Liinc updates

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

@@ -1081,6 +1081,7 @@ public abstract class BaseHapiTerminologySvcImpl implements IHapiTerminologySvc,
 				throw new InternalErrorException(fe);
 			}
 			myConceptMapDao.save(termConceptMap);
+			int codesSaved = 0;
 
 			if (theConceptMap.hasGroup()) {
 				TermConceptMapGroup termConceptMapGroup;
@@ -1116,7 +1117,12 @@ public abstract class BaseHapiTerminologySvcImpl implements IHapiTerminologySvc,
 									termConceptMapGroupElementTarget.setCode(target.getCode());
 									termConceptMapGroupElementTarget.setDisplay(target.getDisplay());
 									termConceptMapGroupElementTarget.setEquivalence(target.getEquivalence());
-									myConceptMapGroupElementTargetDao.saveAndFlush(termConceptMapGroupElementTarget);
+									myConceptMapGroupElementTargetDao.save(termConceptMapGroupElementTarget);
+
+									if (codesSaved++ % 250 == 0) {
+										ourLog.info("Have saved {} codes in conceptmap", codesSaved);
+										myConceptMapGroupElementTargetDao.flush();
+									}
 								}
 							}
 						}

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

@@ -77,6 +77,9 @@ public class TerminologyLoaderSvcImpl implements IHapiTerminologyLoaderSvc {
 	public static final String LOINC_UNIVERSAL_LAB_ORDER_VALUESET_FILE = "LoincUniversalLabOrdersValueSet.csv";
 	public static final String LOINC_IEEE_MEDICAL_DEVICE_CODE_MAPPING_TABLE_CSV = "LoincIeeeMedicalDeviceCodeMappingTable.csv";
 	public static final String LOINC_IMAGING_DOCUMENT_CODES_FILE = "ImagingDocumentCodes.csv";
+	public static final String LOINC_GROUP_FILE = "Group.csv";
+	public static final String LOINC_GROUP_TERMS_FILE = "GroupLoincTerms.csv";
+	public static final String LOINC_PARENT_GROUP_FILE = "ParentGroup.csv";
 	private static final int LOG_INCREMENT = 100000;
 	private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(TerminologyLoaderSvcImpl.class);
 
@@ -124,7 +127,7 @@ public class TerminologyLoaderSvcImpl implements IHapiTerminologyLoaderSvc {
 
 		for (FileDescriptor nextZipBytes : theDescriptors.getUncompressedFileDescriptors()) {
 			String nextFilename = nextZipBytes.getFilename();
-			if (nextFilename.contains(theFileNamePart)) {
+			if (nextFilename.endsWith("/" + theFileNamePart)) {
 				ourLog.info("Processing file {}", nextFilename);
 
 				Reader reader;
@@ -308,6 +311,18 @@ public class TerminologyLoaderSvcImpl implements IHapiTerminologyLoaderSvc {
 		handler = new LoincImagingDocumentCodeHandler(code2concept, valueSets, conceptMaps, uploadProperties);
 		iterateOverZipFile(theDescriptors, LOINC_IMAGING_DOCUMENT_CODES_FILE, handler, ',', QuoteMode.NON_NUMERIC);
 
+		// Group File
+		handler = new LoincGroupFileHandler(code2concept, valueSets, conceptMaps, uploadProperties);
+		iterateOverZipFile(theDescriptors, LOINC_GROUP_FILE, handler, ',', QuoteMode.NON_NUMERIC);
+
+		// Group Terms File
+		handler = new LoincGroupTermsFileHandler(code2concept, valueSets, conceptMaps, uploadProperties);
+		iterateOverZipFile(theDescriptors, LOINC_GROUP_TERMS_FILE, handler, ',', QuoteMode.NON_NUMERIC);
+
+		// Parent Group File
+		handler = new LoincParentGroupFileHandler(code2concept, valueSets, conceptMaps, uploadProperties);
+		iterateOverZipFile(theDescriptors, LOINC_PARENT_GROUP_FILE, handler, ',', QuoteMode.NON_NUMERIC);
+
 		IOUtils.closeQuietly(theDescriptors);
 
 		for (Entry<String, TermConcept> next : code2concept.entrySet()) {

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

@@ -9,9 +9,9 @@ package ca.uhn.fhir.jpa.term.loinc;
  * Licensed under the Apache License, Version 2.0 (the "License");
  * you may not use this file except in compliance with the License.
  * You may obtain a copy of the License at
- * 
+ *
  *      http://www.apache.org/licenses/LICENSE-2.0
- * 
+ *
  * Unless required by applicable law or agreed to in writing, software
  * distributed under the License is distributed on an "AS IS" BASIS,
  * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
@@ -52,8 +52,10 @@ public abstract class BaseLoincHandler implements IRecordHandler {
 
