Merge pull request #2120 from jamesagnew/im_20201005_loincpartlink_fix

Im 20201005 loincpartlink fix

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

@@ -21,6 +21,7 @@ package ca.uhn.fhir.jpa.term;
  */
 
 import ca.uhn.fhir.jpa.term.api.ITermLoaderSvc;
+import ca.uhn.fhir.jpa.util.LogicUtil;
 import ca.uhn.fhir.rest.server.exceptions.InternalErrorException;
 import ca.uhn.fhir.rest.server.exceptions.UnprocessableEntityException;
 import org.apache.commons.io.FileUtils;
@@ -31,6 +32,7 @@ import org.slf4j.LoggerFactory;
 
 import java.io.*;
 import java.util.ArrayList;
+import java.util.Arrays;
 import java.util.HashSet;
 import java.util.List;
 import java.util.Set;
@@ -140,6 +142,24 @@ public class LoadedFileDescriptors implements Closeable {
 		}
 	}
 
+	void verifyPartLinkFilesExist(List<String> theMultiPartLinkFiles, String theSinglePartLinkFile) {
+		List<String> notFoundMulti = notFound(theMultiPartLinkFiles);
+		List<String> notFoundSingle = notFound(Arrays.asList(theSinglePartLinkFile));
+		// Expect all of the files in theMultiPartLinkFiles to be found and theSinglePartLinkFile to not be found,
+		// or none of the files in theMultiPartLinkFiles to be found and the SinglePartLinkFile to be found.
+		boolean multiPartFilesFound = notFoundMulti.isEmpty();
+		boolean singlePartFilesFound = notFoundSingle.isEmpty();
+		if (!LogicUtil.multiXor(multiPartFilesFound, singlePartFilesFound)) {
+			String msg;
+			if (!multiPartFilesFound && !singlePartFilesFound) {
+				msg = "Could not find any of the PartLink files: " + notFoundMulti + " nor " + notFoundSingle;
+			} else {
+				msg = "Only either the single PartLink file or the split PartLink files can be present. Found both the single PartLink file, " + theSinglePartLinkFile + ", and the split PartLink files: " + theMultiPartLinkFiles;
+			}
+			throw new UnprocessableEntityException(msg);
+		}
+	}
+
 
 	private static class NonClosableBOMInputStream extends BOMInputStream {
 		NonClosableBOMInputStream(InputStream theWrap) {

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

@@ -114,8 +114,6 @@ public class TermLoaderSvcImpl implements ITermLoaderSvc {
 				uploadProperties.getProperty(LOINC_IEEE_MEDICAL_DEVICE_CODE_MAPPING_TABLE_FILE.getCode(), LOINC_IEEE_MEDICAL_DEVICE_CODE_MAPPING_TABLE_FILE_DEFAULT.getCode()),
 				uploadProperties.getProperty(LOINC_IMAGING_DOCUMENT_CODES_FILE.getCode(), LOINC_IMAGING_DOCUMENT_CODES_FILE_DEFAULT.getCode()),
 				uploadProperties.getProperty(LOINC_PART_FILE.getCode(), LOINC_PART_FILE_DEFAULT.getCode()),
-				uploadProperties.getProperty(LOINC_PART_LINK_FILE_PRIMARY.getCode(), LOINC_PART_LINK_FILE_PRIMARY_DEFAULT.getCode()),
-				uploadProperties.getProperty(LOINC_PART_LINK_FILE_SUPPLEMENTARY.getCode(), LOINC_PART_LINK_FILE_SUPPLEMENTARY_DEFAULT.getCode()),
 				uploadProperties.getProperty(LOINC_PART_RELATED_CODE_MAPPING_FILE.getCode(), LOINC_PART_RELATED_CODE_MAPPING_FILE_DEFAULT.getCode()),
 				uploadProperties.getProperty(LOINC_RSNA_PLAYBOOK_FILE.getCode(), LOINC_RSNA_PLAYBOOK_FILE_DEFAULT.getCode()),
 				uploadProperties.getProperty(LOINC_TOP2000_COMMON_LAB_RESULTS_SI_FILE.getCode(), LOINC_TOP2000_COMMON_LAB_RESULTS_SI_FILE_DEFAULT.getCode()),
@@ -124,6 +122,12 @@ public class TermLoaderSvcImpl implements ITermLoaderSvc {
 			);
 			descriptors.verifyMandatoryFilesExist(mandatoryFilenameFragments);
 
