Merge pull request #2882 from hapifhir/issue-2881-loinc-terminology-upload-doesnt-load-concepts-when-current-versionfalse

Save version collections also when version is not made current.

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

@@ -473,30 +473,23 @@ public class TermCodeSystemStorageSvcImpl implements ITermCodeSystemStorageSvc {
 		// defaults to true
 		boolean isMakeVersionCurrent = theRequestDetails == null ||
 			(boolean) theRequestDetails.getUserData().getOrDefault(MAKE_LOADING_VERSION_CURRENT, Boolean.TRUE);
+
 		if (isMakeVersionCurrent) {
-			makeCodeSystemCurrentVersion(codeSystem, codeSystemToStore, conceptsToSave, totalCodeCount);
+			codeSystem.setCurrentVersion(codeSystemToStore);
+			if (codeSystem.getPid() == null) {
+				codeSystem = myCodeSystemDao.saveAndFlush(codeSystem);
+			}
 		}
 
+		ourLog.debug("Setting CodeSystemVersion[{}] on {} concepts...", codeSystem.getPid(), totalCodeCount);
+		for (TermConcept next : conceptsToSave) {
+			populateVersion(next, codeSystemToStore);
 		}
 
-
+		ourLog.debug("Saving {} concepts...", totalCodeCount);
-	private void makeCodeSystemCurrentVersion(TermCodeSystem theCodeSystem, TermCodeSystemVersion theCodeSystemToStore,
-			Collection<TermConcept> theConceptsToSave, int theTotalCodeCount) {
-
-		theCodeSystem.setCurrentVersion(theCodeSystemToStore);
-		if (theCodeSystem.getPid() == null) {
-			theCodeSystem = myCodeSystemDao.saveAndFlush(theCodeSystem);
-		}
-
-		ourLog.debug("Setting CodeSystemVersion[{}] on {} concepts...", theCodeSystem.getPid(), theTotalCodeCount);
-		for (TermConcept next : theConceptsToSave) {
-			populateVersion(next, theCodeSystemToStore);
-		}
-
-		ourLog.debug("Saving {} concepts...", theTotalCodeCount);
 		IdentityHashMap<TermConcept, Object> conceptsStack2 = new IdentityHashMap<>();
-		for (TermConcept next : theConceptsToSave) {
+		for (TermConcept next : conceptsToSave) {
-			persistChildren(next, theCodeSystemToStore, conceptsStack2, theTotalCodeCount);
+			persistChildren(next, codeSystemToStore, conceptsStack2, totalCodeCount);
 		}
 
 		ourLog.debug("Done saving concepts, flushing to database");

hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/term/TerminologyLoaderSvcLoincJpaTest.java

@@ -111,6 +111,77 @@ public class TerminologyLoaderSvcLoincJpaTest extends BaseJpaR4Test {
 
