Merge pull request #2120 from jamesagnew/im_20201005_loincpartlink_fix
Im 20201005 loincpartlink fix
This commit is contained in:
IanMMarshall
GitHub
commit
ebbdafb107
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@ -21,6 +21,7 @@ package ca.uhn.fhir.jpa.term;
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*/
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import ca.uhn.fhir.jpa.term.api.ITermLoaderSvc;
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import ca.uhn.fhir.jpa.util.LogicUtil;
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import ca.uhn.fhir.rest.server.exceptions.InternalErrorException;
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import ca.uhn.fhir.rest.server.exceptions.UnprocessableEntityException;
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import org.apache.commons.io.FileUtils;
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@ -31,6 +32,7 @@ import org.slf4j.LoggerFactory;
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import java.io.*;
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import java.util.ArrayList;
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import java.util.Arrays;
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import java.util.HashSet;
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import java.util.List;
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import java.util.Set;
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@ -140,6 +142,24 @@ public class LoadedFileDescriptors implements Closeable {
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}
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}
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void verifyPartLinkFilesExist(List<String> theMultiPartLinkFiles, String theSinglePartLinkFile) {
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List<String> notFoundMulti = notFound(theMultiPartLinkFiles);
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List<String> notFoundSingle = notFound(Arrays.asList(theSinglePartLinkFile));
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// Expect all of the files in theMultiPartLinkFiles to be found and theSinglePartLinkFile to not be found,
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// or none of the files in theMultiPartLinkFiles to be found and the SinglePartLinkFile to be found.
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boolean multiPartFilesFound = notFoundMulti.isEmpty();
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boolean singlePartFilesFound = notFoundSingle.isEmpty();
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if (!LogicUtil.multiXor(multiPartFilesFound, singlePartFilesFound)) {
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String msg;
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if (!multiPartFilesFound && !singlePartFilesFound) {
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msg = "Could not find any of the PartLink files: " + notFoundMulti + " nor " + notFoundSingle;
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} else {
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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;
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}
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throw new UnprocessableEntityException(msg);
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}
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}
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private static class NonClosableBOMInputStream extends BOMInputStream {
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NonClosableBOMInputStream(InputStream theWrap) {
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@ -114,8 +114,6 @@ public class TermLoaderSvcImpl implements ITermLoaderSvc {
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uploadProperties.getProperty(LOINC_IEEE_MEDICAL_DEVICE_CODE_MAPPING_TABLE_FILE.getCode(), LOINC_IEEE_MEDICAL_DEVICE_CODE_MAPPING_TABLE_FILE_DEFAULT.getCode()),
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uploadProperties.getProperty(LOINC_IMAGING_DOCUMENT_CODES_FILE.getCode(), LOINC_IMAGING_DOCUMENT_CODES_FILE_DEFAULT.getCode()),
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uploadProperties.getProperty(LOINC_PART_FILE.getCode(), LOINC_PART_FILE_DEFAULT.getCode()),
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uploadProperties.getProperty(LOINC_PART_LINK_FILE_PRIMARY.getCode(), LOINC_PART_LINK_FILE_PRIMARY_DEFAULT.getCode()),
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uploadProperties.getProperty(LOINC_PART_LINK_FILE_SUPPLEMENTARY.getCode(), LOINC_PART_LINK_FILE_SUPPLEMENTARY_DEFAULT.getCode()),
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uploadProperties.getProperty(LOINC_PART_RELATED_CODE_MAPPING_FILE.getCode(), LOINC_PART_RELATED_CODE_MAPPING_FILE_DEFAULT.getCode()),
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uploadProperties.getProperty(LOINC_RSNA_PLAYBOOK_FILE.getCode(), LOINC_RSNA_PLAYBOOK_FILE_DEFAULT.getCode()),
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uploadProperties.getProperty(LOINC_TOP2000_COMMON_LAB_RESULTS_SI_FILE.getCode(), LOINC_TOP2000_COMMON_LAB_RESULTS_SI_FILE_DEFAULT.getCode()),
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@ -124,6 +122,12 @@ public class TermLoaderSvcImpl implements ITermLoaderSvc {
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);
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descriptors.verifyMandatoryFilesExist(mandatoryFilenameFragments);
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List<String> splitPartLinkFilenameFragments = Arrays.asList(
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uploadProperties.getProperty(LOINC_PART_LINK_FILE_PRIMARY.getCode(), LOINC_PART_LINK_FILE_PRIMARY_DEFAULT.getCode()),
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uploadProperties.getProperty(LOINC_PART_LINK_FILE_SUPPLEMENTARY.getCode(), LOINC_PART_LINK_FILE_SUPPLEMENTARY_DEFAULT.getCode())
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);
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descriptors.verifyPartLinkFilesExist(splitPartLinkFilenameFragments, uploadProperties.getProperty(LOINC_PART_LINK_FILE.getCode(), LOINC_PART_LINK_FILE_DEFAULT.getCode()));