 	BaseLoincHandler(Map<String, TermConcept> theCode2Concept, List<ValueSet> theValueSets, List<ConceptMap> theConceptMaps, Properties theUploadProperties) {
 		myValueSets = theValueSets;
+		myValueSets.forEach(t -> myIdToValueSet.put(t.getId(), t));
 		myCode2Concept = theCode2Concept;
 		myConceptMaps = theConceptMaps;
+		myConceptMaps.forEach(t -> myIdToConceptMaps.put(t.getId(), t));
 		myUploadProperties = theUploadProperties;
 	}
 
@@ -192,7 +194,6 @@ public abstract class BaseLoincHandler implements IRecordHandler {
 			vs.setUrl(theValueSetUri);
 			vs.setId(theValueSetId);
 			vs.setVersion(version);
-			vs.setName(theValueSetName);
 			vs.setStatus(Enumerations.PublicationStatus.ACTIVE);
 			vs.setPublisher(REGENSTRIEF_INSTITUTE_INC);
 			vs.addContact()
@@ -206,6 +207,11 @@ public abstract class BaseLoincHandler implements IRecordHandler {
 		} else {
 			vs = myIdToValueSet.get(theValueSetId);
 		}
+
+		if (isBlank(vs.getName()) && isNotBlank(theValueSetName)) {
+			vs.setName(theValueSetName);
+		}
+
 		return vs;
 	}
 

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

@@ -0,0 +1,62 @@
+package ca.uhn.fhir.jpa.term.loinc;
+
+/*-
+ * #%L
+ * HAPI FHIR JPA Server
+ * %%
+ * Copyright (C) 2014 - 2018 University Health Network
+ * %%
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ *      http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ * #L%
+ */
+
+import ca.uhn.fhir.jpa.entity.TermConcept;
+import ca.uhn.fhir.jpa.term.IRecordHandler;
+import org.apache.commons.csv.CSVRecord;
+import org.hl7.fhir.r4.model.ConceptMap;
+import org.hl7.fhir.r4.model.ValueSet;
+
+import java.util.List;
+import java.util.Map;
+import java.util.Properties;
+
+import static org.apache.commons.lang3.StringUtils.trim;
+
+public class LoincGroupFileHandler extends BaseLoincHandler implements IRecordHandler {
+
+	public static final String VS_URI_PREFIX = "http://loinc.org/fhir/loinc-group-";
+
+	public LoincGroupFileHandler(Map<String, TermConcept> theCode2concept, List<ValueSet> theValueSets, List<ConceptMap> theConceptMaps, Properties theUploadProperties) {
+		super(theCode2concept, theValueSets, theConceptMaps, theUploadProperties);
+	}
+
+	@Override
+	public void accept(CSVRecord theRecord) {
+		//"ParentGroupId","GroupId","Group","Archetype","Status","VersionFirstReleased"
+		String parentGroupId = trim(theRecord.get("ParentGroupId"));
+		String groupId = trim(theRecord.get("GroupId"));
+		String groupName = trim(theRecord.get("Group"));
+
+		ValueSet parentValueSet = getValueSet(parentGroupId, VS_URI_PREFIX + parentGroupId, null, null);
+		parentValueSet
+			.getCompose()
+			.getIncludeFirstRep()
+			.addValueSet(VS_URI_PREFIX + groupId);
+
+		// Create group to set its name (terms are added in a different
+		// handler)
+		getValueSet(groupId, VS_URI_PREFIX + groupId, groupName, null);
+	}
+
+
+}

