Restore ability to load LOINC PartLink data from a single file for pre-2.68 versions.
This commit is contained in:
ianmarshall
parent
ce54d28a23
commit
d9841e59ac
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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 + " or " + notFoundSingle;
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} else {
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msg = "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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@ -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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@ -68,9 +68,54 @@ 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] or [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] or [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("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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@ -413,12 +458,27 @@ public class TerminologyLoaderSvcLoincTest extends BaseLoaderTest {
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}
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}
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public static void addLoincMandatoryFilesAndSinglePartLinkToZip(ZipCollectionBuilder theFiles) throws IOException {
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addBaseLoincMandatoryFilesToZip(theFiles);
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theFiles.addFileZip("/loinc/", "loincupload_singlepartlink.properties");
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theFiles.addFileZip("/loinc/", LOINC_PART_LINK_FILE_DEFAULT.getCode());
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}
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public static void addLoincMandatoryFilesToZip(ZipCollectionBuilder theFiles) throws IOException {
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addLoincMandatoryFilesWithPropertiesFileToZip(theFiles, LOINC_UPLOAD_PROPERTIES_FILE.getCode());
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addBaseLoincMandatoryFilesToZip(theFiles);
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theFiles.addFileZip("/loinc/", LOINC_UPLOAD_PROPERTIES_FILE.getCode());
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theFiles.addFileZip("/loinc/", LOINC_PART_LINK_FILE_PRIMARY_DEFAULT.getCode());
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theFiles.addFileZip("/loinc/", LOINC_PART_LINK_FILE_SUPPLEMENTARY_DEFAULT.getCode());
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}
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public static void addLoincMandatoryFilesWithPropertiesFileToZip(ZipCollectionBuilder theFiles, String thePropertiesFile) throws IOException {
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theFiles.addFileZip("/loinc/", thePropertiesFile);
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theFiles.addFileZip("/loinc/", LOINC_PART_LINK_FILE_PRIMARY_DEFAULT.getCode());
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theFiles.addFileZip("/loinc/", LOINC_PART_LINK_FILE_SUPPLEMENTARY_DEFAULT.getCode());
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addBaseLoincMandatoryFilesToZip(theFiles);
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}
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private static void addBaseLoincMandatoryFilesToZip(ZipCollectionBuilder theFiles) throws IOException{
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theFiles.addFileZip("/loinc/", LOINC_GROUP_FILE_DEFAULT.getCode());
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theFiles.addFileZip("/loinc/", LOINC_GROUP_TERMS_FILE_DEFAULT.getCode());
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theFiles.addFileZip("/loinc/", LOINC_PARENT_GROUP_FILE_DEFAULT.getCode());
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@ -430,8 +490,6 @@ public class TerminologyLoaderSvcLoincTest extends BaseLoaderTest {
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theFiles.addFileZip("/loinc/", LOINC_ANSWERLIST_LINK_FILE_DEFAULT.getCode());
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theFiles.addFileZip("/loinc/", LOINC_ANSWERLIST_LINK_DUPLICATE_FILE_DEFAULT.getCode());
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theFiles.addFileZip("/loinc/", LOINC_PART_FILE_DEFAULT.getCode());
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theFiles.addFileZip("/loinc/", LOINC_PART_LINK_FILE_PRIMARY_DEFAULT.getCode());
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theFiles.addFileZip("/loinc/", LOINC_PART_LINK_FILE_SUPPLEMENTARY_DEFAULT.getCode());
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theFiles.addFileZip("/loinc/", LOINC_PART_RELATED_CODE_MAPPING_FILE_DEFAULT.getCode());
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theFiles.addFileZip("/loinc/", LOINC_DOCUMENT_ONTOLOGY_FILE_DEFAULT.getCode());
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theFiles.addFileZip("/loinc/", LOINC_RSNA_PLAYBOOK_FILE_DEFAULT.getCode());
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@ -0,0 +1,10 @@
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"LoincNumber","LongCommonName","PartNumber","PartName","PartCodeSystem","PartTypeName","LinkTypeName","Property"
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"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"
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"10013-1","R' wave amplitude in lead I","LP6802-5","Elpot","http://loinc.org","PROPERTY","Primary","http://loinc.org/property/PROPERTY"
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"10013-1","R' wave amplitude in lead I","LP6960-1","Pt","http://loinc.org","TIME","Primary","http://loinc.org/property/TIME_ASPCT"
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"10013-1","R' wave amplitude in lead I","LP7289-4","Heart","http://loinc.org","SYSTEM","Primary","http://loinc.org/property/SYSTEM"
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"10013-1","R' wave amplitude in lead I","LP7753-9","Qn","http://loinc.org","SCALE","Primary","http://loinc.org/property/SCALE_TYP"
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"10013-1","R' wave amplitude in lead I","LP6244-0","EKG","http://loinc.org","METHOD","Primary","http://loinc.org/property/METHOD_TYP"
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"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"
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"10013-1","R' wave amplitude in lead I","LP6802-5","Elpot","http://loinc.org","PROPERTY","DetailedModel","http://loinc.org/property/PROPERTY"