+			List<String> splitPartLinkFilenameFragments = Arrays.asList(
+				uploadProperties.getProperty(LOINC_PART_LINK_FILE_PRIMARY.getCode(), LOINC_PART_LINK_FILE_PRIMARY_DEFAULT.getCode()),
+				uploadProperties.getProperty(LOINC_PART_LINK_FILE_SUPPLEMENTARY.getCode(), LOINC_PART_LINK_FILE_SUPPLEMENTARY_DEFAULT.getCode())
+			);
+			descriptors.verifyPartLinkFilesExist(splitPartLinkFilenameFragments, uploadProperties.getProperty(LOINC_PART_LINK_FILE.getCode(), LOINC_PART_LINK_FILE_DEFAULT.getCode()));
+
 			List<String> optionalFilenameFragments = Arrays.asList(
 				uploadProperties.getProperty(LOINC_GROUP_FILE.getCode(), LOINC_GROUP_FILE_DEFAULT.getCode()),
 				uploadProperties.getProperty(LOINC_GROUP_TERMS_FILE.getCode(), LOINC_GROUP_TERMS_FILE_DEFAULT.getCode()),
@@ -475,8 +479,9 @@ public class TermLoaderSvcImpl implements ITermLoaderSvc {
 
 		// Part link
 		handler = new LoincPartLinkHandler(codeSystemVersion, code2concept, propertyNamesToTypes);
-		iterateOverZipFile(theDescriptors, theUploadProperties.getProperty(LOINC_PART_LINK_FILE_PRIMARY.getCode(), LOINC_PART_LINK_FILE_PRIMARY_DEFAULT.getCode()), handler, ',', QuoteMode.NON_NUMERIC, false);
+		iterateOverZipFileOptional(theDescriptors, theUploadProperties.getProperty(LOINC_PART_LINK_FILE.getCode(), LOINC_PART_LINK_FILE_DEFAULT.getCode()), handler, ',', QuoteMode.NON_NUMERIC, false);
-		iterateOverZipFile(theDescriptors, theUploadProperties.getProperty(LOINC_PART_LINK_FILE_SUPPLEMENTARY.getCode(), LOINC_PART_LINK_FILE_SUPPLEMENTARY_DEFAULT.getCode()), handler, ',', QuoteMode.NON_NUMERIC, false);
+		iterateOverZipFileOptional(theDescriptors, theUploadProperties.getProperty(LOINC_PART_LINK_FILE_PRIMARY.getCode(), LOINC_PART_LINK_FILE_PRIMARY_DEFAULT.getCode()), handler, ',', QuoteMode.NON_NUMERIC, false);
+		iterateOverZipFileOptional(theDescriptors, theUploadProperties.getProperty(LOINC_PART_LINK_FILE_SUPPLEMENTARY.getCode(), LOINC_PART_LINK_FILE_SUPPLEMENTARY_DEFAULT.getCode()), handler, ',', QuoteMode.NON_NUMERIC, false);
 
 		IOUtils.closeQuietly(theDescriptors);
 
