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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 2021-08-06 10:59:01 -04:00 committed by GitHub
parent 35d3e3689b
commit 3c598e2ff8
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2 changed files with 32 additions and 50 deletions
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34
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/term/loinc/LoincLinguisticVariantHandler.java
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@ -2,6 +2,7 @@ package ca.uhn.fhir.jpa.term.loinc;
import static org.apache.commons.lang3.StringUtils.isBlank; import static org.apache.commons.lang3.StringUtils.isBlank;
import static org.apache.commons.lang3.StringUtils.trim; import static org.apache.commons.lang3.StringUtils.trim;
import static org.apache.commons.lang3.StringUtils.trimToEmpty;
import java.util.Map; import java.util.Map;
@ -54,18 +55,31 @@ public class LoincLinguisticVariantHandler implements IZipContentsHandlerCsv {
return; return;
} }
addDesignation(theRecord, concept, "COMPONENT"); // The following should be created as designations for each term:
addDesignation(theRecord, concept, "PROPERTY"); // COMPONENT:PROPERTY:TIME_ASPCT:SYSTEM:SCALE_TYP:METHOD_TYP (as colon-separated concatenation - FormalName)
addDesignation(theRecord, concept, "TIME_ASPCT"); // SHORTNAME
addDesignation(theRecord, concept, "SYSTEM"); // LONG_COMMON_NAME
addDesignation(theRecord, concept, "SCALE_TYP"); // LinguisticVariantDisplayName
//-- add formalName designation
StringBuilder formalName = new StringBuilder();
formalName.append(trimToEmpty(theRecord.get("COMPONENT") + ":"));
formalName.append(trimToEmpty(theRecord.get("PROPERTY") + ":"));
formalName.append(trimToEmpty(theRecord.get("TIME_ASPCT") + ":"));
formalName.append(trimToEmpty(theRecord.get("SYSTEM") + ":"));
formalName.append(trimToEmpty(theRecord.get("SCALE_TYP") + ":"));
formalName.append(trimToEmpty(theRecord.get("METHOD_TYP")));
addDesignation(theRecord, concept, "METHOD_TYP"); concept.addDesignation()
addDesignation(theRecord, concept, "CLASS"); .setLanguage(myLanguageCode)
.setUseSystem(ITermLoaderSvc.LOINC_URI)
.setUseCode("FullySpecifiedName")
.setUseDisplay("FullySpecifiedName")
.setValue(formalName.toString());
//-- other designations
addDesignation(theRecord, concept, "SHORTNAME"); addDesignation(theRecord, concept, "SHORTNAME");
addDesignation(theRecord, concept, "LONG_COMMON_NAME"); addDesignation(theRecord, concept, "LONG_COMMON_NAME");
addDesignation(theRecord, concept, "RELATEDNAMES2");
addDesignation(theRecord, concept, "LinguisticVariantDisplayName"); addDesignation(theRecord, concept, "LinguisticVariantDisplayName");
} }

48
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/term/TerminologyLoaderSvcLoincTest.java
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@ -478,13 +478,13 @@ public class TerminologyLoaderSvcLoincTest extends BaseLoaderTest {
// Consumer Name // Consumer Name
if (theIncludeConsumerNameAndLinguisticVariants) { if (theIncludeConsumerNameAndLinguisticVariants) {
code = concepts.get("61438-8"); code = concepts.get("61438-8");
assertEquals(28, code.getDesignations().size()); assertEquals(8, code.getDesignations().size());
verifyConsumerName(code.getDesignations(), "Consumer Name 61438-8"); verifyConsumerName(code.getDesignations(), "Consumer Name 61438-8");
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"); 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");
verifyLinguisticVariant(code.getDesignations(), "fr-CA", "Cellules de Purkinje cytoplasmique type 2 , IgG","Titre","Temps ponctuel","Sérum","Quantitatif","Immunofluorescence","Sérologie","","","",""); verifyLinguisticVariant(code.getDesignations(), "fr-CA", "Cellules de Purkinje cytoplasmique type 2 , IgG","Titre","Temps ponctuel","Sérum","Quantitatif","Immunofluorescence","Sérologie","","","","");
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)",""); 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)","");
code = concepts.get("17787-3"); code = concepts.get("17787-3");
assertEquals(19, code.getDesignations().size()); assertEquals(6, code.getDesignations().size());
verifyConsumerName(code.getDesignations(), "Consumer Name 17787-3"); verifyConsumerName(code.getDesignations(), "Consumer Name 17787-3");
verifyLinguisticVariant(code.getDesignations(), "de-AT", "","","","","","","","","","CoV OC43 RNA ql/SM P","Coronavirus OC43 RNA ql. /Sondermaterial PCR"); verifyLinguisticVariant(code.getDesignations(), "de-AT", "","","","","","","","","","CoV OC43 RNA ql/SM P","Coronavirus OC43 RNA ql. /Sondermaterial PCR");
