Merge branch 'master' into issue-2883-unable-to-load-OpenAPI-docs
This commit is contained in:
katie_smilecdr
commit
f97e703180
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@ -473,30 +473,23 @@ public class TermCodeSystemStorageSvcImpl implements ITermCodeSystemStorageSvc {
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// defaults to true
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boolean isMakeVersionCurrent = theRequestDetails == null ||
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(boolean) theRequestDetails.getUserData().getOrDefault(MAKE_LOADING_VERSION_CURRENT, Boolean.TRUE);
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if (isMakeVersionCurrent) {
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makeCodeSystemCurrentVersion(codeSystem, codeSystemToStore, conceptsToSave, totalCodeCount);
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codeSystem.setCurrentVersion(codeSystemToStore);
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if (codeSystem.getPid() == null) {
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codeSystem = myCodeSystemDao.saveAndFlush(codeSystem);
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}
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}
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}
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private void makeCodeSystemCurrentVersion(TermCodeSystem theCodeSystem, TermCodeSystemVersion theCodeSystemToStore,
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Collection<TermConcept> theConceptsToSave, int theTotalCodeCount) {
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theCodeSystem.setCurrentVersion(theCodeSystemToStore);
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if (theCodeSystem.getPid() == null) {
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theCodeSystem = myCodeSystemDao.saveAndFlush(theCodeSystem);
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ourLog.debug("Setting CodeSystemVersion[{}] on {} concepts...", codeSystem.getPid(), totalCodeCount);
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for (TermConcept next : conceptsToSave) {
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populateVersion(next, codeSystemToStore);
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}
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ourLog.debug("Setting CodeSystemVersion[{}] on {} concepts...", theCodeSystem.getPid(), theTotalCodeCount);
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for (TermConcept next : theConceptsToSave) {
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populateVersion(next, theCodeSystemToStore);
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}
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ourLog.debug("Saving {} concepts...", theTotalCodeCount);
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ourLog.debug("Saving {} concepts...", totalCodeCount);
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IdentityHashMap<TermConcept, Object> conceptsStack2 = new IdentityHashMap<>();
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for (TermConcept next : theConceptsToSave) {
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persistChildren(next, theCodeSystemToStore, conceptsStack2, theTotalCodeCount);
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for (TermConcept next : conceptsToSave) {
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persistChildren(next, codeSystemToStore, conceptsStack2, totalCodeCount);
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}
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ourLog.debug("Done saving concepts, flushing to database");
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@ -62,20 +62,25 @@ public class LoincLinguisticVariantHandler implements IZipContentsHandlerCsv {
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// LinguisticVariantDisplayName
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//-- add formalName designation
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StringBuilder formalName = new StringBuilder();
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formalName.append(trimToEmpty(theRecord.get("COMPONENT") + ":"));
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formalName.append(trimToEmpty(theRecord.get("PROPERTY") + ":"));
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formalName.append(trimToEmpty(theRecord.get("TIME_ASPCT") + ":"));
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formalName.append(trimToEmpty(theRecord.get("SYSTEM") + ":"));
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formalName.append(trimToEmpty(theRecord.get("SCALE_TYP") + ":"));
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formalName.append(trimToEmpty(theRecord.get("METHOD_TYP")));
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StringBuilder fullySpecifiedName = new StringBuilder();
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fullySpecifiedName.append(trimToEmpty(theRecord.get("COMPONENT") + ":"));
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fullySpecifiedName.append(trimToEmpty(theRecord.get("PROPERTY") + ":"));
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fullySpecifiedName.append(trimToEmpty(theRecord.get("TIME_ASPCT") + ":"));
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fullySpecifiedName.append(trimToEmpty(theRecord.get("SYSTEM") + ":"));
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fullySpecifiedName.append(trimToEmpty(theRecord.get("SCALE_TYP") + ":"));
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fullySpecifiedName.append(trimToEmpty(theRecord.get("METHOD_TYP")));
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concept.addDesignation()
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.setLanguage(myLanguageCode)
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.setUseSystem(ITermLoaderSvc.LOINC_URI)
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.setUseCode("FullySpecifiedName")
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.setUseDisplay("FullySpecifiedName")