@@ -598,6 +603,14 @@ public class TermLoaderSvcImpl implements ITermLoaderSvc {
 	}
 
 	public static void iterateOverZipFile(LoadedFileDescriptors theDescriptors, String theFileNamePart, IRecordHandler theHandler, char theDelimiter, QuoteMode theQuoteMode, boolean theIsPartialFilename) {
+		iterateOverZipFile(theDescriptors, theFileNamePart, theHandler, theDelimiter, theQuoteMode, theIsPartialFilename, true);
+	}
+
+	public static void iterateOverZipFileOptional(LoadedFileDescriptors theDescriptors, String theFileNamePart, IRecordHandler theHandler, char theDelimiter, QuoteMode theQuoteMode, boolean theIsPartialFilename) {
+		iterateOverZipFile(theDescriptors, theFileNamePart, theHandler, theDelimiter, theQuoteMode, theIsPartialFilename, false);
+	}
+
+	private static void iterateOverZipFile(LoadedFileDescriptors theDescriptors, String theFileNamePart, IRecordHandler theHandler, char theDelimiter, QuoteMode theQuoteMode, boolean theIsPartialFilename, boolean theRequireMatch) {
 
 		boolean foundMatch = false;
 		for (FileDescriptor nextZipBytes : theDescriptors.getUncompressedFileDescriptors()) {
@@ -644,7 +657,7 @@ public class TermLoaderSvcImpl implements ITermLoaderSvc {
 
 		}
 
-		if (!foundMatch) {
+		if (!foundMatch && theRequireMatch) {
 			throw new InvalidRequestException("Did not find file matching " + theFileNamePart);
 		}
 

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

@@ -192,7 +192,7 @@ public abstract class BaseLoincHandler implements IRecordHandler {
 		if (isNotBlank(theVersionPropertyName)) {
 			version = myUploadProperties.getProperty(theVersionPropertyName);
 		} else {
-			version = myUploadProperties.getProperty(LOINC_CONCEPTMAP_VERSION.getCode());
+			version = myUploadProperties.getProperty(LOINC_CODESYSTEM_VERSION.getCode());
 		}
 
 		ValueSet vs;

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

@@ -85,6 +85,9 @@ public class LoincRsnaPlaybookHandler extends BaseLoincHandler implements IRecor
 		// ConceptMap version from properties files
 		String loincRsnaCmVersion = myUploadProperties.getProperty(LOINC_CONCEPTMAP_VERSION.getCode());
 
+		// CodeSystem version from properties file
+		String codeSystemVersionId = myUploadProperties.getProperty(LOINC_CODESYSTEM_VERSION.getCode());
+
 		// RSNA Codes VS
 		ValueSet vs;
 		if (!myIdToValueSet.containsKey(RSNA_CODES_VS_ID)) {
@@ -93,6 +96,7 @@ public class LoincRsnaPlaybookHandler extends BaseLoincHandler implements IRecor
 			vs.setId(RSNA_CODES_VS_ID);
 			vs.setName(RSNA_CODES_VS_NAME);
 			vs.setStatus(Enumerations.PublicationStatus.ACTIVE);
+			vs.setVersion(codeSystemVersionId);
 			myIdToValueSet.put(RSNA_CODES_VS_ID, vs);
 			myValueSets.add(vs);
 		} else {
@@ -177,7 +181,6 @@ public class LoincRsnaPlaybookHandler extends BaseLoincHandler implements IRecor
 
 		String partConceptMapId;
 		String termConceptMapId;
-		String codeSystemVersionId = myUploadProperties.getProperty(LOINC_CODESYSTEM_VERSION.getCode());
 		if (codeSystemVersionId != null) {
 			partConceptMapId = LoincPartRelatedCodeMappingHandler.LOINC_PART_TO_RID_PART_MAP_ID + "-" + codeSystemVersionId;
 			termConceptMapId = LoincPartRelatedCodeMappingHandler.LOINC_TERM_TO_RPID_PART_MAP_ID + "-" + codeSystemVersionId;

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

@@ -69,6 +69,8 @@ public enum LoincUploadPropertiesEnum {
 	LOINC_PART_FILE_DEFAULT("AccessoryFiles/PartFile/Part.csv"),
 
