcePid);
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List<TermCodeSystemVersion> findByCodeSystemResourcePid(@Param("resource_id") Long theCodeSystemResourcePid);
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@Query("SELECT cs FROM TermCodeSystemVersion cs WHERE cs.myCodeSystemHavingThisVersionAsCurrentVersionIfAny.myResource.myId = :resource_id")
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TermCodeSystemVersion findCurrentVersionForCodeSystemResourcePid(@Param("resource_id") Long theCodeSystemResourcePid);
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@ -53,6 +53,9 @@ public class TermCodeSystemVersion implements Serializable {
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@JoinColumn(name = "RES_ID", referencedColumnName = "RES_ID", nullable = false, updatable = false, foreignKey = @ForeignKey(name = "FK_CODESYSVER_RES_ID"))
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private ResourceTable myResource;
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@Column(name = "RES_ID", insertable = false, updatable = false)
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private Long myResourcePid;
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@Column(name = "CS_VERSION_ID", nullable = true, updatable = false, length = MAX_VERSION_LENGTH)
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private String myCodeSystemVersionId;
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/**
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@ -295,7 +295,8 @@ public abstract class BaseHapiTerminologySvcImpl implements IHapiTerminologySvc,
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myCodeSystemDao.flush();
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int i = 0;
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for (TermCodeSystemVersion next : myCodeSystemVersionDao.findByCodeSystemResource(theCodeSystem.getPid())) {
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List<TermCodeSystemVersion> codeSystemVersions = myCodeSystemVersionDao.findByCodeSystemPid(theCodeSystem.getPid());
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for (TermCodeSystemVersion next : codeSystemVersions) {
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deleteCodeSystemVersion(next.getPid());
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}
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myCodeSystemVersionDao.deleteForCodeSystem(theCodeSystem);
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@ -1647,7 +1648,7 @@ public abstract class BaseHapiTerminologySvcImpl implements IHapiTerminologySvc,
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ValidateUtil.isNotBlankOrThrowInvalidRequest(theSystemUri, "No system URI supplied");
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// Grab the existing versions so we can delete them later
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List<TermCodeSystemVersion> existing = myCodeSystemVersionDao.findByCodeSystemResource(theCodeSystemResourcePid);
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List<TermCodeSystemVersion> existing = myCodeSystemVersionDao.findByCodeSystemResourcePid(theCodeSystemResourcePid);
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/*
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* For now we always delete old versions. At some point it would be nice to allow configuration to keep old versions.
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@ -7,6 +7,7 @@ import ca.uhn.fhir.jpa.dao.*;
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import ca.uhn.fhir.jpa.dao.data.*;
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import ca.uhn.fhir.jpa.dao.dstu2.FhirResourceDaoDstu2SearchNoFtTest;
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import ca.uhn.fhir.jpa.dao.r4.BaseJpaR4Test;
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import ca.uhn.fhir.jpa.entity.TermConcept;
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import ca.uhn.fhir.jpa.model.entity.ModelConfig;
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import ca.uhn.fhir.jpa.model.entity.ResourceIndexedSearchParamString;
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import ca.uhn.fhir.jpa.model.entity.ResourceTable;
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@ -105,6 +106,8 @@ public abstract class BaseJpaDstu3Test extends BaseJpaTest {
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@Qualifier("myConceptMapDaoDstu3")
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protected IFhirResourceDaoConceptMap<ConceptMap> myConceptMapDao;
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@Autowired
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protected ITermConceptDao myConceptDao;
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@Autowired
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@Qualifier("myConditionDaoDstu3")
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protected IFhirResourceDao<Condition> myConditionDao;
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@Autowired
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@ -1,12 +1,16 @@
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package ca.uhn.fhir.jpa.dao.dstu3;
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import static org.junit.Assert.assertNotEquals;
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import static org.hamcrest.Matchers.greaterThan;
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import static org.junit.Assert.*;
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import java.nio.charset.StandardCharsets;
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import ca.uhn.fhir.jpa.term.BaseHapiTerminologySvcImpl;
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import org.apache.commons.io.IOUtils;
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import org.hl7.fhir.dstu3.model.CodeSystem;
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import org.hl7.fhir.dstu3.model.Enumerations;
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import org.hl7.fhir.dstu3.model.IdType;
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import org.hl7.fhir.instance.model.api.IIdType;
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import org.junit.AfterClass;
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import org.junit.Test;
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@ -39,5 +43,41 @@ public class FhirResourceDaoDstu3CodeSystemTest extends BaseJpaDstu3Test {
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}
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@Test
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public void testDeleteCodeSystemComplete() {
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BaseHapiTerminologySvcImpl.setForceSaveDeferredAlwaysForUnitTest(false);
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// Create the code system
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CodeSystem cs = new CodeSystem();
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cs.setUrl("http://foo");
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cs.setContent(CodeSystem.CodeSystemContentMode.COMPLETE);
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cs.setStatus(Enumerations.PublicationStatus.ACTIVE);
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cs.addConcept().setCode("A");
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IIdType id = myCodeSystemDao.create(cs, mySrd).getId().toUnqualifiedVersionless();
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runInTransaction(()->{
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assertEquals(1, myConceptDao.count());
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});
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// Update the code system
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cs = new CodeSystem();
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cs.setId(id);
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cs.setUrl("http://foo");
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cs.setContent(CodeSystem.CodeSystemContentMode.COMPLETE);
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cs.setStatus(Enumerations.PublicationStatus.ACTIVE);
