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Problem found in LOINC loader.

This commit is contained in:
ianmarshall 2020-08-30 17:11:48 -04:00
parent ff7aab2924
commit 1c55d87b10
4 changed files with 89 additions and 5 deletions
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1
hapi-fhir-base/src/main/resources/ca/uhn/fhir/i18n/hapi-messages.properties
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@ -142,6 +142,7 @@ ca.uhn.fhir.jpa.binstore.BinaryAccessProvider.unknownType=Content in resource of
ca.uhn.fhir.jpa.term.BaseTermReadSvcImpl.cannotCreateDuplicateCodeSystemUrl=Can not create multiple CodeSystem resources with CodeSystem.url "{0}", already have one with resource ID: {1}
ca.uhn.fhir.jpa.term.BaseTermReadSvcImpl.cannotCreateDuplicateCodeSystemUrlAndVersion=Can not create multiple CodeSystem resources with CodeSystem.url "{0}" and CodeSystem.version "{1}", already have one with resource ID: {2}
ca.uhn.fhir.jpa.term.BaseTermReadSvcImpl.cannotUpdateVersionForExistingCodeSystemVersion=Updated CodeSystem has wrong version id. Existing CodeSystem resource has CodeSystem.url "{0}" and CodeSystem.version "{1}", already have one with resource ID: {2}
ca.uhn.fhir.jpa.term.BaseTermReadSvcImpl.cannotCreateDuplicateConceptMapUrl=Can not create multiple ConceptMap resources with ConceptMap.url "{0}", already have one with resource ID: {1}
ca.uhn.fhir.jpa.term.BaseTermReadSvcImpl.cannotCreateDuplicateValueSetUrl=Can not create multiple ValueSet resources with ValueSet.url "{0}", already have one with resource ID: {1}
ca.uhn.fhir.jpa.term.BaseTermReadSvcImpl.expansionTooLarge=Expansion of ValueSet produced too many codes (maximum {0}) - Operation aborted!

2
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/data/ITermCodeSystemVersionDao.java
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@ -49,7 +49,7 @@ public interface ITermCodeSystemVersionDao extends JpaRepository<TermCodeSystemV
TermCodeSystemVersion findByCodeSystemPidVersionIsNull(@Param("codesystem_pid") Long theCodeSystemPid);
@Query("SELECT cs FROM TermCodeSystemVersion cs WHERE cs.myResourcePid = :resource_id")
List<TermCodeSystemVersion> findByCodeSystemResourcePid(@Param("resource_id") Long theCodeSystemResourcePid);
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);

12
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/term/TermCodeSystemStorageSvcImpl.java
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@ -715,14 +715,18 @@ public class TermCodeSystemStorageSvcImpl implements ITermCodeSystemStorageSvc {
if (theSystemVersionId == null) {
codeSystemVersionEntity = myCodeSystemVersionDao.findByCodeSystemPidVersionIsNull(theCodeSystem.getPid());
if (codeSystemVersionEntity != null) {
msg = myContext.getLocalizer().getMessage(BaseTermReadSvcImpl.class, "cannotCreateDuplicateCodeSystemUrl", theSystemUri,
codeSystemVersionEntity.getResource().getIdDt().toUnqualifiedVersionless().getValue());
msg = myContext.getLocalizer().getMessage(BaseTermReadSvcImpl.class, "cannotCreateDuplicateCodeSystemUrl", theSystemUri, codeSystemVersionEntity.getResource().getIdDt().toUnqualifiedVersionless().getValue());
}
} else {
codeSystemVersionEntity = myCodeSystemVersionDao.findByCodeSystemPidAndVersion(theCodeSystem.getPid(), theSystemVersionId);
if (codeSystemVersionEntity != null) {
msg = myContext.getLocalizer().getMessage(BaseTermReadSvcImpl.class, "cannotCreateDuplicateCodeSystemUrlAndVersion", theSystemUri,
theSystemVersionId, codeSystemVersionEntity.getResource().getIdDt().toUnqualifiedVersionless().getValue());
msg = myContext.getLocalizer().getMessage(BaseTermReadSvcImpl.class, "cannotCreateDuplicateCodeSystemUrlAndVersion", theSystemUri, theSystemVersionId, codeSystemVersionEntity.getResource().getIdDt().toUnqualifiedVersionless().getValue());
} else {
codeSystemVersionEntity = myCodeSystemVersionDao.findByCodeSystemResourcePid(theCodeSystemResourceTable.getId());
if (codeSystemVersionEntity != null) {
msg = myContext.getLocalizer().getMessage(BaseTermReadSvcImpl.class, "cannotCreateDuplicateCodeSystemUrlAndVersion", theSystemUri, theSystemVersionId, codeSystemVersionEntity.getResource().getIdDt().toUnqualifiedVersionless().getValue());
throw new UnprocessableEntityException(msg);
}
}
}
// Throw exception if the CodeSystemVersion is being duplicated.