 	// Part link
+	LOINC_PART_LINK_FILE("loinc.part.link.file"),
+	LOINC_PART_LINK_FILE_DEFAULT("AccessoryFiles/PartFile/LoincPartLink.csv"),
 	LOINC_PART_LINK_FILE_PRIMARY("loinc.part.link.primary.file"),
 	LOINC_PART_LINK_FILE_PRIMARY_DEFAULT("AccessoryFiles/PartFile/LoincPartLink_Primary.csv"),
 	LOINC_PART_LINK_FILE_SUPPLEMENTARY("loinc.part.link.supplementary.file"),

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

@@ -39,6 +39,7 @@ import static org.hamcrest.Matchers.contains;
 import static org.hamcrest.Matchers.containsString;
 import static org.hamcrest.Matchers.empty;
 import static org.junit.jupiter.api.Assertions.assertEquals;
+import static org.junit.jupiter.api.Assertions.assertNull;
 import static org.junit.jupiter.api.Assertions.assertTrue;
 import static org.junit.jupiter.api.Assertions.fail;
 import static org.mockito.ArgumentMatchers.any;
@@ -68,9 +69,54 @@ public class TerminologyLoaderSvcLoincTest extends BaseLoaderTest {
 	}
 
 	@Test
-	public void testLoadLoinc() throws Exception {
+	public void testLoadLoincWithSplitPartLink() throws Exception {
 		addLoincMandatoryFilesToZip(myFiles);
+		verifyLoadLoinc();
+	}
 
+	@Test
+	public void testLoadLoincWithSinglePartLink() throws Exception {
+		addLoincMandatoryFilesAndSinglePartLinkToZip(myFiles);
+		verifyLoadLoinc();
+	}
+
+	@Test
+	public void testLoadLoincInvalidPartLinkFiles() throws IOException {
+
+		// Missing all PartLinkFiles
+		addBaseLoincMandatoryFilesToZip(myFiles);
+		myFiles.addFileZip("/loinc/", LOINC_UPLOAD_PROPERTIES_FILE.getCode());
+
+		try {
+			mySvc.loadLoinc(myFiles.getFiles(), mySrd);
+			fail();
+		} catch (UnprocessableEntityException e) {
+			assertEquals("Could not find any of the PartLink files: [AccessoryFiles/PartFile/LoincPartLink_Primary.csv, AccessoryFiles/PartFile/LoincPartLink_Supplementary.csv] nor [AccessoryFiles/PartFile/LoincPartLink.csv]", e.getMessage());
+		}
+
+		// Missing LoincPartLink_Supplementary
+		myFiles.addFileZip("/loinc/", LOINC_PART_LINK_FILE_PRIMARY_DEFAULT.getCode());
+		try {
+			mySvc.loadLoinc(myFiles.getFiles(), mySrd);
+			fail();
+		} catch (UnprocessableEntityException e) {
+			assertEquals("Could not find any of the PartLink files: [AccessoryFiles/PartFile/LoincPartLink_Supplementary.csv] nor [AccessoryFiles/PartFile/LoincPartLink.csv]", e.getMessage());
+		}
+
+		// Both Split and Single PartLink files
+		myFiles.addFileZip("/loinc/", LOINC_PART_LINK_FILE_SUPPLEMENTARY_DEFAULT.getCode());
+		myFiles.addFileZip("/loinc/", LOINC_PART_LINK_FILE_DEFAULT.getCode());
+		try {
+			mySvc.loadLoinc(myFiles.getFiles(), mySrd);
+			fail();
+		} catch (UnprocessableEntityException e) {
+			assertEquals("Only either the single PartLink file or the split PartLink files can be present. Found both the single PartLink file, AccessoryFiles/PartFile/LoincPartLink.csv, and the split PartLink files: [AccessoryFiles/PartFile/LoincPartLink_Primary.csv, AccessoryFiles/PartFile/LoincPartLink_Supplementary.csv]", e.getMessage());
+		}
+
+	}
+
+
+	private void verifyLoadLoinc() throws Exception {
 		// Actually do the load
 		mySvc.loadLoinc(myFiles.getFiles(), mySrd);
 