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List<String> optionalFilenameFragments = Arrays.asList(
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uploadProperties.getProperty(LOINC_GROUP_FILE.getCode(), LOINC_GROUP_FILE_DEFAULT.getCode()),
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uploadProperties.getProperty(LOINC_GROUP_TERMS_FILE.getCode(), LOINC_GROUP_TERMS_FILE_DEFAULT.getCode()),
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@ -475,8 +479,9 @@ public class TermLoaderSvcImpl implements ITermLoaderSvc {
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// Part link
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handler = new LoincPartLinkHandler(codeSystemVersion, code2concept, propertyNamesToTypes);
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iterateOverZipFile(theDescriptors, theUploadProperties.getProperty(LOINC_PART_LINK_FILE_PRIMARY.getCode(), LOINC_PART_LINK_FILE_PRIMARY_DEFAULT.getCode()), handler, ',', QuoteMode.NON_NUMERIC, false);
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iterateOverZipFile(theDescriptors, theUploadProperties.getProperty(LOINC_PART_LINK_FILE_SUPPLEMENTARY.getCode(), LOINC_PART_LINK_FILE_SUPPLEMENTARY_DEFAULT.getCode()), handler, ',', QuoteMode.NON_NUMERIC, false);
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iterateOverZipFileOptional(theDescriptors, theUploadProperties.getProperty(LOINC_PART_LINK_FILE.getCode(), LOINC_PART_LINK_FILE_DEFAULT.getCode()), handler, ',', QuoteMode.NON_NUMERIC, false);
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iterateOverZipFileOptional(theDescriptors, theUploadProperties.getProperty(LOINC_PART_LINK_FILE_PRIMARY.getCode(), LOINC_PART_LINK_FILE_PRIMARY_DEFAULT.getCode()), handler, ',', QuoteMode.NON_NUMERIC, false);
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iterateOverZipFileOptional(theDescriptors, theUploadProperties.getProperty(LOINC_PART_LINK_FILE_SUPPLEMENTARY.getCode(), LOINC_PART_LINK_FILE_SUPPLEMENTARY_DEFAULT.getCode()), handler, ',', QuoteMode.NON_NUMERIC, false);
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IOUtils.closeQuietly(theDescriptors);
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@ -598,6 +603,14 @@ public class TermLoaderSvcImpl implements ITermLoaderSvc {
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}
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public static void iterateOverZipFile(LoadedFileDescriptors theDescriptors, String theFileNamePart, IRecordHandler theHandler, char theDelimiter, QuoteMode theQuoteMode, boolean theIsPartialFilename) {
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iterateOverZipFile(theDescriptors, theFileNamePart, theHandler, theDelimiter, theQuoteMode, theIsPartialFilename, true);
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}
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public static void iterateOverZipFileOptional(LoadedFileDescriptors theDescriptors, String theFileNamePart, IRecordHandler theHandler, char theDelimiter, QuoteMode theQuoteMode, boolean theIsPartialFilename) {
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iterateOverZipFile(theDescriptors, theFileNamePart, theHandler, theDelimiter, theQuoteMode, theIsPartialFilename, false);
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}
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private static void iterateOverZipFile(LoadedFileDescriptors theDescriptors, String theFileNamePart, IRecordHandler theHandler, char theDelimiter, QuoteMode theQuoteMode, boolean theIsPartialFilename, boolean theRequireMatch) {
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boolean foundMatch = false;
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for (FileDescriptor nextZipBytes : theDescriptors.getUncompressedFileDescriptors()) {
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@ -644,7 +657,7 @@ public class TermLoaderSvcImpl implements ITermLoaderSvc {
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}
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if (!foundMatch) {
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if (!foundMatch && theRequireMatch) {
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throw new InvalidRequestException("Did not find file matching " + theFileNamePart);
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}
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@ -192,7 +192,7 @@ public abstract class BaseLoincHandler implements IRecordHandler {
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if (isNotBlank(theVersionPropertyName)) {
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version = myUploadProperties.getProperty(theVersionPropertyName);
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} else {
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version = myUploadProperties.getProperty(LOINC_CONCEPTMAP_VERSION.getCode());
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version = myUploadProperties.getProperty(LOINC_CODESYSTEM_VERSION.getCode());
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}
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ValueSet vs;
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@ -84,7 +84,10 @@ public class LoincRsnaPlaybookHandler extends BaseLoincHandler implements IRecor
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// ConceptMap version from properties files
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String loincRsnaCmVersion = myUploadProperties.getProperty(LOINC_CONCEPTMAP_VERSION.getCode());
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// CodeSystem version from properties file
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String codeSystemVersionId = myUploadProperties.getProperty(LOINC_CODESYSTEM_VERSION.getCode());
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// RSNA Codes VS
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ValueSet vs;
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if (!myIdToValueSet.containsKey(RSNA_CODES_VS_ID)) {
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@ -93,6 +96,7 @@ public class LoincRsnaPlaybookHandler extends BaseLoincHandler implements IRecor