79
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/term/TerminologyLoaderSvcLoincIntegratedTest.java Normal file
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@ -0,0 +1,79 @@
package ca.uhn.fhir.jpa.term;
import ca.uhn.fhir.jpa.dao.r4.BaseJpaR4Test;
import ca.uhn.fhir.jpa.entity.TermCodeSystem;
import ca.uhn.fhir.jpa.entity.TermCodeSystemVersion;
import org.eclipse.jetty.http.HttpStatus;
import org.hl7.fhir.r4.model.CodeSystem;
import org.junit.jupiter.api.BeforeEach;
import org.junit.jupiter.api.Test;
import java.io.IOException;
import static org.junit.jupiter.api.Assertions.assertEquals;
public class TerminologyLoaderSvcLoincIntegratedTest extends BaseJpaR4Test {
private TermLoaderSvcImpl mySvc;
private ZipCollectionBuilder myFiles;
@BeforeEach
public void before() {
mySvc = new TermLoaderSvcImpl();
mySvc.setTermCodeSystemStorageSvcForUnitTests(myTermCodeSystemStorageSvc);
mySvc.setTermDeferredStorageSvc(myTerminologyDeferredStorageSvc);
myFiles = new ZipCollectionBuilder();
}
@Test
public void testLoadLoincMultipleVersions() throws IOException {
// Load LOINC marked as version 2.67
TerminologyLoaderSvcLoincTest.addLoincMandatoryFilesWithPropertiesFileToZip(myFiles, "v267_loincupload.properties");
mySvc.loadLoinc(myFiles.getFiles(), mySrd);
runInTransaction(() -> {
assertEquals(1, myTermCodeSystemDao.count());
assertEquals(1, myTermCodeSystemVersionDao.count());
assertEquals(1, myResourceTableDao.count());
TermCodeSystem myTermCodeSystem = myTermCodeSystemDao.findByCodeSystemUri("http://loinc.org");
TermCodeSystemVersion myTermCodeSystemVersion = myTermCodeSystemVersionDao.findByCodeSystemPidAndVersion(myTermCodeSystem.getPid(), "2.67");
assertEquals(myTermCodeSystem.getCurrentVersion().getPid(), myTermCodeSystemVersion.getPid());
assertEquals(myTermCodeSystem.getResource().getId(), myTermCodeSystemVersion.getResource().getId());
});
// Update LOINC marked as version 2.67
myFiles = new ZipCollectionBuilder();
TerminologyLoaderSvcLoincTest.addLoincMandatoryFilesWithPropertiesFileToZip(myFiles, "v267_loincupload.properties");
mySvc.loadLoinc(myFiles.getFiles(), mySrd);
runInTransaction(() -> {
assertEquals(1, myTermCodeSystemDao.count());
assertEquals(1, myTermCodeSystemVersionDao.count());
TermCodeSystem myTermCodeSystem = myTermCodeSystemDao.findByCodeSystemUri("http://loinc.org");
TermCodeSystemVersion myTermCodeSystemVersion = myTermCodeSystemVersionDao.findByCodeSystemPidAndVersion(myTermCodeSystem.getPid(), "2.67");
assertEquals(myTermCodeSystem.getCurrentVersion().getPid(), myTermCodeSystemVersion.getPid());
assertEquals(myTermCodeSystem.getResource().getId(), myTermCodeSystemVersion.getResource().getId());
});
// Load LOINC marked as version 2.68
myFiles = new ZipCollectionBuilder();
TerminologyLoaderSvcLoincTest.addLoincMandatoryFilesWithPropertiesFileToZip(myFiles, "v268_loincupload.properties");
mySvc.loadLoinc(myFiles.getFiles(), mySrd);
runInTransaction(() -> {
assertEquals(1, myTermCodeSystemDao.count());
assertEquals(2, myTermCodeSystemVersionDao.count());
TermCodeSystem myTermCodeSystem = myTermCodeSystemDao.findByCodeSystemUri("http://loinc.org");
TermCodeSystemVersion mySecondTermCodeSystemVersion = myTermCodeSystemVersionDao.findByCodeSystemPidAndVersion(myTermCodeSystem.getPid(), "2.68");
assertEquals(myTermCodeSystem.getCurrentVersion().getPid(), mySecondTermCodeSystemVersion.getPid());
assertEquals(myTermCodeSystem.getResource().getId(), mySecondTermCodeSystemVersion.getResource().getId());
});
}
}