Allw successful deletion of concept maps
This commit is contained in:
James Agnew
parent
7b809f059a
commit
32fefefcd8
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@ -160,13 +160,16 @@ public class FhirResourceDaoConceptMapDstu3 extends FhirResourceDaoDstu3<Concept
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boolean theUpdateVersion, Date theUpdateTime, boolean theForceUpdate, boolean theCreateNewHistoryEntry) {
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ResourceTable retVal = super.updateEntity(theRequestDetails, theResource, theEntity, theDeletedTimestampOrNull, thePerformIndexing, theUpdateVersion, theUpdateTime, theForceUpdate, theCreateNewHistoryEntry);
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ConceptMap conceptMap = (ConceptMap) theResource;
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// Convert from DSTU3 to R4
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try {
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myHapiTerminologySvc.storeTermConceptMapAndChildren(retVal, VersionConvertor_30_40.convertConceptMap(conceptMap));
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} catch (FHIRException fe) {
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throw new InternalErrorException(fe);
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if (retVal.getDeleted() == null) {
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try {
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ConceptMap conceptMap = (ConceptMap) theResource;
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org.hl7.fhir.r4.model.ConceptMap converted = VersionConvertor_30_40.convertConceptMap(conceptMap);
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myHapiTerminologySvc.storeTermConceptMapAndChildren(retVal, converted);
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} catch (FHIRException fe) {
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throw new InternalErrorException(fe);
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}
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} else {
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myHapiTerminologySvc.deleteConceptMapAndChildren(retVal);
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}
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return retVal;
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@ -156,9 +156,12 @@ public class FhirResourceDaoConceptMapR4 extends FhirResourceDaoR4<ConceptMap> i
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boolean theUpdateVersion, Date theUpdateTime, boolean theForceUpdate, boolean theCreateNewHistoryEntry) {
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ResourceTable retVal = super.updateEntity(theRequestDetails, theResource, theEntity, theDeletedTimestampOrNull, thePerformIndexing, theUpdateVersion, theUpdateTime, theForceUpdate, theCreateNewHistoryEntry);
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ConceptMap conceptMap = (ConceptMap) theResource;
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myHapiTerminologySvc.storeTermConceptMapAndChildren(retVal, conceptMap);
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if (retVal.getDeleted() == null) {
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ConceptMap conceptMap = (ConceptMap) theResource;
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myHapiTerminologySvc.storeTermConceptMapAndChildren(retVal, conceptMap);
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} else {
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myHapiTerminologySvc.deleteConceptMapAndChildren(retVal);
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}
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return retVal;
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}
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@ -9,9 +9,9 @@ package ca.uhn.fhir.jpa.term;
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* Licensed under the Apache License, Version 2.0 (the "License");
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* you may not use this file except in compliance with the License.