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"10013-1","R' wave amplitude in lead I","LP6960-1","Pt","http://loinc.org","TIME","DetailedModel","http://loinc.org/property/time-core"
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@ -0,0 +1,82 @@
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#################
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### MANDATORY ###
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#################
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# Answer lists (ValueSets of potential answers/values for LOINC "questions")
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## File must be present
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loinc.answerlist.file=AccessoryFiles/AnswerFile/AnswerList.csv
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# Answer list links (connects LOINC observation codes to answer list codes)
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## File must be present
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loinc.answerlist.link.file=AccessoryFiles/AnswerFile/LoincAnswerListLink.csv
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# Document ontology
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## File must be present
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loinc.document.ontology.file=AccessoryFiles/DocumentOntology/DocumentOntology.csv
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# LOINC codes
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## File must be present
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loinc.file=LoincTable/Loinc.csv
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# LOINC hierarchy
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## File must be present
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loinc.hierarchy.file=AccessoryFiles/MultiAxialHierarchy/MultiAxialHierarchy.csv
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# IEEE medical device codes
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## File must be present
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loinc.ieee.medical.device.code.mapping.table.file=AccessoryFiles/LoincIeeeMedicalDeviceCodeMappingTable/LoincIeeeMedicalDeviceCodeMappingTable.csv
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# Imaging document codes
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## File must be present
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loinc.imaging.document.codes.file=AccessoryFiles/ImagingDocuments/ImagingDocumentCodes.csv
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# Part
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## File must be present
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loinc.part.file=AccessoryFiles/PartFile/Part.csv
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# Part link
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## File must be present
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loinc.part.link.file=AccessoryFiles/PartFile/LoincPartLink.csv
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# Part related code mapping
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## File must be present
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loinc.part.related.code.mapping.file=AccessoryFiles/PartFile/PartRelatedCodeMapping.csv
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# RSNA playbook
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## File must be present
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loinc.rsna.playbook.file=AccessoryFiles/LoincRsnaRadiologyPlaybook/LoincRsnaRadiologyPlaybook.csv
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# Top 2000 codes - SI
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## File must be present
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loinc.top2000.common.lab.results.si.file=AccessoryFiles/Top2000Results/SI/Top2000CommonLabResultsSi.csv
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# Top 2000 codes - US
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## File must be present
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loinc.top2000.common.lab.results.us.file=AccessoryFiles/Top2000Results/US/Top2000CommonLabResultsUs.csv
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# Universal lab order ValueSet
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## File must be present
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loinc.universal.lab.order.valueset.file=AccessoryFiles/LoincUniversalLabOrdersValueSet/LoincUniversalLabOrdersValueSet.csv
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################
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### OPTIONAL ###
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################
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# This is the version identifier for the answer list file
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## Key may be omitted
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loinc.answerlist.version=Beta.1
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# This is the version identifier for uploaded ConceptMap resources
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## Key may be omitted
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loinc.conceptmap.version=Beta.1
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# Group
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## Default value if key not provided: AccessoryFiles/GroupFile/Group.csv
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## File may be omitted
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loinc.group.file=AccessoryFiles/GroupFile/Group.csv
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# Group terms
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## Default value if key not provided: AccessoryFiles/GroupFile/GroupLoincTerms.csv
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## File may be omitted
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loinc.group.terms.file=AccessoryFiles/GroupFile/GroupLoincTerms.csv
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# Parent group
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## Default value if key not provided: AccessoryFiles/GroupFile/ParentGroup.csv
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## File may be omitted
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loinc.parent.group.file=AccessoryFiles/GroupFile/ParentGroup.csv
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