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Fixes to terminology loader.

This commit is contained in:
ianmarshall 2020-09-25 21:43:15 -04:00
parent 47244c54dc
commit 1dc4a533d6
18 changed files with 139 additions and 38 deletions
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2
hapi-fhir-jpaserver-api/src/main/java/ca/uhn/fhir/jpa/api/dao/IFhirResourceDaoCodeSystem.java
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@ -42,6 +42,8 @@ public interface IFhirResourceDaoCodeSystem<T extends IBaseResource, CD, CC> ext
SubsumesResult subsumes(IPrimitiveType<String> theCodeA, IPrimitiveType<String> theCodeB, IPrimitiveType<String> theSystem, CD theCodingA, CD theCodingB, RequestDetails theRequestDetails);
IValidationSupport.CodeValidationResult validateCode(IIdType theCodeSystemId, IPrimitiveType<String> theCodeSystemUrl, IPrimitiveType<String> theVersion, IPrimitiveType<String> theCode, IPrimitiveType<String> theDisplay, CD theCoding, CC theCodeableConcept, RequestDetails theRequestDetails);
class SubsumesResult {
private final ConceptSubsumptionOutcome myOutcome;

5
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/term/BaseTermReadSvcImpl.java
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@ -129,6 +129,7 @@ import org.quartz.JobExecutionContext;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.context.ApplicationContext;
import org.springframework.data.domain.PageRequest;
import org.springframework.data.domain.Pageable;
import org.springframework.data.domain.Slice;
import org.springframework.transaction.PlatformTransactionManager;
import org.springframework.transaction.TransactionDefinition;
@ -147,7 +148,9 @@ import javax.persistence.PersistenceContextType;
import javax.persistence.TypedQuery;
import javax.persistence.criteria.CriteriaBuilder;
import javax.persistence.criteria.CriteriaQuery;
import javax.persistence.criteria.Fetch;
import javax.persistence.criteria.Join;
import javax.persistence.criteria.JoinType;
import javax.persistence.criteria.Predicate;
import javax.persistence.criteria.Root;
import javax.validation.constraints.NotNull;
@ -2706,7 +2709,7 @@ public abstract class BaseTermReadSvcImpl implements ITermReadSvc {
CriteriaQuery<TermConcept> query = criteriaBuilder.createQuery(TermConcept.class);
Root<TermConcept> root = query.from(TermConcept.class);
Fetch<TermCodeSystemVersion, TermConcept> systemVersionFetch = root.fetch("myCodeSystem", JoinType.INNER);
Fetch<TermCodeSystemVersion, TermConcept> systemVersionFetch = root.fetch("myCodeSystem", JoinType.INNER);
Join<TermCodeSystemVersion, TermConcept> systemVersionJoin = (Join<TermCodeSystemVersion, TermConcept>)systemVersionFetch;
Fetch<TermCodeSystem, TermCodeSystemVersion> systemFetch = systemVersionFetch.fetch("myCodeSystem", JoinType.INNER);
Join<TermCodeSystem, TermCodeSystemVersion> systemJoin = (Join<TermCodeSystem, TermCodeSystemVersion>)systemFetch;

16
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/term/TermLoaderSvcImpl.java
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@ -480,7 +480,7 @@ public class TermLoaderSvcImpl implements ITermLoaderSvc {
IOUtils.closeQuietly(theDescriptors);
valueSets.add(getValueSetLoincAll());
valueSets.add(getValueSetLoincAll(theUploadProperties));
for (Entry<String, TermConcept> next : code2concept.entrySet()) {
TermConcept nextConcept = next.getValue();
@ -499,12 +499,20 @@ public class TermLoaderSvcImpl implements ITermLoaderSvc {
return new UploadStatistics(conceptCount, target);
}
private ValueSet getValueSetLoincAll() {
private ValueSet getValueSetLoincAll(Properties theUploadProperties) {
ValueSet retVal = new ValueSet();
retVal.setId("loinc-all");
String codeSystemVersionId = theUploadProperties.getProperty(LOINC_CODESYSTEM_VERSION.getCode());
String valueSetId;
if (codeSystemVersionId != null) {
valueSetId = "loinc-all" + "-" + codeSystemVersionId;
} else {
valueSetId = "loinc-all";
codeSystemVersionId = "1.0.0";
}
retVal.setId(valueSetId);
retVal.setUrl("http://loinc.org/vs");
retVal.setVersion("1.0.0");
retVal.setVersion(codeSystemVersionId);
retVal.setName("All LOINC codes");
retVal.setStatus(Enumerations.PublicationStatus.ACTIVE);
retVal.setDate(new Date());