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* You may obtain a copy of the License at
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*
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*
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* http://www.apache.org/licenses/LICENSE-2.0
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*
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*
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* Unless required by applicable law or agreed to in writing, software
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* distributed under the License is distributed on an "AS IS" BASIS,
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* WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
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@ -162,14 +162,6 @@ public abstract class BaseHapiTerminologySvcImpl implements IHapiTerminologySvc,
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}
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}
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private void removeCodeFromExpansion(String theCodeSystem, String theCode, ValueSet.ValueSetExpansionComponent theExpansionComponent) {
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theExpansionComponent
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.getContains()
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.removeIf(t ->
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theCodeSystem.equals(t.getSystem()) &&
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theCode.equals(t.getCode()));
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}
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private void addConceptsToList(ValueSet.ValueSetExpansionComponent theExpansionComponent, Set<String> theAddedCodes, String theSystem, List<CodeSystem.ConceptDefinitionComponent> theConcept, boolean theAdd) {
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for (CodeSystem.ConceptDefinitionComponent next : theConcept) {
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if (theAdd && theAddedCodes.add(next.getCode())) {
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@ -281,6 +273,130 @@ public abstract class BaseHapiTerminologySvcImpl implements IHapiTerminologySvc,
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myEntityManager.flush();
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}
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public void deleteCodeSystemVersion(Long theCodeSystemVersionPid) {
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ourLog.info(" * Deleting code system version {}", theCodeSystemVersionPid);
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PageRequest page = PageRequest.of(0, 1000);
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int count;
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// Parent/Child links
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ourLog.info(" * Deleting parent/child links");
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count = 0;
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while (true) {
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Slice<TermConceptParentChildLink> link = myConceptParentChildLinkDao.findByCodeSystemVersion(page, theCodeSystemVersionPid);
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if (link.hasContent() == false) {
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break;
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}
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myConceptParentChildLinkDao.deleteInBatch(link);
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count += link.getNumberOfElements();
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ourLog.info(" * {} parent/child links deleted", count);
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}
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myConceptParentChildLinkDao.flush();
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// Properties
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ourLog.info(" * Deleting properties");
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count = 0;
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while (true) {
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Slice<TermConceptProperty> link = myConceptPropertyDao.findByCodeSystemVersion(page, theCodeSystemVersionPid);
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if (link.hasContent() == false) {
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break;
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}
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myConceptPropertyDao.deleteInBatch(link);
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count += link.getNumberOfElements();
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ourLog.info(" * {} concept properties deleted", count);
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}
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myConceptPropertyDao.flush();
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// Properties
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ourLog.info(" * Deleting designations");
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count = 0;
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while (true) {
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Slice<TermConceptDesignation> link = myConceptDesignationDao.findByCodeSystemVersion(page, theCodeSystemVersionPid);
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if (link.hasContent() == false) {
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break;
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}
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myConceptDesignationDao.deleteInBatch(link);
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count += link.getNumberOfElements();
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ourLog.info(" * {} concept designations deleted", count);
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}
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myConceptDesignationDao.flush();
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// Concepts
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ourLog.info(" * Deleting concepts");
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count = 0;
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while (true) {
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Slice<TermConcept> link = myConceptDao.findByCodeSystemVersion(page, theCodeSystemVersionPid);
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if (link.hasContent() == false) {
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break;
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}
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myConceptDao.deleteInBatch(link);
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myConceptDao.flush();
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count += link.getNumberOfElements();
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ourLog.info(" * {} concepts deleted", count);
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}
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Optional<TermCodeSystem> codeSystemOpt = myCodeSystemDao.findWithCodeSystemVersionAsCurrentVersion(theCodeSystemVersionPid);
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if (codeSystemOpt.isPresent()) {
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TermCodeSystem codeSystem = codeSystemOpt.get();
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ourLog.info(" * Removing code system version {} as current version of code system {}", theCodeSystemVersionPid, codeSystem.getPid());
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codeSystem.setCurrentVersion(null);
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myCodeSystemDao.save(codeSystem);
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}
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ourLog.info(" * Deleting code system version");
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myCodeSystemVersionDao.deleteById(theCodeSystemVersionPid);
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}
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public void deleteConceptMap(ResourceTable theResourceTable) {
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// Get existing entity so it can be deleted.