@@ -138,10 +184,12 @@ public class TerminologyLoaderSvcLoincTest extends BaseLoaderTest {
 		assertEquals(ITermLoaderSvc.LOINC_URI, vs.getCompose().getInclude().get(0).getSystem());
 		assertEquals("LA6270-8", vs.getCompose().getInclude().get(0).getConcept().get(0).getCode());
 		assertEquals("Never", vs.getCompose().getInclude().get(0).getConcept().get(0).getDisplay());
+		assertEquals("Beta.1", vs.getVersion());
 
 		// External AnswerList
 		vs = valueSets.get("LL1892-0");
 		assertEquals(0, vs.getCompose().getIncludeFirstRep().getConcept().size());
+		assertEquals("Beta.1", vs.getVersion());
 
 		// Part
 		code = concepts.get("LP101394-7");
@@ -175,6 +223,7 @@ public class TerminologyLoaderSvcLoincTest extends BaseLoaderTest {
 		assertEquals(3, vs.getCompose().getInclude().get(0).getConcept().size());
 		assertEquals("11488-4", vs.getCompose().getInclude().get(0).getConcept().get(0).getCode());
 		assertEquals("Consult note", vs.getCompose().getInclude().get(0).getConcept().get(0).getDisplay());
+		assertNull(vs.getVersion());
 
 		// Document ontology parts
 		code = concepts.get("11488-4");
@@ -192,6 +241,7 @@ public class TerminologyLoaderSvcLoincTest extends BaseLoaderTest {
 		assertEquals(ITermLoaderSvc.LOINC_URI, vs.getCompose().getInclude().get(0).getSystem());
 		assertEquals("17787-3", vs.getCompose().getInclude().get(0).getConcept().get(0).getCode());
 		assertEquals("NM Thyroid gland Study report", vs.getCompose().getInclude().get(0).getConcept().get(0).getDisplay());
+		assertNull(vs.getVersion());
 
 		// RSNA Playbook Code Parts - Region Imaged
 		code = concepts.get("17787-3");
@@ -260,6 +310,7 @@ public class TerminologyLoaderSvcLoincTest extends BaseLoaderTest {
 		assertEquals("Creatinine [Mass/volume] in Serum or Plasma", vs.getCompose().getInclude().get(0).getConcept().get(0).getDisplay());
 		assertEquals("718-7", vs.getCompose().getInclude().get(0).getConcept().get(1).getCode());
 		assertEquals("Hemoglobin [Mass/volume] in Blood", vs.getCompose().getInclude().get(0).getConcept().get(1).getDisplay());
+		assertNull(vs.getVersion());
 
 		// TOP 2000 - SI
 		vs = valueSets.get(LoincTop2000LabResultsSiHandler.TOP_2000_SI_VS_ID);
@@ -272,6 +323,7 @@ public class TerminologyLoaderSvcLoincTest extends BaseLoaderTest {
 		assertEquals("Creatinine [Moles/volume] in Serum or Plasma", vs.getCompose().getInclude().get(0).getConcept().get(0).getDisplay());
 		assertEquals("718-7", vs.getCompose().getInclude().get(0).getConcept().get(1).getCode());
 		assertEquals("Hemoglobin [Mass/volume] in Blood", vs.getCompose().getInclude().get(0).getConcept().get(1).getDisplay());
+		assertNull(vs.getVersion());
 
 		// Universal lab order VS
 		vs = valueSets.get(LoincUniversalOrderSetHandler.VS_ID_BASE);
@@ -280,6 +332,7 @@ public class TerminologyLoaderSvcLoincTest extends BaseLoaderTest {
 		assertEquals(9, vs.getCompose().getInclude().get(0).getConcept().size());
 		assertEquals("42176-8", vs.getCompose().getInclude().get(0).getConcept().get(0).getCode());
 		assertEquals("1,3 beta glucan [Mass/volume] in Serum", vs.getCompose().getInclude().get(0).getConcept().get(0).getDisplay());
+		assertNull(vs.getVersion());
 