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vs.setId(RSNA_CODES_VS_ID);
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vs.setName(RSNA_CODES_VS_NAME);
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vs.setStatus(Enumerations.PublicationStatus.ACTIVE);
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vs.setVersion(codeSystemVersionId);
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myIdToValueSet.put(RSNA_CODES_VS_ID, vs);
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myValueSets.add(vs);
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} else {
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@ -177,7 +181,6 @@ public class LoincRsnaPlaybookHandler extends BaseLoincHandler implements IRecor
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String partConceptMapId;
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String termConceptMapId;
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String codeSystemVersionId = myUploadProperties.getProperty(LOINC_CODESYSTEM_VERSION.getCode());
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if (codeSystemVersionId != null) {
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partConceptMapId = LoincPartRelatedCodeMappingHandler.LOINC_PART_TO_RID_PART_MAP_ID + "-" + codeSystemVersionId;
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termConceptMapId = LoincPartRelatedCodeMappingHandler.LOINC_TERM_TO_RPID_PART_MAP_ID + "-" + codeSystemVersionId;
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@ -69,6 +69,8 @@ public enum LoincUploadPropertiesEnum {
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LOINC_PART_FILE_DEFAULT("AccessoryFiles/PartFile/Part.csv"),
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// Part link
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LOINC_PART_LINK_FILE("loinc.part.link.file"),
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LOINC_PART_LINK_FILE_DEFAULT("AccessoryFiles/PartFile/LoincPartLink.csv"),
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LOINC_PART_LINK_FILE_PRIMARY("loinc.part.link.primary.file"),
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LOINC_PART_LINK_FILE_PRIMARY_DEFAULT("AccessoryFiles/PartFile/LoincPartLink_Primary.csv"),
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LOINC_PART_LINK_FILE_SUPPLEMENTARY("loinc.part.link.supplementary.file"),
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@ -39,6 +39,7 @@ import static org.hamcrest.Matchers.contains;
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import static org.hamcrest.Matchers.containsString;
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import static org.hamcrest.Matchers.empty;
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import static org.junit.jupiter.api.Assertions.assertEquals;
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import static org.junit.jupiter.api.Assertions.assertNull;
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import static org.junit.jupiter.api.Assertions.assertTrue;
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import static org.junit.jupiter.api.Assertions.fail;
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import static org.mockito.ArgumentMatchers.any;
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@ -68,9 +69,54 @@ public class TerminologyLoaderSvcLoincTest extends BaseLoaderTest {
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}
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@Test
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public void testLoadLoinc() throws Exception {
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public void testLoadLoincWithSplitPartLink() throws Exception {
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addLoincMandatoryFilesToZip(myFiles);
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verifyLoadLoinc();
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}
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@Test
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public void testLoadLoincWithSinglePartLink() throws Exception {
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addLoincMandatoryFilesAndSinglePartLinkToZip(myFiles);
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verifyLoadLoinc();
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}
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@Test
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public void testLoadLoincInvalidPartLinkFiles() throws IOException {
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// Missing all PartLinkFiles
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addBaseLoincMandatoryFilesToZip(myFiles);
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myFiles.addFileZip("/loinc/", LOINC_UPLOAD_PROPERTIES_FILE.getCode());
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try {
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mySvc.loadLoinc(myFiles.getFiles(), mySrd);
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fail();
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} catch (UnprocessableEntityException e) {
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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());
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}
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// Missing LoincPartLink_Supplementary
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myFiles.addFileZip("/loinc/", LOINC_PART_LINK_FILE_PRIMARY_DEFAULT.getCode());
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try {
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mySvc.loadLoinc(myFiles.getFiles(), mySrd);
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fail();
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} catch (UnprocessableEntityException e) {
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assertEquals("Could not find any of the PartLink files: [AccessoryFiles/PartFile/LoincPartLink_Supplementary.csv] nor [AccessoryFiles/PartFile/LoincPartLink.csv]", e.getMessage());
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}
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// Both Split and Single PartLink files