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Optional<TermConceptMap> optionalExistingTermConceptMapById = myConceptMapDao.findTermConceptMapByResourcePid(theResourceTable.getId());
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if (optionalExistingTermConceptMapById.isPresent()) {
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TermConceptMap existingTermConceptMap = optionalExistingTermConceptMapById.get();
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ourLog.info("Deleting existing TermConceptMap {} and its children...", existingTermConceptMap.getId());
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for (TermConceptMapGroup group : existingTermConceptMap.getConceptMapGroups()) {
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for (TermConceptMapGroupElement element : group.getConceptMapGroupElements()) {
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for (TermConceptMapGroupElementTarget target : element.getConceptMapGroupElementTargets()) {
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myConceptMapGroupElementTargetDao.deleteTermConceptMapGroupElementTargetById(target.getId());
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}
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myConceptMapGroupElementDao.deleteTermConceptMapGroupElementById(element.getId());
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}
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myConceptMapGroupDao.deleteTermConceptMapGroupById(group.getId());
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}
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myConceptMapDao.deleteTermConceptMapById(existingTermConceptMap.getId());
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ourLog.info("Done deleting existing TermConceptMap {} and its children.", existingTermConceptMap.getId());
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ourLog.info("Flushing...");
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myConceptMapGroupElementTargetDao.flush();
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myConceptMapGroupElementDao.flush();
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myConceptMapGroupDao.flush();
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myConceptMapDao.flush();
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ourLog.info("Done flushing.");
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}
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}
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@Override
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@Transactional
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public void deleteConceptMapAndChildren(ResourceTable theResourceTable) {
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deleteConceptMap(theResourceTable);
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}
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private int ensureParentsSaved(Collection<TermConceptParentChildLink> theParents) {
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ourLog.trace("Checking {} parents", theParents.size());
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int retVal = 0;
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@ -323,6 +439,19 @@ public abstract class BaseHapiTerminologySvcImpl implements IHapiTerminologySvc,
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return valueSet;
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}
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protected List<VersionIndependentConcept> expandValueSetAndReturnVersionIndependentConcepts(org.hl7.fhir.r4.model.ValueSet theValueSetToExpandR4) {
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org.hl7.fhir.r4.model.ValueSet.ValueSetExpansionComponent expandedR4 = expandValueSet(theValueSetToExpandR4).getExpansion();
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ArrayList<VersionIndependentConcept> retVal = new ArrayList<>();
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for (org.hl7.fhir.r4.model.ValueSet.ValueSetExpansionContainsComponent nextContains : expandedR4.getContains()) {
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retVal.add(
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new VersionIndependentConcept()
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.setSystem(nextContains.getSystem())
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.setCode(nextContains.getCode()));
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}
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return retVal;
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}
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public void expandValueSetHandleIncludeOrExclude(ValueSet.ValueSetExpansionComponent theExpansionComponent, Set<String> theAddedCodes, ValueSet.ConceptSetComponent include, boolean theAdd) {
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String system = include.getSystem();
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if (isNotBlank(system)) {
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@ -479,19 +608,6 @@ public abstract class BaseHapiTerminologySvcImpl implements IHapiTerminologySvc,
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}
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}
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protected List<VersionIndependentConcept> expandValueSetAndReturnVersionIndependentConcepts(org.hl7.fhir.r4.model.ValueSet theValueSetToExpandR4) {
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org.hl7.fhir.r4.model.ValueSet.ValueSetExpansionComponent expandedR4 = expandValueSet(theValueSetToExpandR4).getExpansion();
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ArrayList<VersionIndependentConcept> retVal = new ArrayList<>();
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for (org.hl7.fhir.r4.model.ValueSet.ValueSetExpansionContainsComponent nextContains : expandedR4.getContains()) {
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retVal.add(
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new VersionIndependentConcept()
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.setSystem(nextContains.getSystem())
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.setCode(nextContains.getCode()));
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}
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return retVal;
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}
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private void fetchChildren(TermConcept theConcept, Set<TermConcept> theSetToPopulate) {
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for (TermConceptParentChildLink nextChildLink : theConcept.getChildren()) {
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TermConcept nextChild = nextChildLink.getChild();
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@ -794,6 +910,14 @@ public abstract class BaseHapiTerminologySvcImpl implements IHapiTerminologySvc,
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}
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private void removeCodeFromExpansion(String theCodeSystem, String theCode, ValueSet.ValueSetExpansionComponent theExpansionComponent) {
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theExpansionComponent
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.getContains()
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.removeIf(t ->