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

@@ -0,0 +1,53 @@
+package ca.uhn.fhir.jpa.term.loinc;
+
+/*-
+ * #%L
+ * HAPI FHIR JPA Server
+ * %%
+ * Copyright (C) 2014 - 2018 University Health Network
+ * %%
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ * 
+ *      http://www.apache.org/licenses/LICENSE-2.0
+ * 
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ * #L%
+ */
+
+import ca.uhn.fhir.jpa.entity.TermConcept;
+import ca.uhn.fhir.jpa.term.IHapiTerminologyLoaderSvc;
+import ca.uhn.fhir.jpa.term.IRecordHandler;
+import org.apache.commons.csv.CSVRecord;
+import org.hl7.fhir.r4.model.ConceptMap;
+import org.hl7.fhir.r4.model.ValueSet;
+
+import java.util.List;
+import java.util.Map;
+import java.util.Properties;
+
+import static org.apache.commons.lang3.StringUtils.trim;
+
+public class LoincGroupTermsFileHandler extends BaseLoincHandler implements IRecordHandler {
+
+	public LoincGroupTermsFileHandler(Map<String, TermConcept> theCode2concept, List<ValueSet> theValueSets, List<ConceptMap> theConceptMaps, Properties theUploadProperties) {
+		super(theCode2concept, theValueSets, theConceptMaps, theUploadProperties);
+	}
+
+	@Override
+	public void accept(CSVRecord theRecord) {
+		//"Category","GroupId","Archetype","LoincNumber","LongCommonName"
+		String groupId = trim(theRecord.get("GroupId"));
+		String loincNumber = trim(theRecord.get("LoincNumber"));
+
+		ValueSet valueSet = getValueSet(groupId, LoincGroupFileHandler.VS_URI_PREFIX + groupId, null, null);
+		addCodeAsIncludeToValueSet(valueSet, IHapiTerminologyLoaderSvc.LOINC_URI, loincNumber, null);
+	}
+
+
+}

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

@@ -0,0 +1,51 @@
+package ca.uhn.fhir.jpa.term.loinc;
+
+/*-
+ * #%L
+ * HAPI FHIR JPA Server
+ * %%
+ * Copyright (C) 2014 - 2018 University Health Network
+ * %%
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ *      http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ * #L%
+ */
+
+import ca.uhn.fhir.jpa.entity.TermConcept;
+import ca.uhn.fhir.jpa.term.IRecordHandler;
+import org.apache.commons.csv.CSVRecord;
+import org.hl7.fhir.r4.model.ConceptMap;
+import org.hl7.fhir.r4.model.ValueSet;
+
+import java.util.List;
+import java.util.Map;
+import java.util.Properties;
+
+import static org.apache.commons.lang3.StringUtils.trim;
+
+public class LoincParentGroupFileHandler extends BaseLoincHandler implements IRecordHandler {
+
+	public LoincParentGroupFileHandler(Map<String, TermConcept> theCode2concept, List<ValueSet> theValueSets, List<ConceptMap> theConceptMaps, Properties theUploadProperties) {
+		super(theCode2concept, theValueSets, theConceptMaps, theUploadProperties);
+	}
+
+	@Override
+	public void accept(CSVRecord theRecord) {
+		// "ParentGroupId","ParentGroup","Status"
+		String parentGroupId = trim(theRecord.get("ParentGroupId"));
+		String parentGroupName = trim(theRecord.get("ParentGroup"));
+
+		getValueSet(parentGroupId, LoincGroupFileHandler.VS_URI_PREFIX + parentGroupId, parentGroupName, null);
+	}
+
+
+}

hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/provider/dstu3/TerminologyUploaderProviderDstu3Test.java

@@ -42,6 +42,9 @@ public class TerminologyUploaderProviderDstu3Test extends BaseResourceProviderDs
 		addFile(zos, TerminologyLoaderSvcImpl.LOINC_HIERARCHY_FILE);
 		addFile(zos, TerminologyLoaderSvcImpl.LOINC_ANSWERLIST_FILE);
 		addFile(zos, TerminologyLoaderSvcImpl.LOINC_ANSWERLIST_LINK_FILE);
+		addFile(zos, TerminologyLoaderSvcImpl.LOINC_GROUP_FILE);
+		addFile(zos, TerminologyLoaderSvcImpl.LOINC_GROUP_TERMS_FILE);
+		addFile(zos, TerminologyLoaderSvcImpl.LOINC_PARENT_GROUP_FILE);
 		addFile(zos, TerminologyLoaderSvcImpl.LOINC_PART_FILE);
 		addFile(zos, TerminologyLoaderSvcImpl.LOINC_PART_LINK_FILE);
 		addFile(zos, TerminologyLoaderSvcImpl.LOINC_PART_RELATED_CODE_MAPPING_FILE);

hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/term/TerminologyLoaderSvcIntegrationDstu3Test.java