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cs.addConcept().setCode("A");
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cs.addConcept().setCode("B");
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myCodeSystemDao.update(cs, mySrd);
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runInTransaction(()->{
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assertEquals(2, myConceptDao.count());
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});
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// Delete the code system
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myCodeSystemDao.delete(id);
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runInTransaction(()->{
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assertEquals(0L, myConceptDao.count());
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});
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}
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}
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@ -2,6 +2,7 @@ package ca.uhn.fhir.jpa.provider.dstu3;
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import ca.uhn.fhir.context.FhirContext;
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import ca.uhn.fhir.jpa.dao.dstu3.FhirResourceDaoDstu3TerminologyTest;
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import ca.uhn.fhir.jpa.term.BaseHapiTerminologySvcImpl;
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import ca.uhn.fhir.rest.server.exceptions.InvalidRequestException;
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import ca.uhn.fhir.rest.server.exceptions.ResourceNotFoundException;
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import ca.uhn.fhir.util.TestUtil;
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@ -86,6 +87,53 @@ public class ResourceProviderDstu3CodeSystemTest extends BaseResourceProviderDst
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}
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@Test
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public void testDeleteCodeSystemComplete2() {
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BaseHapiTerminologySvcImpl.setForceSaveDeferredAlwaysForUnitTest(false);
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String input = "{\n" +
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" \"resourceType\": \"CodeSystem\",\n" +
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" \"id\": \"CDRTestCodeSystem\",\n" +
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" \"url\": \"http://fkcfhir.org/fhir/cs/CDRTestCodeSystem\",\n" +
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" \"identifier\": {\n" +
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" \"value\": \"CDRTestCodeSystem\"\n" +
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" },\n" +
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" \"name\": \"CDRTestCodeSystem\",\n" +
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" \"status\": \"retired\",\n" +
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" \"publisher\": \"FMCNA\",\n" +
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" \"description\": \"Smile CDR Test Code System \",\n" +
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" \"hierarchyMeaning\": \"grouped-by\",\n" +
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" \"content\": \"complete\",\n" +
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" \"concept\": [\n" +
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" {\n" +
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" \"code\": \"IHD\",\n" +
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" \"display\": \"IHD\"\n" +
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" },\n" +
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" {\n" +
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" \"code\": \"HHD\",\n" +
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" \"display\": \"HHD\"\n" +
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" }\n" +
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" ]\n" +
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"}";
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// Create the code system
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CodeSystem cs = (CodeSystem) myFhirCtx.newJsonParser().parseResource(input);
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ourClient.update().resource(cs).execute();
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runInTransaction(()->{
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assertEquals(26, myConceptDao.count());
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});
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// Delete the code system
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ourClient.delete().resource(cs).execute();
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runInTransaction(()->{
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assertEquals(24L, myConceptDao.count());
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});
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}
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@Test
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public void testLookupOperationByCodeAndSystemBuiltInCode() {
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Parameters respParam = ourClient
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@ -298,7 +298,7 @@ public class InterceptorDstu3Test {
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@Create()
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public MethodOutcome create(@ResourceParam Patient theResource) {
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ourLastPatient = theResource;
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return new MethodOutcome();
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return new MethodOutcome().setCreated(true);
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}
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@Operation(name="$postOperation")
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@ -7,7 +7,7 @@ import ca.uhn.fhir.model.dstu2.resource.ValueSet;
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import ca.uhn.fhir.tinder.model.*;
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import ca.uhn.fhir.tinder.util.XMLUtils;
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import org.apache.commons.lang3.StringUtils;
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import org.apache.commons.lang3.text.WordUtils;
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import org.apache.commons.text.WordUtils;
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import org.apache.maven.plugin.MojoExecutionException;
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import org.apache.maven.plugin.MojoFailureException;
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import org.w3c.dom.Document;
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@ -89,6 +89,11 @@
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The informational message returned in an OperationOutcome when a delete failed due to cascades not being enabled
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contained an incorrect example. This has been corrected.
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</action>
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<action type="fix">
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In some cases, deleting a CodeSystem resource would fail because the underlying
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codes were not correctly deleted from the terminology service tables. This is
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fixed.
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</action>
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<action type="change">
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Two foreign keys have been dropped from the HFJ_SEARCH_RESULT table used by the FHIR search query cache. These
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constraints did not add value and caused unneccessary contention when used under high load.
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