Fix loinc designation issue with FormalName (#2865)
* Fix loinc designation issue with FormalName * Changed Loinc designation name to 'FullySpecifiedName'
This commit is contained in:
Frank Tao
GitHub
parent
35d3e3689b
commit
3c598e2ff8
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@ -2,6 +2,7 @@ package ca.uhn.fhir.jpa.term.loinc;
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import static org.apache.commons.lang3.StringUtils.isBlank;
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import static org.apache.commons.lang3.StringUtils.trim;
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import static org.apache.commons.lang3.StringUtils.trimToEmpty;
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import java.util.Map;
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@ -54,18 +55,31 @@ public class LoincLinguisticVariantHandler implements IZipContentsHandlerCsv {
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return;
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}
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addDesignation(theRecord, concept, "COMPONENT");
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addDesignation(theRecord, concept, "PROPERTY");
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addDesignation(theRecord, concept, "TIME_ASPCT");
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addDesignation(theRecord, concept, "SYSTEM");
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addDesignation(theRecord, concept, "SCALE_TYP");
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// The following should be created as designations for each term:
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// COMPONENT:PROPERTY:TIME_ASPCT:SYSTEM:SCALE_TYP:METHOD_TYP (as colon-separated concatenation - FormalName)
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// SHORTNAME
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// LONG_COMMON_NAME
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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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addDesignation(theRecord, concept, "METHOD_TYP");
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addDesignation(theRecord, concept, "CLASS");
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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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//-- other designations
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addDesignation(theRecord, concept, "SHORTNAME");
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addDesignation(theRecord, concept, "LONG_COMMON_NAME");
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addDesignation(theRecord, concept, "RELATEDNAMES2");
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addDesignation(theRecord, concept, "LONG_COMMON_NAME");
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addDesignation(theRecord, concept, "LinguisticVariantDisplayName");
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}
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@ -478,13 +478,13 @@ public class TerminologyLoaderSvcLoincTest extends BaseLoaderTest {
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// Consumer Name
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if (theIncludeConsumerNameAndLinguisticVariants) {
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code = concepts.get("61438-8");
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assertEquals(28, code.getDesignations().size());
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assertEquals(8, code.getDesignations().size());
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verifyConsumerName(code.getDesignations(), "Consumer Name 61438-8");
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verifyLinguisticVariant(code.getDesignations(), "de-AT", "Entlassungsbrief Ärztlich","Ergebnis","Zeitpunkt","{Setting}","Dokument","Dermatologie","DOC.ONTOLOGY","de shortname","de long common name","de related names 2","de linguistic variant display name");
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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(19, code.getDesignations().size());
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assertEquals(6, 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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@ -958,61 +958,29 @@ public class TerminologyLoaderSvcLoincTest extends BaseLoaderTest {
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String methodType, String theClass, String theShortName, String theLongCommonName, String theRelatedName2,
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String theLinguisticVariantDisplayName) {
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TermConceptDesignation componentDes = null;
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TermConceptDesignation propertyDes = null;
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TermConceptDesignation timeAspctDes = null;
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TermConceptDesignation systemDes = null;
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TermConceptDesignation scaleTypDes = null;
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TermConceptDesignation methodTypDes = null;
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TermConceptDesignation classDes = null;
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TermConceptDesignation formalNameDes = null;
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TermConceptDesignation shortNameDes = null;
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TermConceptDesignation longCommonNameDes = null;
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TermConceptDesignation relatedNames2Des = null;
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TermConceptDesignation longCommonNameDes = null;
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TermConceptDesignation linguisticVariantDisplayNameDes = null;
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for (TermConceptDesignation designation : designationList) {
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if (theLanguage.equals(designation.getLanguage())) {
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if ("COMPONENT".equals(designation.getUseDisplay()))
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componentDes = designation;
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if ("PROPERTY".equals(designation.getUseDisplay()))
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propertyDes = designation;
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if ("TIME_ASPCT".equals(designation.getUseDisplay()))
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timeAspctDes = designation;
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if ("SYSTEM".equals(designation.getUseDisplay()))
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systemDes = designation;
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if ("SCALE_TYP".equals(designation.getUseDisplay()))
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scaleTypDes = designation;
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if ("FullySpecifiedName".equals(designation.getUseDisplay()))
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formalNameDes = designation;
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if ("METHOD_TYP".equals(designation.getUseDisplay()))
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methodTypDes = designation;
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if ("CLASS".equals(designation.getUseDisplay()))
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classDes = designation;
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if ("SHORTNAME".equals(designation.getUseDisplay()))
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shortNameDes = designation;
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if ("LONG_COMMON_NAME".equals(designation.getUseDisplay()))
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longCommonNameDes = designation;
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if ("RELATEDNAMES2".equals(designation.getUseDisplay()))
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relatedNames2Des = designation;
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if ("LinguisticVariantDisplayName".equals(designation.getUseDisplay()))
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linguisticVariantDisplayNameDes = designation;
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}
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}
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verifyDesignation(componentDes, ITermLoaderSvc.LOINC_URI, "COMPONENT", theComponent);
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verifyDesignation(propertyDes, ITermLoaderSvc.LOINC_URI, "PROPERTY", theProperty);
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verifyDesignation(timeAspctDes, ITermLoaderSvc.LOINC_URI, "TIME_ASPCT", theTimeAspct);
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verifyDesignation(systemDes, ITermLoaderSvc.LOINC_URI, "SYSTEM", theSystem);
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verifyDesignation(scaleTypDes, ITermLoaderSvc.LOINC_URI, "SCALE_TYP", theScaleTyp);
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verifyDesignation(methodTypDes, ITermLoaderSvc.LOINC_URI, "METHOD_TYP", methodType);
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verifyDesignation(classDes, ITermLoaderSvc.LOINC_URI, "CLASS", theClass);
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verifyDesignation(formalNameDes, ITermLoaderSvc.LOINC_URI, "FullySpecifiedName", theComponent+":"+theProperty+":"+theTimeAspct+":"+theSystem+":"+theScaleTyp+":"+methodType);
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verifyDesignation(shortNameDes, ITermLoaderSvc.LOINC_URI, "SHORTNAME", theShortName);
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verifyDesignation(longCommonNameDes, ITermLoaderSvc.LOINC_URI, "LONG_COMMON_NAME", theLongCommonName);
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verifyDesignation(relatedNames2Des, ITermLoaderSvc.LOINC_URI, "RELATEDNAMES2", theRelatedName2);
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verifyDesignation(longCommonNameDes, ITermLoaderSvc.LOINC_URI, "LONG_COMMON_NAME", theLongCommonName);
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verifyDesignation(linguisticVariantDisplayNameDes, ITermLoaderSvc.LOINC_URI, "LinguisticVariantDisplayName", theLinguisticVariantDisplayName);
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}
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