@@ -67,7 +67,6 @@ public class TerminologyLoaderSvcIntegrationDstu3Test extends BaseJpaDstu3Test {
 	public void testExpandWithPropertyCoding() throws Exception {
 		ZipCollectionBuilder files = new ZipCollectionBuilder();
 		TerminologyLoaderSvcLoincTest.addLoincMandatoryFilesToZip(files);
-		TerminologyLoaderSvcLoincTest.addLoincOptionalFilesToZip(files);
 		myLoader.loadLoinc(files.getFiles(), mySrd);
 
 		// Search by code
@@ -121,7 +120,6 @@ public class TerminologyLoaderSvcIntegrationDstu3Test extends BaseJpaDstu3Test {
 	public void testExpandWithPropertyString() throws Exception {
 		ZipCollectionBuilder files = new ZipCollectionBuilder();
 		TerminologyLoaderSvcLoincTest.addLoincMandatoryFilesToZip(files);
-		TerminologyLoaderSvcLoincTest.addLoincOptionalFilesToZip(files);
 		myLoader.loadLoinc(files.getFiles(), mySrd);
 
 		ValueSet input = new ValueSet();
@@ -144,7 +142,6 @@ public class TerminologyLoaderSvcIntegrationDstu3Test extends BaseJpaDstu3Test {
 	public void testLookupWithProperties() throws Exception {
 		ZipCollectionBuilder files = new ZipCollectionBuilder();
 		TerminologyLoaderSvcLoincTest.addLoincMandatoryFilesToZip(files);
-		TerminologyLoaderSvcLoincTest.addLoincOptionalFilesToZip(files);
 		myLoader.loadLoinc(files.getFiles(), mySrd);
 
 		IFhirResourceDaoCodeSystem.LookupCodeResult result = myCodeSystemDao.lookupCode(new StringType("10013-1"), new StringType(IHapiTerminologyLoaderSvc.LOINC_URI), null, mySrd);
@@ -176,7 +173,6 @@ public class TerminologyLoaderSvcIntegrationDstu3Test extends BaseJpaDstu3Test {
 	public void testLookupWithPropertiesExplicit() throws Exception {
 		ZipCollectionBuilder files = new ZipCollectionBuilder();
 		TerminologyLoaderSvcLoincTest.addLoincMandatoryFilesToZip(files);
-		TerminologyLoaderSvcLoincTest.addLoincOptionalFilesToZip(files);
 		myLoader.loadLoinc(files.getFiles(), mySrd);
 
 		IFhirResourceDaoCodeSystem.LookupCodeResult result = myCodeSystemDao.lookupCode(new StringType("10013-1"), new StringType(IHapiTerminologyLoaderSvc.LOINC_URI), null, mySrd);

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

@@ -93,7 +93,6 @@ public class TerminologyLoaderSvcLoincTest {
 	@Test
 	public void testLoadLoinc() throws Exception {
 		addLoincMandatoryFilesToZip(myFiles);
-		addLoincOptionalFilesToZip(myFiles);
 
 		// Actually do the load
 		mySvc.loadLoinc(myFiles.getFiles(), details);
@@ -287,7 +286,7 @@ public class TerminologyLoaderSvcLoincTest {
 