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myFiles.addFileZip("/loinc/", LOINC_PART_LINK_FILE_SUPPLEMENTARY_DEFAULT.getCode());
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myFiles.addFileZip("/loinc/", LOINC_PART_LINK_FILE_DEFAULT.getCode());
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try {
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mySvc.loadLoinc(myFiles.getFiles(), mySrd);
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fail();
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} catch (UnprocessableEntityException e) {
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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());
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}
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}
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private void verifyLoadLoinc() throws Exception {
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// Actually do the load
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mySvc.loadLoinc(myFiles.getFiles(), mySrd);
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@ -138,10 +184,12 @@ public class TerminologyLoaderSvcLoincTest extends BaseLoaderTest {
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assertEquals(ITermLoaderSvc.LOINC_URI, vs.getCompose().getInclude().get(0).getSystem());
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assertEquals("LA6270-8", vs.getCompose().getInclude().get(0).getConcept().get(0).getCode());
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assertEquals("Never", vs.getCompose().getInclude().get(0).getConcept().get(0).getDisplay());
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assertEquals("Beta.1", vs.getVersion());
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// External AnswerList
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vs = valueSets.get("LL1892-0");
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assertEquals(0, vs.getCompose().getIncludeFirstRep().getConcept().size());
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assertEquals("Beta.1", vs.getVersion());
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// Part
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code = concepts.get("LP101394-7");
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@ -175,6 +223,7 @@ public class TerminologyLoaderSvcLoincTest extends BaseLoaderTest {
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assertEquals(3, vs.getCompose().getInclude().get(0).getConcept().size());
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assertEquals("11488-4", vs.getCompose().getInclude().get(0).getConcept().get(0).getCode());
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assertEquals("Consult note", vs.getCompose().getInclude().get(0).getConcept().get(0).getDisplay());
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assertNull(vs.getVersion());
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// Document ontology parts
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code = concepts.get("11488-4");
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@ -192,6 +241,7 @@ public class TerminologyLoaderSvcLoincTest extends BaseLoaderTest {
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assertEquals(ITermLoaderSvc.LOINC_URI, vs.getCompose().getInclude().get(0).getSystem());
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assertEquals("17787-3", vs.getCompose().getInclude().get(0).getConcept().get(0).getCode());
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assertEquals("NM Thyroid gland Study report", vs.getCompose().getInclude().get(0).getConcept().get(0).getDisplay());
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assertNull(vs.getVersion());
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// RSNA Playbook Code Parts - Region Imaged
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code = concepts.get("17787-3");
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@ -260,6 +310,7 @@ public class TerminologyLoaderSvcLoincTest extends BaseLoaderTest {
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assertEquals("Creatinine [Mass/volume] in Serum or Plasma", vs.getCompose().getInclude().get(0).getConcept().get(0).getDisplay());
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assertEquals("718-7", vs.getCompose().getInclude().get(0).getConcept().get(1).getCode());
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assertEquals("Hemoglobin [Mass/volume] in Blood", vs.getCompose().getInclude().get(0).getConcept().get(1).getDisplay());
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assertNull(vs.getVersion());
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// TOP 2000 - SI
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vs = valueSets.get(LoincTop2000LabResultsSiHandler.TOP_2000_SI_VS_ID);
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@ -272,6 +323,7 @@ public class TerminologyLoaderSvcLoincTest extends BaseLoaderTest {
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assertEquals("Creatinine [Moles/volume] in Serum or Plasma", vs.getCompose().getInclude().get(0).getConcept().get(0).getDisplay());
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assertEquals("718-7", vs.getCompose().getInclude().get(0).getConcept().get(1).getCode());
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assertEquals("Hemoglobin [Mass/volume] in Blood", vs.getCompose().getInclude().get(0).getConcept().get(1).getDisplay());
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assertNull(vs.getVersion());
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// Universal lab order VS
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vs = valueSets.get(LoincUniversalOrderSetHandler.VS_ID_BASE);
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@ -280,6 +332,7 @@ public class TerminologyLoaderSvcLoincTest extends BaseLoaderTest {
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assertEquals(9, vs.getCompose().getInclude().get(0).getConcept().size());
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assertEquals("42176-8", vs.getCompose().getInclude().get(0).getConcept().get(0).getCode());