9
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/term/loinc/BaseLoincTop2000LabResultsHandler.java
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@ -31,7 +31,7 @@ import java.util.List;
import java.util.Map;
import java.util.Properties;
import static ca.uhn.fhir.jpa.term.loinc.LoincUploadPropertiesEnum.LOINC_CONCEPTMAP_VERSION;
import static ca.uhn.fhir.jpa.term.loinc.LoincUploadPropertiesEnum.LOINC_CODESYSTEM_VERSION;
import static org.apache.commons.lang3.StringUtils.trim;
public class BaseLoincTop2000LabResultsHandler extends BaseLoincHandler implements IRecordHandler {
@ -42,7 +42,12 @@ public class BaseLoincTop2000LabResultsHandler extends BaseLoincHandler implemen
public BaseLoincTop2000LabResultsHandler(Map<String, TermConcept> theCode2concept, List<ValueSet> theValueSets, String theValueSetId, String theValueSetUri, String theValueSetName, List<ConceptMap> theConceptMaps, Properties theUploadProperties) {
super(theCode2concept, theValueSets, theConceptMaps, theUploadProperties);
myValueSetId = theValueSetId + "-" + myUploadProperties.getProperty(LOINC_CONCEPTMAP_VERSION.getCode());
String versionId = myUploadProperties.getProperty(LOINC_CODESYSTEM_VERSION.getCode());
if (versionId != null) {
myValueSetId = theValueSetId + "-" + versionId;
} else {
myValueSetId = theValueSetId;
}
myValueSetUri = theValueSetUri;
myValueSetName = theValueSetName;
}

11
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/term/loinc/LoincAnswerListHandler.java
View File

@ -50,7 +50,7 @@ public class LoincAnswerListHandler extends BaseLoincHandler {
public void accept(CSVRecord theRecord) {
// this is the code for the list (will repeat)
String answerListId = trim(theRecord.get("AnswerListId")) + "-" + myUploadProperties.getProperty(LOINC_CONCEPTMAP_VERSION.getCode());
String answerListId = trim(theRecord.get("AnswerListId"));
String answerListName = trim(theRecord.get("AnswerListName"));
String answerListOid = trim(theRecord.get("AnswerListOID"));
String externallyDefined = trim(theRecord.get("ExtDefinedYN"));
@ -74,7 +74,14 @@ public class LoincAnswerListHandler extends BaseLoincHandler {
}
// Answer list ValueSet
ValueSet vs = getValueSet(answerListId, "http://loinc.org/vs/" + answerListId, answerListName, LOINC_ANSWERLIST_VERSION.getCode());
String valueSetId;
String codeSystemVersionId = myUploadProperties.getProperty(LOINC_CODESYSTEM_VERSION.getCode());
if (codeSystemVersionId != null) {
valueSetId = answerListId + "-" + codeSystemVersionId;
} else {
valueSetId = answerListId;
}
ValueSet vs = getValueSet(valueSetId, "http://loinc.org/vs/" + answerListId, answerListName, LOINC_ANSWERLIST_VERSION.getCode());
if (vs.getIdentifier().isEmpty()) {
vs.addIdentifier()
.setSystem("urn:ietf:rfc:3986")