 		// All LOINC codes
 		assertTrue(valueSets.containsKey("loinc-all"));
@@ -296,6 +349,7 @@ public class TerminologyLoaderSvcLoincTest extends BaseLoaderTest {
 		assertTrue(vs.getCompose().hasInclude());
 		assertEquals(1, vs.getCompose().getInclude().size());
 		assertEquals(ITermLoaderSvc.LOINC_URI, vs.getCompose().getInclude().get(0).getSystem());
+		assertEquals("1.0.0", vs.getVersion());
 
 		// IEEE Medical Device Codes
 		conceptMap = conceptMaps.get(LoincIeeeMedicalDeviceCodeHandler.LOINC_IEEE_CM_ID);
@@ -353,6 +407,18 @@ public class TerminologyLoaderSvcLoincTest extends BaseLoaderTest {
 		verify(myTermCodeSystemStorageSvc, times(1)).storeNewCodeSystemVersion(mySystemCaptor.capture(), myCsvCaptor.capture(), any(RequestDetails.class), myValueSetsCaptor.capture(), myConceptMapCaptor.capture());
 		CodeSystem loincCS = mySystemCaptor.getValue();
 		assertEquals("2.67", loincCS.getVersion());
+		List<ValueSet> loincVS_resources = myValueSetsCaptor.getValue();
+		for (ValueSet loincVS : loincVS_resources) {
+			if (loincVS.getId().startsWith("LL1000-0") || loincVS.getId().startsWith("LL1001-8") || loincVS.getId().startsWith("LL1892-0")) {
+				assertEquals("2.67.Beta.1", loincVS.getVersion());
+			} else {
+				assertEquals("2.67", loincVS.getVersion());
+			}
+		}
+		List<ConceptMap> loincCM_resources = myConceptMapCaptor.getValue();
+		for (ConceptMap loincCM : loincCM_resources) {
+			assertEquals("2.67.Beta.1", loincCM.getVersion());
+		}
 
 		// Update LOINC marked as version 2.67
 		myFiles = new ZipCollectionBuilder();
@@ -362,6 +428,18 @@ public class TerminologyLoaderSvcLoincTest extends BaseLoaderTest {
 		verify(myTermCodeSystemStorageSvc, times(2)).storeNewCodeSystemVersion(mySystemCaptor.capture(), myCsvCaptor.capture(), any(RequestDetails.class), myValueSetsCaptor.capture(), myConceptMapCaptor.capture());
 		loincCS = mySystemCaptor.getValue();
 		assertEquals("2.67", loincCS.getVersion());
+		loincVS_resources = myValueSetsCaptor.getValue();
+		for (ValueSet loincVS : loincVS_resources) {
+			if (loincVS.getId().startsWith("LL1000-0") || loincVS.getId().startsWith("LL1001-8") || loincVS.getId().startsWith("LL1892-0")) {
+				assertEquals("2.67.Beta.1", loincVS.getVersion());
+			} else {
+				assertEquals("2.67", loincVS.getVersion());
+			}
+		}
+		loincCM_resources = myConceptMapCaptor.getValue();
+		for (ConceptMap loincCM : loincCM_resources) {
+			assertEquals("2.67.Beta.1", loincCM.getVersion());
+		}
 