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assertEquals("1,3 beta glucan [Mass/volume] in Serum", vs.getCompose().getInclude().get(0).getConcept().get(0).getDisplay());
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assertNull(vs.getVersion());
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// All LOINC codes
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assertTrue(valueSets.containsKey("loinc-all"));
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@ -296,6 +349,7 @@ public class TerminologyLoaderSvcLoincTest extends BaseLoaderTest {
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assertTrue(vs.getCompose().hasInclude());
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assertEquals(1, vs.getCompose().getInclude().size());
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assertEquals(ITermLoaderSvc.LOINC_URI, vs.getCompose().getInclude().get(0).getSystem());
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assertEquals("1.0.0", vs.getVersion());
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// IEEE Medical Device Codes
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conceptMap = conceptMaps.get(LoincIeeeMedicalDeviceCodeHandler.LOINC_IEEE_CM_ID);
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@ -353,6 +407,18 @@ public class TerminologyLoaderSvcLoincTest extends BaseLoaderTest {
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verify(myTermCodeSystemStorageSvc, times(1)).storeNewCodeSystemVersion(mySystemCaptor.capture(), myCsvCaptor.capture(), any(RequestDetails.class), myValueSetsCaptor.capture(), myConceptMapCaptor.capture());
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CodeSystem loincCS = mySystemCaptor.getValue();
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assertEquals("2.67", loincCS.getVersion());
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List<ValueSet> loincVS_resources = myValueSetsCaptor.getValue();
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for (ValueSet loincVS : loincVS_resources) {
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if (loincVS.getId().startsWith("LL1000-0") || loincVS.getId().startsWith("LL1001-8") || loincVS.getId().startsWith("LL1892-0")) {
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assertEquals("2.67.Beta.1", loincVS.getVersion());
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} else {
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assertEquals("2.67", loincVS.getVersion());
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}
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}
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List<ConceptMap> loincCM_resources = myConceptMapCaptor.getValue();
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for (ConceptMap loincCM : loincCM_resources) {
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assertEquals("2.67.Beta.1", loincCM.getVersion());
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}
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// Update LOINC marked as version 2.67
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myFiles = new ZipCollectionBuilder();
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@ -362,6 +428,18 @@ public class TerminologyLoaderSvcLoincTest extends BaseLoaderTest {
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verify(myTermCodeSystemStorageSvc, times(2)).storeNewCodeSystemVersion(mySystemCaptor.capture(), myCsvCaptor.capture(), any(RequestDetails.class), myValueSetsCaptor.capture(), myConceptMapCaptor.capture());
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loincCS = mySystemCaptor.getValue();
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assertEquals("2.67", loincCS.getVersion());
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loincVS_resources = myValueSetsCaptor.getValue();
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for (ValueSet loincVS : loincVS_resources) {
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if (loincVS.getId().startsWith("LL1000-0") || loincVS.getId().startsWith("LL1001-8") || loincVS.getId().startsWith("LL1892-0")) {
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assertEquals("2.67.Beta.1", loincVS.getVersion());
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} else {
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assertEquals("2.67", loincVS.getVersion());
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}
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}
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loincCM_resources = myConceptMapCaptor.getValue();
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for (ConceptMap loincCM : loincCM_resources) {
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assertEquals("2.67.Beta.1", loincCM.getVersion());
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}
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// Load LOINC marked as version 2.68
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myFiles = new ZipCollectionBuilder();
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@ -371,6 +449,18 @@ public class TerminologyLoaderSvcLoincTest extends BaseLoaderTest {
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verify(myTermCodeSystemStorageSvc, times(3)).storeNewCodeSystemVersion(mySystemCaptor.capture(), myCsvCaptor.capture(), any(RequestDetails.class), myValueSetsCaptor.capture(), myConceptMapCaptor.capture());
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loincCS = mySystemCaptor.getValue();
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assertEquals("2.68", loincCS.getVersion());
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loincVS_resources = myValueSetsCaptor.getValue();
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for (ValueSet loincVS : loincVS_resources) {
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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());
|
||||
|
|
|
|||
|
|
@ -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"
|
||||
|
|
|
@ -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
|
||||
|
|
@ -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
|
||||
|
|
|
|||
|
|
@ -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
|
||||
|
|
|
|||
Loading…
Reference in New Issue