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.setValue(formalName.toString());
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String fullySpecifiedNameStr = fullySpecifiedName.toString();
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// skip if COMPONENT, PROPERTY, TIME_ASPCT, SYSTEM, SCALE_TYP and METHOD_TYP are all empty
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if (!fullySpecifiedNameStr.equals(":::::")) {
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concept.addDesignation()
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.setLanguage(myLanguageCode)
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.setUseSystem(ITermLoaderSvc.LOINC_URI)
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.setUseCode("FullySpecifiedName")
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.setUseDisplay("FullySpecifiedName")
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.setValue(fullySpecifiedNameStr);
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}
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//-- other designations
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addDesignation(theRecord, concept, "SHORTNAME");
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@ -111,6 +111,77 @@ public class TerminologyLoaderSvcLoincJpaTest extends BaseJpaR4Test {
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}
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@Test
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public void testLoadLoincVersionNotCurrent() throws IOException {
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// Load LOINC marked as version 2.67
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TerminologyLoaderSvcLoincTest.addLoincMandatoryFilesWithPropertiesFileToZip(myFiles, "v267_loincupload.properties");
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mySvc.loadLoinc(myFiles.getFiles(), mySrd);
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myTerminologyDeferredStorageSvc.saveAllDeferred();
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// array just to make it final and populate it into following lambda
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final TermCodeSystemVersion[] currentCodeSystemVersion_before_loading_v2_68 = new TermCodeSystemVersion[1];
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runInTransaction(() -> {
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assertEquals(1, myTermCodeSystemDao.count());
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assertEquals(2, myTermCodeSystemVersionDao.count());
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assertEquals(24, myTermValueSetDao.count());
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assertEquals(162, myTermConceptDao.count());
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assertEquals(12, myTermConceptMapDao.count());
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assertEquals(38, myResourceTableDao.count());
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TermCodeSystem myTermCodeSystem = myTermCodeSystemDao.findByCodeSystemUri("http://loinc.org");
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TermCodeSystemVersion myTermCodeSystemVersion_versioned =
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myTermCodeSystemVersionDao.findByCodeSystemPidAndVersion(myTermCodeSystem.getPid(), "2.67");
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assertNotEquals(myTermCodeSystem.getCurrentVersion().getPid(), myTermCodeSystemVersion_versioned.getPid());
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assertNotEquals(myTermCodeSystem.getResource().getId(), myTermCodeSystemVersion_versioned.getResource().getId());
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TermCodeSystemVersion myTermCodeSystemVersion_nonversioned =
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myTermCodeSystemVersionDao.findByCodeSystemPidVersionIsNull(myTermCodeSystem.getPid());
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assertEquals(myTermCodeSystem.getCurrentVersion().getPid(), myTermCodeSystemVersion_nonversioned.getPid());
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assertEquals(myTermCodeSystem.getResource().getId(), myTermCodeSystemVersion_nonversioned.getResource().getId());
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// current should be null loaded after 2.67
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currentCodeSystemVersion_before_loading_v2_68[0] =
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myTermCodeSystemVersionDao.findByCodeSystemPidVersionIsNull(myTermCodeSystem.getPid());
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});
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// Load LOINC marked as version 2.68 and not making it current (so 2.67 should remain current)
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myFiles = new ZipCollectionBuilder();
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TerminologyLoaderSvcLoincTest.addLoincMandatoryFilesWithPropertiesFileToZip(
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myFiles, "v268_curr_false_loincupload.properties");
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mySvc.loadLoinc(myFiles.getFiles(), mySrd);
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myTerminologyDeferredStorageSvc.saveAllDeferred();
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runInTransaction(() -> {
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assertEquals(1, myTermCodeSystemDao.count());
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assertEquals(3, myTermCodeSystemVersionDao.count());
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assertEquals(36, myTermValueSetDao.count());
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assertEquals(243, myTermConceptDao.count());
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assertEquals(18, myTermConceptMapDao.count());
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assertEquals(57, myResourceTableDao.count());