 		// IEEE Medical Device Codes
 		conceptMap = conceptMaps.get(LoincIeeeMedicalDeviceCodeHandler.LOINC_IEEE_CM_ID);
-		ourLog.info(FhirContext.forR4().newXmlParser().setPrettyPrint(true).encodeResourceToString(conceptMap));
+		ourLog.debug(FhirContext.forR4().newXmlParser().setPrettyPrint(true).encodeResourceToString(conceptMap));
 		assertEquals(LoincIeeeMedicalDeviceCodeHandler.LOINC_IEEE_CM_NAME, conceptMap.getName());
 		assertEquals(LoincIeeeMedicalDeviceCodeHandler.LOINC_IEEE_CM_URI, conceptMap.getUrl());
 		assertEquals(1, conceptMap.getGroup().size());
@@ -309,6 +308,25 @@ public class TerminologyLoaderSvcLoincTest {
 		assertEquals(9, vs.getCompose().getInclude().get(0).getConcept().size());
 		assertEquals("11525-3", vs.getCompose().getInclude().get(0).getConcept().get(0).getCode());
 		assertEquals("US Pelvis Fetus for pregnancy", vs.getCompose().getInclude().get(0).getConcept().get(0).getDisplay());
+
+		// Group - Parent
+		vs = valueSets.get("LG100-4");
+		ourLog.info(FhirContext.forR4().newXmlParser().setPrettyPrint(true).encodeResourceToString(vs));
+		assertEquals("Chem_DrugTox_Chal_Sero_Allergy<SAME:Comp|Prop|Tm|Syst (except intravascular and urine)><ANYBldSerPlas,ANYUrineUrineSed><ROLLUP:Method>", vs.getName());
+		assertEquals("http://loinc.org/fhir/loinc-group-LG100-4", vs.getUrl());
+		assertEquals(1, vs.getCompose().getInclude().size());
+		assertEquals(1, vs.getCompose().getInclude().get(0).getValueSet().size());
+		assertEquals("http://loinc.org/fhir/loinc-group-LG1695-8", vs.getCompose().getInclude().get(0).getValueSet().get(0).getValueAsString());
+
+		// Group - Child
+		vs = valueSets.get("LG1695-8");
+		ourLog.info(FhirContext.forR4().newXmlParser().setPrettyPrint(true).encodeResourceToString(vs));
+		assertEquals("1,4-Dichlorobenzene|MCnc|Pt|ANYBldSerPl", vs.getName());
+		assertEquals("http://loinc.org/fhir/loinc-group-LG1695-8", vs.getUrl());
+		assertEquals(1, vs.getCompose().getInclude().size());
+		assertEquals(2, vs.getCompose().getInclude().get(0).getConcept().size());
+		assertEquals("17424-3", vs.getCompose().getInclude().get(0).getConcept().get(0).getCode());
+		assertEquals("13006-2", vs.getCompose().getInclude().get(0).getConcept().get(1).getCode());
 	}
 
 	@Test
@@ -336,7 +354,8 @@ public class TerminologyLoaderSvcLoincTest {
 
 	@Test
 	public void testLoadLoincMissingMandatoryFiles() throws IOException {
-		addLoincOptionalFilesToZip(myFiles);
+		myFiles.addFileZip("/loinc/", TerminologyLoaderSvcImpl.LOINC_UPLOAD_PROPERTIES_FILE);
+		myFiles.addFileZip("/loinc/", TerminologyLoaderSvcImpl.LOINC_GROUP_FILE);
 
 		// Actually do the load
 		try {
@@ -349,13 +368,13 @@ public class TerminologyLoaderSvcLoincTest {
 