12
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/term/loinc/LoincDocumentOntologyHandler.java
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@ -33,7 +33,7 @@ import java.util.List;
import java.util.Map;
import java.util.Properties;
import static ca.uhn.fhir.jpa.term.loinc.LoincUploadPropertiesEnum.LOINC_CONCEPTMAP_VERSION;
import static ca.uhn.fhir.jpa.term.loinc.LoincUploadPropertiesEnum.LOINC_CODESYSTEM_VERSION;
import static org.apache.commons.lang3.StringUtils.trim;
public class LoincDocumentOntologyHandler extends BaseLoincHandler implements IRecordHandler {
@ -58,8 +58,14 @@ public class LoincDocumentOntologyHandler extends BaseLoincHandler implements IR
String partName = trim(theRecord.get("PartName"));
// RSNA Codes VS
ValueSet vs = getValueSet(DOCUMENT_ONTOLOGY_CODES_VS_ID + "-" + myUploadProperties.getProperty(LOINC_CONCEPTMAP_VERSION.getCode()),
DOCUMENT_ONTOLOGY_CODES_VS_URI, DOCUMENT_ONTOLOGY_CODES_VS_NAME, null);
String valueSetId;
String codeSystemVersionId = myUploadProperties.getProperty(LOINC_CODESYSTEM_VERSION.getCode());
if (codeSystemVersionId != null) {
valueSetId = DOCUMENT_ONTOLOGY_CODES_VS_ID + "-" + codeSystemVersionId;
} else {
valueSetId = DOCUMENT_ONTOLOGY_CODES_VS_ID;
}
ValueSet vs = getValueSet(valueSetId, DOCUMENT_ONTOLOGY_CODES_VS_URI, DOCUMENT_ONTOLOGY_CODES_VS_NAME, null);
addCodeAsIncludeToValueSet(vs, ITermLoaderSvc.LOINC_URI, loincNumber, null);
// Part Properties

19
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/term/loinc/LoincGroupFileHandler.java
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@ -30,7 +30,7 @@ import java.util.List;
import java.util.Map;
import java.util.Properties;
import static ca.uhn.fhir.jpa.term.loinc.LoincUploadPropertiesEnum.LOINC_CONCEPTMAP_VERSION;
import static ca.uhn.fhir.jpa.term.loinc.LoincUploadPropertiesEnum.LOINC_CODESYSTEM_VERSION;
import static org.apache.commons.lang3.StringUtils.trim;
public class LoincGroupFileHandler extends BaseLoincHandler implements IRecordHandler {
@ -44,11 +44,22 @@ public class LoincGroupFileHandler extends BaseLoincHandler implements IRecordHa
@Override
public void accept(CSVRecord theRecord) {
//"ParentGroupId","GroupId","Group","Archetype","Status","VersionFirstReleased"
String parentGroupId = trim(theRecord.get("ParentGroupId")) + "-" + myUploadProperties.getProperty(LOINC_CONCEPTMAP_VERSION.getCode());
String parentGroupId = trim(theRecord.get("ParentGroupId"));
String groupId = trim(theRecord.get("GroupId"));
String groupName = trim(theRecord.get("Group"));
ValueSet parentValueSet = getValueSet(parentGroupId, VS_URI_PREFIX + parentGroupId, null, null);
String codeSystemVersionId = myUploadProperties.getProperty(LOINC_CODESYSTEM_VERSION.getCode());
String parentGroupValueSetId;
String groupValueSetId;
if (codeSystemVersionId != null) {
parentGroupValueSetId = parentGroupId + "-" + codeSystemVersionId;
groupValueSetId = groupId + "-" + codeSystemVersionId;
} else {
parentGroupValueSetId = parentGroupId;
groupValueSetId = groupId;
}
ValueSet parentValueSet = getValueSet(parentGroupValueSetId, VS_URI_PREFIX + parentGroupId, null, null);
parentValueSet
.getCompose()
.getIncludeFirstRep()
@ -56,7 +67,7 @@ public class LoincGroupFileHandler extends BaseLoincHandler implements IRecordHa
// Create group to set its name (terms are added in a different
// handler)
getValueSet(groupId, VS_URI_PREFIX + groupId + "-" + myUploadProperties.getProperty(LOINC_CONCEPTMAP_VERSION.getCode()), groupName, null);
getValueSet(groupValueSetId, VS_URI_PREFIX + groupId, groupName, null);
}

12
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/term/loinc/LoincGroupTermsFileHandler.java
View File

@ -31,6 +31,7 @@ import java.util.List;
import java.util.Map;
import java.util.Properties;
import static ca.uhn.fhir.jpa.term.loinc.LoincUploadPropertiesEnum.LOINC_CODESYSTEM_VERSION;
import static ca.uhn.fhir.jpa.term.loinc.LoincUploadPropertiesEnum.LOINC_CONCEPTMAP_VERSION;
import static org.apache.commons.lang3.StringUtils.trim;
@ -43,10 +44,17 @@ public class LoincGroupTermsFileHandler extends BaseLoincHandler implements IRec
@Override
public void accept(CSVRecord theRecord) {
//"Category","GroupId","Archetype","LoincNumber","LongCommonName"
String groupId = trim(theRecord.get("GroupId")) + "-" + myUploadProperties.getProperty(LOINC_CONCEPTMAP_VERSION.getCode());
String groupId = trim(theRecord.get("GroupId"));
String codeSystemVersionId = myUploadProperties.getProperty(LOINC_CODESYSTEM_VERSION.getCode());
String valueSetId;
if (codeSystemVersionId != null) {
valueSetId = groupId + "-" + codeSystemVersionId;
} else {
valueSetId = groupId;
}
String loincNumber = trim(theRecord.get("LoincNumber"));
ValueSet valueSet = getValueSet(groupId, LoincGroupFileHandler.VS_URI_PREFIX + groupId, null, null);
ValueSet valueSet = getValueSet(valueSetId, LoincGroupFileHandler.VS_URI_PREFIX + groupId, null, null);
addCodeAsIncludeToValueSet(valueSet, ITermLoaderSvc.LOINC_URI, loincNumber, null);
}