 		// Load LOINC marked as version 2.68
 		myFiles = new ZipCollectionBuilder();
@@ -371,6 +449,18 @@ public class TerminologyLoaderSvcLoincTest extends BaseLoaderTest {
 		verify(myTermCodeSystemStorageSvc, times(3)).storeNewCodeSystemVersion(mySystemCaptor.capture(), myCsvCaptor.capture(), any(RequestDetails.class), myValueSetsCaptor.capture(), myConceptMapCaptor.capture());
 		loincCS = mySystemCaptor.getValue();
 		assertEquals("2.68", loincCS.getVersion());
+		loincVS_resources = myValueSetsCaptor.getValue();
+		for (ValueSet loincVS : loincVS_resources) {
+			if (loincVS.getId().startsWith("LL1000-0") || loincVS.getId().startsWith("LL1001-8") || loincVS.getId().startsWith("LL1892-0")) {
+				assertEquals("2.68.Beta.1", loincVS.getVersion());
+			} else {
+				assertEquals("2.68", loincVS.getVersion());
+			}
+		}
+		loincCM_resources = myConceptMapCaptor.getValue();
+		for (ConceptMap loincCM : loincCM_resources) {
+			assertEquals("2.68.Beta.1", loincCM.getVersion());
+		}
 
 	}
 
@@ -413,12 +503,27 @@ public class TerminologyLoaderSvcLoincTest extends BaseLoaderTest {
 		}
 	}
 
+	public static void addLoincMandatoryFilesAndSinglePartLinkToZip(ZipCollectionBuilder theFiles) throws IOException {
+		addBaseLoincMandatoryFilesToZip(theFiles);
+		theFiles.addFileZip("/loinc/", "loincupload_singlepartlink.properties");
+		theFiles.addFileZip("/loinc/", LOINC_PART_LINK_FILE_DEFAULT.getCode());
+	}
+
 	public static void addLoincMandatoryFilesToZip(ZipCollectionBuilder theFiles) throws IOException {
-		addLoincMandatoryFilesWithPropertiesFileToZip(theFiles, LOINC_UPLOAD_PROPERTIES_FILE.getCode());
+		addBaseLoincMandatoryFilesToZip(theFiles);
+		theFiles.addFileZip("/loinc/", LOINC_UPLOAD_PROPERTIES_FILE.getCode());
+		theFiles.addFileZip("/loinc/", LOINC_PART_LINK_FILE_PRIMARY_DEFAULT.getCode());
+		theFiles.addFileZip("/loinc/", LOINC_PART_LINK_FILE_SUPPLEMENTARY_DEFAULT.getCode());
 	}
 
 	public static void addLoincMandatoryFilesWithPropertiesFileToZip(ZipCollectionBuilder theFiles, String thePropertiesFile) throws IOException {
 		theFiles.addFileZip("/loinc/", thePropertiesFile);
+		theFiles.addFileZip("/loinc/", LOINC_PART_LINK_FILE_PRIMARY_DEFAULT.getCode());
+		theFiles.addFileZip("/loinc/", LOINC_PART_LINK_FILE_SUPPLEMENTARY_DEFAULT.getCode());
+		addBaseLoincMandatoryFilesToZip(theFiles);
+	}
+
+	private static void addBaseLoincMandatoryFilesToZip(ZipCollectionBuilder theFiles) throws IOException{
 		theFiles.addFileZip("/loinc/", LOINC_GROUP_FILE_DEFAULT.getCode());
 		theFiles.addFileZip("/loinc/", LOINC_GROUP_TERMS_FILE_DEFAULT.getCode());
 		theFiles.addFileZip("/loinc/", LOINC_PARENT_GROUP_FILE_DEFAULT.getCode());
@@ -430,8 +535,6 @@ public class TerminologyLoaderSvcLoincTest extends BaseLoaderTest {
 		theFiles.addFileZip("/loinc/", LOINC_ANSWERLIST_LINK_FILE_DEFAULT.getCode());
 		theFiles.addFileZip("/loinc/", LOINC_ANSWERLIST_LINK_DUPLICATE_FILE_DEFAULT.getCode());
 		theFiles.addFileZip("/loinc/", LOINC_PART_FILE_DEFAULT.getCode());
-		theFiles.addFileZip("/loinc/", LOINC_PART_LINK_FILE_PRIMARY_DEFAULT.getCode());
-		theFiles.addFileZip("/loinc/", LOINC_PART_LINK_FILE_SUPPLEMENTARY_DEFAULT.getCode());
 		theFiles.addFileZip("/loinc/", LOINC_PART_RELATED_CODE_MAPPING_FILE_DEFAULT.getCode());
 		theFiles.addFileZip("/loinc/", LOINC_DOCUMENT_ONTOLOGY_FILE_DEFAULT.getCode());
 		theFiles.addFileZip("/loinc/", LOINC_RSNA_PLAYBOOK_FILE_DEFAULT.getCode());