 
 	public static void addLoincMandatoryFilesToZip(ZipCollectionBuilder theFiles) throws IOException {
-		theFiles.addFileZip("/loinc/", "Loinc.csv", TerminologyLoaderSvcImpl.LOINC_FILE);
-		theFiles.addFileZip("/loinc/", "MultiAxialHierarchy.csv", TerminologyLoaderSvcImpl.LOINC_HIERARCHY_FILE);
-	}
-
-	public static void addLoincOptionalFilesToZip(ZipCollectionBuilder theFiles) throws IOException {
-		theFiles.addFileZip("/loinc/", "loincupload.properties");
-		theFiles.addFileZip("/loinc/", "AnswerList.csv", TerminologyLoaderSvcImpl.LOINC_ANSWERLIST_FILE);
+		theFiles.addFileZip("/loinc/", TerminologyLoaderSvcImpl.LOINC_UPLOAD_PROPERTIES_FILE);
+		theFiles.addFileZip("/loinc/", TerminologyLoaderSvcImpl.LOINC_GROUP_FILE);
+		theFiles.addFileZip("/loinc/", TerminologyLoaderSvcImpl.LOINC_GROUP_TERMS_FILE);
+		theFiles.addFileZip("/loinc/", TerminologyLoaderSvcImpl.LOINC_PARENT_GROUP_FILE);
+		theFiles.addFileZip("/loinc/", TerminologyLoaderSvcImpl.LOINC_FILE, TerminologyLoaderSvcImpl.LOINC_FILE);
+		theFiles.addFileZip("/loinc/", TerminologyLoaderSvcImpl.LOINC_HIERARCHY_FILE, TerminologyLoaderSvcImpl.LOINC_HIERARCHY_FILE);
+		theFiles.addFileZip("/loinc/", TerminologyLoaderSvcImpl.LOINC_ANSWERLIST_FILE, TerminologyLoaderSvcImpl.LOINC_ANSWERLIST_FILE);
 		theFiles.addFileZip("/loinc/", TerminologyLoaderSvcImpl.LOINC_ANSWERLIST_LINK_FILE, TerminologyLoaderSvcImpl.LOINC_ANSWERLIST_LINK_FILE);
 		theFiles.addFileZip("/loinc/", TerminologyLoaderSvcImpl.LOINC_PART_FILE, TerminologyLoaderSvcImpl.LOINC_PART_FILE);
 		theFiles.addFileZip("/loinc/", TerminologyLoaderSvcImpl.LOINC_PART_LINK_FILE, TerminologyLoaderSvcImpl.LOINC_PART_LINK_FILE);
@@ -365,13 +384,8 @@ public class TerminologyLoaderSvcLoincTest {
 		theFiles.addFileZip("/loinc/", TerminologyLoaderSvcImpl.LOINC_UNIVERSAL_LAB_ORDER_VALUESET_FILE);
 		theFiles.addFileZip("/loinc/", TerminologyLoaderSvcImpl.LOINC_IEEE_MEDICAL_DEVICE_CODE_MAPPING_TABLE_CSV);
 		theFiles.addFileZip("/loinc/", TerminologyLoaderSvcImpl.LOINC_IMAGING_DOCUMENT_CODES_FILE);
-
-		/*
-		 * Top 2000 files have versions in the filename so don't use the
-		 * constant.. that way this is a better test
-		 */
-		theFiles.addFilePlain("/loinc/", TerminologyLoaderSvcImpl.LOINC_TOP2000_COMMON_LAB_RESULTS_SI_FILE);
-		theFiles.addFilePlain("/loinc/", TerminologyLoaderSvcImpl.LOINC_TOP2000_COMMON_LAB_RESULTS_US_FILE);
+		theFiles.addFileZip("/loinc/", TerminologyLoaderSvcImpl.LOINC_TOP2000_COMMON_LAB_RESULTS_SI_FILE);
+		theFiles.addFileZip("/loinc/", TerminologyLoaderSvcImpl.LOINC_TOP2000_COMMON_LAB_RESULTS_US_FILE);
 	}
 
 	@AfterClass

hapi-fhir-jpaserver-base/src/test/resources/loinc/Group.csv

@@ -0,0 +1,2 @@
+"ParentGroupId","GroupId","Group","Archetype","Status","VersionFirstReleased"
+"LG100-4","LG1695-8","1,4-Dichlorobenzene|MCnc|Pt|ANYBldSerPl","","Active",""

hapi-fhir-jpaserver-base/src/test/resources/loinc/GroupLoincTerms.csv

@@ -0,0 +1,3 @@
+"Category","GroupId","Archetype","LoincNumber","LongCommonName"
+"Flowsheet","LG1695-8","","17424-3","1,4-Dichlorobenzene [Mass/volume] in Blood"
+"Flowsheet","LG1695-8","","13006-2","1,4-Dichlorobenzene [Mass/volume] in Serum or Plasma"

hapi-fhir-jpaserver-base/src/test/resources/loinc/ParentGroup.csv

@@ -0,0 +1,2 @@
+"ParentGroupId","ParentGroup","Status"
+"LG100-4","Chem_DrugTox_Chal_Sero_Allergy<SAME:Comp|Prop|Tm|Syst (except intravascular and urine)><ANYBldSerPlas,ANYUrineUrineSed><ROLLUP:Method>","ACTIVE"