12
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/term/loinc/LoincIeeeMedicalDeviceCodeHandler.java
View File

@ -32,6 +32,7 @@ import java.util.List;
import java.util.Map;
import java.util.Properties;
import static ca.uhn.fhir.jpa.term.loinc.LoincUploadPropertiesEnum.LOINC_CODESYSTEM_VERSION;
import static ca.uhn.fhir.jpa.term.loinc.LoincUploadPropertiesEnum.LOINC_CONCEPTMAP_VERSION;
import static org.apache.commons.lang3.StringUtils.trim;
@ -61,9 +62,16 @@ public class LoincIeeeMedicalDeviceCodeHandler extends BaseLoincHandler implemen
// LOINC Part -> IEEE 11073:10101 Mappings
String sourceCodeSystemUri = ITermLoaderSvc.LOINC_URI;
String targetCodeSystemUri = ITermLoaderSvc.IEEE_11073_10101_URI;
String conceptMapId;
String codeSystemVersionId = myUploadProperties.getProperty(LOINC_CODESYSTEM_VERSION.getCode());
if (codeSystemVersionId != null) {
conceptMapId = LOINC_IEEE_CM_ID + "-" + codeSystemVersionId;
} else {
conceptMapId = LOINC_IEEE_CM_ID;
}
addConceptMapEntry(
new ConceptMapping()
.setConceptMapId(LOINC_IEEE_CM_ID + "-" + myUploadProperties.getProperty(LOINC_CONCEPTMAP_VERSION.getCode()))
.setConceptMapId(conceptMapId)
.setConceptMapUri(LOINC_IEEE_CM_URI)
.setConceptMapVersion(loincIeeeCmVersion)
.setConceptMapName(LOINC_IEEE_CM_NAME)
@ -74,7 +82,7 @@ public class LoincIeeeMedicalDeviceCodeHandler extends BaseLoincHandler implemen
.setTargetCode(ieeeCode)
.setTargetDisplay(ieeeDisplayName)
.setEquivalence(Enumerations.ConceptMapEquivalence.EQUAL),
CM_COPYRIGHT);
CM_COPYRIGHT);
}

14
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/term/loinc/LoincImagingDocumentCodeHandler.java
View File

@ -31,12 +31,12 @@ import java.util.List;
import java.util.Map;
import java.util.Properties;
import static ca.uhn.fhir.jpa.term.loinc.LoincUploadPropertiesEnum.LOINC_CONCEPTMAP_VERSION;
import static ca.uhn.fhir.jpa.term.loinc.LoincUploadPropertiesEnum.LOINC_CODESYSTEM_VERSION;
import static org.apache.commons.lang3.StringUtils.trim;
public class LoincImagingDocumentCodeHandler extends BaseLoincHandler implements IRecordHandler {
public final String VS_ID = "loinc-imaging-document-codes" + "-" + myUploadProperties.getProperty(LOINC_CONCEPTMAP_VERSION.getCode());
public static final String VS_ID_BASE = "loinc-imaging-document-codes";
public static final String VS_URI = "http://loinc.org/vs/loinc-imaging-document-codes";
public static final String VS_NAME = "LOINC Imaging Document Codes";
@ -49,7 +49,15 @@ public class LoincImagingDocumentCodeHandler extends BaseLoincHandler implements
String loincNumber = trim(theRecord.get("LOINC_NUM"));
String displayName = trim(theRecord.get("LONG_COMMON_NAME"));
ValueSet valueSet = getValueSet(VS_ID, VS_URI, VS_NAME,null);
String codeSystemVersionId = myUploadProperties.getProperty(LOINC_CODESYSTEM_VERSION.getCode());
String valueSetId;
if (codeSystemVersionId != null) {
valueSetId = VS_ID_BASE + "-" + codeSystemVersionId;
} else {
valueSetId = VS_ID_BASE;
}
ValueSet valueSet = getValueSet(valueSetId, VS_URI, VS_NAME,null);
addCodeAsIncludeToValueSet(valueSet, ITermLoaderSvc.LOINC_URI, loincNumber, displayName);
}