 	}
 
+	@Test
+	public void testLoadLoincVersionNotCurrent() throws IOException {
+
+		// Load LOINC marked as version 2.67
+		TerminologyLoaderSvcLoincTest.addLoincMandatoryFilesWithPropertiesFileToZip(myFiles, "v267_loincupload.properties");
+
+		mySvc.loadLoinc(myFiles.getFiles(), mySrd);
+
+		myTerminologyDeferredStorageSvc.saveAllDeferred();
+
+		// array just to make it final and populate it into following lambda
+		final TermCodeSystemVersion[] currentCodeSystemVersion_before_loading_v2_68 = new TermCodeSystemVersion[1];
+
+		runInTransaction(() -> {
+			assertEquals(1, myTermCodeSystemDao.count());
+			assertEquals(2, myTermCodeSystemVersionDao.count());
+			assertEquals(24, myTermValueSetDao.count());
+			assertEquals(162, myTermConceptDao.count());
+			assertEquals(12, myTermConceptMapDao.count());
+			assertEquals(38, myResourceTableDao.count());
+			TermCodeSystem myTermCodeSystem = myTermCodeSystemDao.findByCodeSystemUri("http://loinc.org");
+
+			TermCodeSystemVersion myTermCodeSystemVersion_versioned =
+				myTermCodeSystemVersionDao.findByCodeSystemPidAndVersion(myTermCodeSystem.getPid(), "2.67");
+			assertNotEquals(myTermCodeSystem.getCurrentVersion().getPid(), myTermCodeSystemVersion_versioned.getPid());
+			assertNotEquals(myTermCodeSystem.getResource().getId(), myTermCodeSystemVersion_versioned.getResource().getId());
+
+			TermCodeSystemVersion myTermCodeSystemVersion_nonversioned =
+				myTermCodeSystemVersionDao.findByCodeSystemPidVersionIsNull(myTermCodeSystem.getPid());
+			assertEquals(myTermCodeSystem.getCurrentVersion().getPid(), myTermCodeSystemVersion_nonversioned.getPid());
+			assertEquals(myTermCodeSystem.getResource().getId(), myTermCodeSystemVersion_nonversioned.getResource().getId());
+
+			// current should be null loaded after 2.67
+			currentCodeSystemVersion_before_loading_v2_68[0] =
+				myTermCodeSystemVersionDao.findByCodeSystemPidVersionIsNull(myTermCodeSystem.getPid());
+		});
+
+		// Load LOINC marked as version 2.68 and not making it current (so 2.67 should remain current)
+		myFiles = new ZipCollectionBuilder();
+		TerminologyLoaderSvcLoincTest.addLoincMandatoryFilesWithPropertiesFileToZip(
+			myFiles, "v268_curr_false_loincupload.properties");
+		mySvc.loadLoinc(myFiles.getFiles(), mySrd);
+		myTerminologyDeferredStorageSvc.saveAllDeferred();
+
+		runInTransaction(() -> {
+			assertEquals(1, myTermCodeSystemDao.count());
+			assertEquals(3, myTermCodeSystemVersionDao.count());
+			assertEquals(36, myTermValueSetDao.count());
+			assertEquals(243, myTermConceptDao.count());
+			assertEquals(18, myTermConceptMapDao.count());
+			assertEquals(57, myResourceTableDao.count());
+			TermCodeSystem myTermCodeSystem = myTermCodeSystemDao.findByCodeSystemUri("http://loinc.org");
+
+			TermCodeSystemVersion currentCodeSystemVersion_after_loading_v2_68 =
+				myTermCodeSystemVersionDao.findByCodeSystemPidVersionIsNull(myTermCodeSystem.getPid());
+
+			// current should be same as before loading 2.68
+			assertEquals(currentCodeSystemVersion_before_loading_v2_68[0].getPid(), currentCodeSystemVersion_after_loading_v2_68.getPid());
+
+			TermCodeSystemVersion termCodeSystemVersion_267 =
+				myTermCodeSystemVersionDao.findByCodeSystemPidAndVersion(myTermCodeSystem.getPid(), "2.67");
+			assertNotEquals(myTermCodeSystem.getCurrentVersion().getPid(), termCodeSystemVersion_267.getPid());
+
+			TermCodeSystemVersion termCodeSystemVersion_268 =
+				myTermCodeSystemVersionDao.findByCodeSystemPidAndVersion(myTermCodeSystem.getPid(), "2.68");
+			assertNotEquals(myTermCodeSystem.getCurrentVersion().getPid(), termCodeSystemVersion_268.getPid());
+		});
+
+	}
+
+
 	/**
 	 * Loinc distro includes loinc.xml as of 2.70
 	 */

hapi-fhir-jpaserver-base/src/test/resources/loinc/v268_curr_false_loincupload.properties