hapi-fhir-jpaserver-base/src/test/resources/loinc/AccessoryFiles/PartFile/LoincPartLink.csv

@@ -0,0 +1,10 @@
+"LoincNumber","LongCommonName","PartNumber","PartName","PartCodeSystem","PartTypeName","LinkTypeName","Property"
+"10013-1","R' wave amplitude in lead I","LP31101-6","R' wave amplitude.lead I","http://loinc.org","COMPONENT","Primary","http://loinc.org/property/COMPONENT"
+"10013-1","R' wave amplitude in lead I","LP6802-5","Elpot","http://loinc.org","PROPERTY","Primary","http://loinc.org/property/PROPERTY"
+"10013-1","R' wave amplitude in lead I","LP6960-1","Pt","http://loinc.org","TIME","Primary","http://loinc.org/property/TIME_ASPCT"
+"10013-1","R' wave amplitude in lead I","LP7289-4","Heart","http://loinc.org","SYSTEM","Primary","http://loinc.org/property/SYSTEM"
+"10013-1","R' wave amplitude in lead I","LP7753-9","Qn","http://loinc.org","SCALE","Primary","http://loinc.org/property/SCALE_TYP"
+"10013-1","R' wave amplitude in lead I","LP6244-0","EKG","http://loinc.org","METHOD","Primary","http://loinc.org/property/METHOD_TYP"
+"10013-1","R' wave amplitude in lead I","LP31101-6","R' wave amplitude.lead I","http://loinc.org","COMPONENT","DetailedModel","http://loinc.org/property/analyte"
+"10013-1","R' wave amplitude in lead I","LP6802-5","Elpot","http://loinc.org","PROPERTY","DetailedModel","http://loinc.org/property/PROPERTY"
+"10013-1","R' wave amplitude in lead I","LP6960-1","Pt","http://loinc.org","TIME","DetailedModel","http://loinc.org/property/time-core"

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

@@ -0,0 +1,82 @@
+#################
+### 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.file=AccessoryFiles/PartFile/LoincPartLink.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 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

hapi-fhir-jpaserver-base/src/test/resources/loinc/v267_loincupload.properties

@@ -67,11 +67,11 @@ loinc.codesystem.version=2.67
 
 # This is the version identifier for the answer list file
 ## Key may be omitted
-loinc.answerlist.version=Beta.1
+loinc.answerlist.version=2.67.Beta.1
 
 # This is the version identifier for uploaded ConceptMap resources
 ## Key may be omitted
-loinc.conceptmap.version=Beta.1
+loinc.conceptmap.version=2.67.Beta.1
 
 # Group
 ## Default value if key not provided: AccessoryFiles/GroupFile/Group.csv

hapi-fhir-jpaserver-base/src/test/resources/loinc/v268_loincupload.properties

@@ -67,11 +67,11 @@ loinc.codesystem.version=2.68
 
 # This is the version identifier for the answer list file
 ## Key may be omitted
-loinc.answerlist.version=Beta.1
+loinc.answerlist.version=2.68.Beta.1
 
 # This is the version identifier for uploaded ConceptMap resources
 ## Key may be omitted
-loinc.conceptmap.version=Beta.1
+loinc.conceptmap.version=2.68.Beta.1
 
 # Group
 ## Default value if key not provided: AccessoryFiles/GroupFile/Group.csv