13
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/term/loinc/LoincParentGroupFileHandler.java
View File

@ -30,7 +30,7 @@ import java.util.List;
import java.util.Map;
import java.util.Properties;
import static ca.uhn.fhir.jpa.term.loinc.LoincUploadPropertiesEnum.LOINC_CONCEPTMAP_VERSION;
import static ca.uhn.fhir.jpa.term.loinc.LoincUploadPropertiesEnum.LOINC_CODESYSTEM_VERSION;
import static org.apache.commons.lang3.StringUtils.trim;
public class LoincParentGroupFileHandler extends BaseLoincHandler implements IRecordHandler {
@ -42,10 +42,17 @@ public class LoincParentGroupFileHandler extends BaseLoincHandler implements IRe
@Override
public void accept(CSVRecord theRecord) {
// "ParentGroupId","ParentGroup","Status"
String parentGroupId = trim(theRecord.get("ParentGroupId")) + "-" + myUploadProperties.getProperty(LOINC_CONCEPTMAP_VERSION.getCode());
String parentGroupId = trim(theRecord.get("ParentGroupId"));
String codeSystemVersionId = myUploadProperties.getProperty(LOINC_CODESYSTEM_VERSION.getCode());
String valueSetId;
if (codeSystemVersionId != null) {
valueSetId = parentGroupId + "-" + codeSystemVersionId;
} else {
valueSetId = parentGroupId;
}
String parentGroupName = trim(theRecord.get("ParentGroup"));
getValueSet(parentGroupId, LoincGroupFileHandler.VS_URI_PREFIX + parentGroupId, parentGroupName, null);
getValueSet(valueSetId, LoincGroupFileHandler.VS_URI_PREFIX + parentGroupId, parentGroupName, null);
}

10
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/term/loinc/LoincPartRelatedCodeMappingHandler.java
View File

@ -33,6 +33,7 @@ import java.util.List;
import java.util.Map;
import java.util.Properties;
import static ca.uhn.fhir.jpa.term.loinc.LoincUploadPropertiesEnum.LOINC_CODESYSTEM_VERSION;
import static ca.uhn.fhir.jpa.term.loinc.LoincUploadPropertiesEnum.LOINC_CONCEPTMAP_VERSION;
import static org.apache.commons.lang3.StringUtils.defaultString;
import static org.apache.commons.lang3.StringUtils.trim;
@ -129,10 +130,17 @@ public class LoincPartRelatedCodeMappingHandler extends BaseLoincHandler impleme
loincPartMapName = "Unknown Mapping";
break;
}
String conceptMapId;
String codeSystemVersionId = myUploadProperties.getProperty(LOINC_CODESYSTEM_VERSION.getCode());
if (codeSystemVersionId != null) {
conceptMapId = loincPartMapId + "-" + codeSystemVersionId;
} else {
conceptMapId = loincPartMapId;
}
addConceptMapEntry(
new ConceptMapping()
.setConceptMapId(loincPartMapId + "-" + myUploadProperties.getProperty(LOINC_CONCEPTMAP_VERSION.getCode()))
.setConceptMapId(conceptMapId)
.setConceptMapUri(loincPartMapUri)
.setConceptMapVersion(loincPartMapVersion)
.setConceptMapName(loincPartMapName)

16
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/term/loinc/LoincRsnaPlaybookHandler.java
View File