@@ -0,0 +1,99 @@
+#################
+### MANDATORY ###
+#################
+
+# Answer lists (ValueSets of potential answers/values for LOINC "questions")
+## File must be present
+loinc.answerlist.file=AccessoryFiles/AnswerFile/AnswerList.csv
+# Answer list links (connects LOINC observation codes to answer list codes)
+## File must be present
+loinc.answerlist.link.file=AccessoryFiles/AnswerFile/LoincAnswerListLink.csv
+
+# Document ontology
+## File must be present
+loinc.document.ontology.file=AccessoryFiles/DocumentOntology/DocumentOntology.csv
+
+# LOINC codes
+## File must be present
+loinc.file=LoincTable/Loinc.csv
+
+# LOINC hierarchy
+## File must be present
+loinc.hierarchy.file=AccessoryFiles/MultiAxialHierarchy/MultiAxialHierarchy.csv
+
+# IEEE medical device codes
+## File must be present
+loinc.ieee.medical.device.code.mapping.table.file=AccessoryFiles/LoincIeeeMedicalDeviceCodeMappingTable/LoincIeeeMedicalDeviceCodeMappingTable.csv
+
+# Imaging document codes
+## File must be present
+loinc.imaging.document.codes.file=AccessoryFiles/ImagingDocuments/ImagingDocumentCodes.csv
+
+# Part
+## File must be present
+loinc.part.file=AccessoryFiles/PartFile/Part.csv
+
+# Part link
+## File must be present
+loinc.part.link.primary.file=AccessoryFiles/PartFile/LoincPartLink_Primary.csv
+loinc.part.link.supplementary.file=AccessoryFiles/PartFile/LoincPartLink_Supplementary.csv
+
+# Part related code mapping
+## File must be present
+loinc.part.related.code.mapping.file=AccessoryFiles/PartFile/PartRelatedCodeMapping.csv
+
+# RSNA playbook
+## File must be present
+loinc.rsna.playbook.file=AccessoryFiles/LoincRsnaRadiologyPlaybook/LoincRsnaRadiologyPlaybook.csv
+
+# Top 2000 codes - SI
+## File must be present
+loinc.top2000.common.lab.results.si.file=AccessoryFiles/Top2000Results/SI/Top2000CommonLabResultsSi.csv
+# Top 2000 codes - US
+## File must be present
+loinc.top2000.common.lab.results.us.file=AccessoryFiles/Top2000Results/US/Top2000CommonLabResultsUs.csv
+
+# Universal lab order ValueSet
+## File must be present
+loinc.universal.lab.order.valueset.file=AccessoryFiles/LoincUniversalLabOrdersValueSet/LoincUniversalLabOrdersValueSet.csv
+
+################
+### OPTIONAL ###
+################
+
+# This is the version identifier for the LOINC code system
+## Key may be omitted if only a single version of LOINC is being kept.
+loinc.codesystem.version=2.68
+
+loinc.codesystem.make.current=false
+
+# This is the version identifier for the answer list file
+## Key may be omitted
+loinc.answerlist.version=Beta.1
+
+# This is the version identifier for uploaded ConceptMap resources
+## Key may be omitted
+loinc.conceptmap.version=Beta.1
+
+# Group
+## Default value if key not provided: AccessoryFiles/GroupFile/Group.csv
+## File may be omitted
+loinc.group.file=AccessoryFiles/GroupFile/Group.csv
+# Group terms
+## Default value if key not provided: AccessoryFiles/GroupFile/GroupLoincTerms.csv
+## File may be omitted
+loinc.group.terms.file=AccessoryFiles/GroupFile/GroupLoincTerms.csv
+# Parent group
+## Default value if key not provided: AccessoryFiles/GroupFile/ParentGroup.csv
+## File may be omitted
+loinc.parent.group.file=AccessoryFiles/GroupFile/ParentGroup.csv
+
+# Consumer Names
+## Default value if key not provided: AccessoryFiles/ConsumerName/ConsumerName.csv
+## File may be omitted
+loinc.consumer.name.file=AccessoryFiles/ConsumerName/ConsumerName.csv
+
+# Linguistic Variants
+## Default value if key not provided: AccessoryFiles/LinguisticVariants/LinguisticVariants.csv
+## File may be omitted
+loinc.linguistic.variants.file=AccessoryFiles/LinguisticVariants/LinguisticVariants.csv