verifyLinguisticVariant(code.getDesignations(), "fr-CA", "Virus respiratoire syncytial bovin","Présence-Seuil","Temps ponctuel","XXX","Ordinal","Culture spécifique à un microorganisme","Microbiologie","","","",""); verifyLinguisticVariant(code.getDesignations(), "fr-CA", "Virus respiratoire syncytial bovin","Présence-Seuil","Temps ponctuel","XXX","Ordinal","Culture spécifique à un microorganisme","Microbiologie","","","","");
@ -958,61 +958,29 @@ public class TerminologyLoaderSvcLoincTest extends BaseLoaderTest {
String methodType, String theClass, String theShortName, String theLongCommonName, String theRelatedName2, String methodType, String theClass, String theShortName, String theLongCommonName, String theRelatedName2,
String theLinguisticVariantDisplayName) { String theLinguisticVariantDisplayName) {
TermConceptDesignation componentDes = null; TermConceptDesignation formalNameDes = null;
TermConceptDesignation propertyDes = null;
TermConceptDesignation timeAspctDes = null;
TermConceptDesignation systemDes = null;
TermConceptDesignation scaleTypDes = null;
TermConceptDesignation methodTypDes = null;
TermConceptDesignation classDes = null;
TermConceptDesignation shortNameDes = null; TermConceptDesignation shortNameDes = null;
TermConceptDesignation longCommonNameDes = null; TermConceptDesignation longCommonNameDes = null;
TermConceptDesignation relatedNames2Des = null;
TermConceptDesignation linguisticVariantDisplayNameDes = null; TermConceptDesignation linguisticVariantDisplayNameDes = null;
for (TermConceptDesignation designation : designationList) { for (TermConceptDesignation designation : designationList) {
if (theLanguage.equals(designation.getLanguage())) { if (theLanguage.equals(designation.getLanguage())) {
if ("COMPONENT".equals(designation.getUseDisplay())) if ("FullySpecifiedName".equals(designation.getUseDisplay()))
componentDes = designation; formalNameDes = designation;
if ("PROPERTY".equals(designation.getUseDisplay()))
propertyDes = designation;
if ("TIME_ASPCT".equals(designation.getUseDisplay()))
timeAspctDes = designation;
if ("SYSTEM".equals(designation.getUseDisplay()))
systemDes = designation;
if ("SCALE_TYP".equals(designation.getUseDisplay()))
scaleTypDes = designation;
if ("METHOD_TYP".equals(designation.getUseDisplay()))
methodTypDes = designation;
if ("CLASS".equals(designation.getUseDisplay()))
classDes = designation;
if ("SHORTNAME".equals(designation.getUseDisplay())) if ("SHORTNAME".equals(designation.getUseDisplay()))
shortNameDes = designation; shortNameDes = designation;
if ("LONG_COMMON_NAME".equals(designation.getUseDisplay())) if ("LONG_COMMON_NAME".equals(designation.getUseDisplay()))
longCommonNameDes = designation; longCommonNameDes = designation;
if ("RELATEDNAMES2".equals(designation.getUseDisplay()))
relatedNames2Des = designation;
if ("LinguisticVariantDisplayName".equals(designation.getUseDisplay())) if ("LinguisticVariantDisplayName".equals(designation.getUseDisplay()))
linguisticVariantDisplayNameDes = designation; linguisticVariantDisplayNameDes = designation;
} }
} }
verifyDesignation(componentDes, ITermLoaderSvc.LOINC_URI, "COMPONENT", theComponent);
verifyDesignation(propertyDes, ITermLoaderSvc.LOINC_URI, "PROPERTY", theProperty);
verifyDesignation(timeAspctDes, ITermLoaderSvc.LOINC_URI, "TIME_ASPCT", theTimeAspct);
verifyDesignation(systemDes, ITermLoaderSvc.LOINC_URI, "SYSTEM", theSystem);
verifyDesignation(scaleTypDes, ITermLoaderSvc.LOINC_URI, "SCALE_TYP", theScaleTyp);
verifyDesignation(methodTypDes, ITermLoaderSvc.LOINC_URI, "METHOD_TYP", methodType); verifyDesignation(formalNameDes, ITermLoaderSvc.LOINC_URI, "FullySpecifiedName", theComponent+":"+theProperty+":"+theTimeAspct+":"+theSystem+":"+theScaleTyp+":"+methodType);
verifyDesignation(classDes, ITermLoaderSvc.LOINC_URI, "CLASS", theClass);
verifyDesignation(shortNameDes, ITermLoaderSvc.LOINC_URI, "SHORTNAME", theShortName); verifyDesignation(shortNameDes, ITermLoaderSvc.LOINC_URI, "SHORTNAME", theShortName);
verifyDesignation(longCommonNameDes, ITermLoaderSvc.LOINC_URI, "LONG_COMMON_NAME", theLongCommonName); verifyDesignation(longCommonNameDes, ITermLoaderSvc.LOINC_URI, "LONG_COMMON_NAME", theLongCommonName);
verifyDesignation(relatedNames2Des, ITermLoaderSvc.LOINC_URI, "RELATEDNAMES2", theRelatedName2);
verifyDesignation(linguisticVariantDisplayNameDes, ITermLoaderSvc.LOINC_URI, "LinguisticVariantDisplayName", theLinguisticVariantDisplayName); verifyDesignation(linguisticVariantDisplayNameDes, ITermLoaderSvc.LOINC_URI, "LinguisticVariantDisplayName", theLinguisticVariantDisplayName);
} }