@ -31,6 +31,7 @@ import org.hl7.fhir.r4.model.ValueSet;
import java.util.*;
import static ca.uhn.fhir.jpa.term.loinc.LoincUploadPropertiesEnum.LOINC_CODESYSTEM_VERSION;
import static ca.uhn.fhir.jpa.term.loinc.LoincUploadPropertiesEnum.LOINC_CONCEPTMAP_VERSION;
import static org.apache.commons.lang3.StringUtils.isNotBlank;
import static org.apache.commons.lang3.StringUtils.trim;
@ -174,11 +175,22 @@ public class LoincRsnaPlaybookHandler extends BaseLoincHandler implements IRecor
code.addPropertyCoding(loincCodePropName, ITermLoaderSvc.LOINC_URI, partNumber, partName);
}
String partConceptMapId;
String termConceptMapId;
String codeSystemVersionId = myUploadProperties.getProperty(LOINC_CODESYSTEM_VERSION.getCode());
if (codeSystemVersionId != null) {
partConceptMapId = LoincPartRelatedCodeMappingHandler.LOINC_PART_TO_RID_PART_MAP_ID + "-" + codeSystemVersionId;
termConceptMapId = LoincPartRelatedCodeMappingHandler.LOINC_TERM_TO_RPID_PART_MAP_ID + "-" + codeSystemVersionId;
} else {
partConceptMapId = LoincPartRelatedCodeMappingHandler.LOINC_PART_TO_RID_PART_MAP_ID;
termConceptMapId = LoincPartRelatedCodeMappingHandler.LOINC_TERM_TO_RPID_PART_MAP_ID;
}
// LOINC Part -> Radlex RID code mappings
if (isNotBlank(rid)) {
addConceptMapEntry(
new ConceptMapping()
.setConceptMapId(LoincPartRelatedCodeMappingHandler.LOINC_PART_TO_RID_PART_MAP_ID + "-" + myUploadProperties.getProperty(LOINC_CONCEPTMAP_VERSION.getCode()))
.setConceptMapId(partConceptMapId)
.setConceptMapUri(LoincPartRelatedCodeMappingHandler.LOINC_PART_TO_RID_PART_MAP_URI)
.setConceptMapVersion(loincRsnaCmVersion)
.setConceptMapName(LoincPartRelatedCodeMappingHandler.LOINC_PART_TO_RID_PART_MAP_NAME)
@ -196,7 +208,7 @@ public class LoincRsnaPlaybookHandler extends BaseLoincHandler implements IRecor
if (isNotBlank(rpid)) {
addConceptMapEntry(
new ConceptMapping()
.setConceptMapId(LoincPartRelatedCodeMappingHandler.LOINC_TERM_TO_RPID_PART_MAP_ID + "-" + myUploadProperties.getProperty(LOINC_CONCEPTMAP_VERSION.getCode()))
.setConceptMapId(termConceptMapId)
.setConceptMapUri(LoincPartRelatedCodeMappingHandler.LOINC_TERM_TO_RPID_PART_MAP_URI)
.setConceptMapVersion(loincRsnaCmVersion)
.setConceptMapName(LoincPartRelatedCodeMappingHandler.LOINC_TERM_TO_RPID_PART_MAP_NAME)

14
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/term/loinc/LoincUniversalOrderSetHandler.java
View File

@ -29,12 +29,12 @@ import org.hl7.fhir.r4.model.ValueSet;
import java.util.*;
import static ca.uhn.fhir.jpa.term.loinc.LoincUploadPropertiesEnum.LOINC_CONCEPTMAP_VERSION;
import static ca.uhn.fhir.jpa.term.loinc.LoincUploadPropertiesEnum.LOINC_CODESYSTEM_VERSION;
import static org.apache.commons.lang3.StringUtils.trim;
public class LoincUniversalOrderSetHandler extends BaseLoincHandler implements IRecordHandler {
public final String VS_ID = "loinc-universal-order-set" + "-" + myUploadProperties.getProperty(LOINC_CONCEPTMAP_VERSION.getCode());
public static final String VS_ID_BASE = "loinc-universal-order-set";
public static final String VS_URI = "http://loinc.org/vs/loinc-universal-order-set";
public static final String VS_NAME = "LOINC Universal Order Set";
@ -48,7 +48,15 @@ public class LoincUniversalOrderSetHandler extends BaseLoincHandler implements I
String displayName = trim(theRecord.get("LONG_COMMON_NAME"));
String orderObs = trim(theRecord.get("ORDER_OBS"));
ValueSet valueSet = getValueSet(VS_ID, VS_URI, VS_NAME, null);
String codeSystemVersionId = myUploadProperties.getProperty(LOINC_CODESYSTEM_VERSION.getCode());
String valueSetId;
if (codeSystemVersionId != null) {
valueSetId = VS_ID_BASE + "-" + codeSystemVersionId;
} else {
valueSetId = VS_ID_BASE;
}
ValueSet valueSet = getValueSet(valueSetId, VS_URI, VS_NAME, null);
addCodeAsIncludeToValueSet(valueSet, ITermLoaderSvc.LOINC_URI, loincNumber, displayName);
}