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TermCodeSystem myTermCodeSystem = myTermCodeSystemDao.findByCodeSystemUri("http://loinc.org");
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TermCodeSystemVersion currentCodeSystemVersion_after_loading_v2_68 =
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myTermCodeSystemVersionDao.findByCodeSystemPidVersionIsNull(myTermCodeSystem.getPid());
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// current should be same as before loading 2.68
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assertEquals(currentCodeSystemVersion_before_loading_v2_68[0].getPid(), currentCodeSystemVersion_after_loading_v2_68.getPid());
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TermCodeSystemVersion termCodeSystemVersion_267 =
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myTermCodeSystemVersionDao.findByCodeSystemPidAndVersion(myTermCodeSystem.getPid(), "2.67");
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assertNotEquals(myTermCodeSystem.getCurrentVersion().getPid(), termCodeSystemVersion_267.getPid());
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TermCodeSystemVersion termCodeSystemVersion_268 =
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myTermCodeSystemVersionDao.findByCodeSystemPidAndVersion(myTermCodeSystem.getPid(), "2.68");
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assertNotEquals(myTermCodeSystem.getCurrentVersion().getPid(), termCodeSystemVersion_268.getPid());
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});
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}
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/**
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* Loinc distro includes loinc.xml as of 2.70
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*/
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@ -484,7 +484,7 @@ public class TerminologyLoaderSvcLoincTest extends BaseLoaderTest {
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verifyLinguisticVariant(code.getDesignations(), "fr-CA", "Cellules de Purkinje cytoplasmique type 2 , IgG","Titre","Temps ponctuel","Sérum","Quantitatif","Immunofluorescence","Sérologie","","","","");
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verifyLinguisticVariant(code.getDesignations(), "zh-CN", "血流速度.收缩期.最大值","速度","时间点","大脑中动脉","定量型","超声.多普勒","产科学检查与测量指标.超声","","", "Cereb 动态 可用数量表示的;定量性;数值型;数量型;连续数值型标尺 大脑（Cerebral） 时刻;随机;随意;瞬间 术语\"cerebral\"指的是主要由中枢半球（大脑皮质和基底神经节）组成的那部分脑结构 流 流量;流速;流体 血;全血 血流量;血液流量 速度(距离/时间);速率;速率(距离/时间)","");
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code = concepts.get("17787-3");
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assertEquals(6, code.getDesignations().size());
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assertEquals(5, code.getDesignations().size());
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verifyConsumerName(code.getDesignations(), "Consumer Name 17787-3");
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verifyLinguisticVariant(code.getDesignations(), "de-AT", "","","","","","","","","","CoV OC43 RNA ql/SM P","Coronavirus OC43 RNA ql. /Sondermaterial PCR");
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verifyLinguisticVariant(code.getDesignations(), "fr-CA", "Virus respiratoire syncytial bovin","Présence-Seuil","Temps ponctuel","XXX","Ordinal","Culture spécifique à un microorganisme","Microbiologie","","","","");
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@ -986,7 +986,7 @@ public class TerminologyLoaderSvcLoincTest extends BaseLoaderTest {
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private static void verifyDesignation(TermConceptDesignation theDesignation, String theUseSystem, String theUseCode, String theValue) {
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if (theDesignation == null)
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return;
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return;
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assertEquals(theUseSystem, theDesignation.getUseSystem());
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assertEquals(theUseCode, theDesignation.getUseCode());
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assertEquals(theValue, theDesignation.getValue());
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@ -0,0 +1,99 @@
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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.primary.file=AccessoryFiles/PartFile/LoincPartLink_Primary.csv
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loinc.part.link.supplementary.file=AccessoryFiles/PartFile/LoincPartLink_Supplementary.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 LOINC code system
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## Key may be omitted if only a single version of LOINC is being kept.
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loinc.codesystem.version=2.68
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loinc.codesystem.make.current=false
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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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# Consumer Names
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## Default value if key not provided: AccessoryFiles/ConsumerName/ConsumerName.csv
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## File may be omitted
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loinc.consumer.name.file=AccessoryFiles/ConsumerName/ConsumerName.csv
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# Linguistic Variants
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## Default value if key not provided: AccessoryFiles/LinguisticVariants/LinguisticVariants.csv
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## File may be omitted
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loinc.linguistic.variants.file=AccessoryFiles/LinguisticVariants/LinguisticVariants.csv
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