2
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/term/loinc/LoincUploadPropertiesEnum.java
View File

@ -96,7 +96,7 @@ public enum LoincUploadPropertiesEnum {
/*
* OPTIONAL
*/
// This is the version identifier for the answer list file
// This is the version identifier for the LOINC code system
LOINC_CODESYSTEM_VERSION("loinc.codesystem.version"),
// This is the version identifier for the answer list file

2
hapi-fhir-jpaserver-base/src/main/resources/ca/uhn/fhir/jpa/term/loinc/loincupload.properties
View File

@ -63,7 +63,7 @@ loinc.universal.lab.order.valueset.file=AccessoryFiles/LoincUniversalLabOrdersVa
# This is the version identifier for the LOINC code system
## Key may be omitted if only a single version of LOINC is being kept.
loinc.codesystem.version=2.68
#loinc.codesystem.version=2.68
# This is the version identifier for the answer list file
## Key may be omitted

6
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/term/TerminologyLoaderSvcLoincTest.java
View File

@ -165,7 +165,7 @@ public class TerminologyLoaderSvcLoincTest extends BaseLoaderTest {
assertEquals(1, group.getElement().get(0).getTarget().size());
assertEquals("420710006", group.getElement().get(0).getTarget().get(0).getCode());
assertEquals("Interferon beta (substance)", group.getElement().get(0).getTarget().get(0).getDisplay());
// Document Ontology ValueSet
vs = valueSets.get(LoincDocumentOntologyHandler.DOCUMENT_ONTOLOGY_CODES_VS_ID);
assertEquals(LoincDocumentOntologyHandler.DOCUMENT_ONTOLOGY_CODES_VS_NAME, vs.getName());
@ -274,7 +274,7 @@ public class TerminologyLoaderSvcLoincTest extends BaseLoaderTest {
assertEquals("Hemoglobin [Mass/volume] in Blood", vs.getCompose().getInclude().get(0).getConcept().get(1).getDisplay());
// Universal lab order VS
vs = valueSets.get(LoincUniversalOrderSetHandler.VS_ID);
vs = valueSets.get(LoincUniversalOrderSetHandler.VS_ID_BASE);
assertEquals(1, vs.getCompose().getInclude().size());
assertEquals(ITermLoaderSvc.LOINC_URI, vs.getCompose().getInclude().get(0).getSystem());
assertEquals(9, vs.getCompose().getInclude().get(0).getConcept().size());
@ -314,7 +314,7 @@ public class TerminologyLoaderSvcLoincTest extends BaseLoaderTest {
assertEquals("MDC_CONC_GLU_VENOUS_PLASMA", conceptMap.getGroup().get(0).getElement().get(4).getTarget().get(0).getDisplay());
// Imaging Document Codes
vs = valueSets.get(LoincImagingDocumentCodeHandler.VS_ID);
vs = valueSets.get(LoincImagingDocumentCodeHandler.VS_ID_BASE);
assertEquals(LoincImagingDocumentCodeHandler.VS_URI, vs.getUrl());
assertEquals(LoincImagingDocumentCodeHandler.VS_NAME, vs.getName());
assertEquals(1, vs.getCompose().getInclude().size());

2
hapi-fhir-jpaserver-migrate/src/main/java/ca/uhn/fhir/jpa/migrate/tasks/HapiFhirJpaMigrationTasks.java
View File

@ -156,7 +156,7 @@ public class HapiFhirJpaMigrationTasks extends BaseMigrationTasks<VersionEnum> {
Builder.BuilderWithTableName trmValueSet = version.onTable("TRM_VALUESET");
trmValueSet.addColumn("20200923.2", "VER").nullable().type(ColumnTypeEnum.STRING, TermValueSet.MAX_VER_LENGTH);
trmValueSet.dropIndex("20200923.3", "IDX_VALUESET_URL");
trmValueSet.addIndex("20200923.4", "IDX_VALUESET_URL").unique(true).withColumns("URL", "VAR");
trmValueSet.addIndex("20200923.4", "IDX_VALUESET_URL").unique(true).withColumns("URL", "VER");
}
protected void init510_20200725() {