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theCodeSystem.equals(t.getSystem()) &&
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theCode.equals(t.getCode()));
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}
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private int saveConcept(TermConcept theConcept) {
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int retVal = 0;
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@ -841,7 +965,7 @@ public abstract class BaseHapiTerminologySvcImpl implements IHapiTerminologySvc,
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TransactionTemplate tt = new TransactionTemplate(myTransactionMgr);
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tt.setPropagationBehavior(TransactionTemplate.PROPAGATION_REQUIRES_NEW);
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if(!myDeferredConcepts.isEmpty() || !myConceptLinksToSaveLater.isEmpty()) {
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if (!myDeferredConcepts.isEmpty() || !myConceptLinksToSaveLater.isEmpty()) {
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tt.execute(t -> {
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processDeferredConcepts();
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return null;
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@ -972,89 +1096,6 @@ public abstract class BaseHapiTerminologySvcImpl implements IHapiTerminologySvc,
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}
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}
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public void deleteCodeSystemVersion(Long theCodeSystemVersionPid) {
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ourLog.info(" * Deleting code system version {}", theCodeSystemVersionPid);
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PageRequest page = PageRequest.of(0, 1000);
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int count;
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// Parent/Child links
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ourLog.info(" * Deleting parent/child links");
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count = 0;
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while (true) {
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Slice<TermConceptParentChildLink> link = myConceptParentChildLinkDao.findByCodeSystemVersion(page, theCodeSystemVersionPid);
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if (link.hasContent() == false) {
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break;
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}
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myConceptParentChildLinkDao.deleteInBatch(link);
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count += link.getNumberOfElements();
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ourLog.info(" * {} parent/child links deleted", count);
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}
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myConceptParentChildLinkDao.flush();
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// Properties
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ourLog.info(" * Deleting properties");
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count = 0;
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while (true) {
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Slice<TermConceptProperty> link = myConceptPropertyDao.findByCodeSystemVersion(page, theCodeSystemVersionPid);
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if (link.hasContent() == false) {
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break;
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}
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myConceptPropertyDao.deleteInBatch(link);
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count += link.getNumberOfElements();
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ourLog.info(" * {} concept properties deleted", count);
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}
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myConceptPropertyDao.flush();
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// Properties
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ourLog.info(" * Deleting designations");
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count = 0;
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while (true) {
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Slice<TermConceptDesignation> link = myConceptDesignationDao.findByCodeSystemVersion(page, theCodeSystemVersionPid);
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if (link.hasContent() == false) {
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break;
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}
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myConceptDesignationDao.deleteInBatch(link);
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count += link.getNumberOfElements();
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ourLog.info(" * {} concept designations deleted", count);
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}
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myConceptDesignationDao.flush();
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// Concepts
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ourLog.info(" * Deleting concepts");
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count = 0;
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while (true) {
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Slice<TermConcept> link = myConceptDao.findByCodeSystemVersion(page, theCodeSystemVersionPid);
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if (link.hasContent() == false) {
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break;
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}
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myConceptDao.deleteInBatch(link);
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myConceptDao.flush();
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count += link.getNumberOfElements();
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ourLog.info(" * {} concepts deleted", count);
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}
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Optional<TermCodeSystem> codeSystemOpt = myCodeSystemDao.findWithCodeSystemVersionAsCurrentVersion(theCodeSystemVersionPid);
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if (codeSystemOpt.isPresent()) {
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TermCodeSystem codeSystem = codeSystemOpt.get();
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ourLog.info(" * Removing code system version {} as current version of code system {}", theCodeSystemVersionPid, codeSystem.getPid());
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codeSystem.setCurrentVersion(null);
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myCodeSystemDao.save(codeSystem);
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}
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ourLog.info(" * Deleting code system version");
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myCodeSystemVersionDao.deleteById(theCodeSystemVersionPid);
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}
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@Override
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@Transactional(propagation = Propagation.REQUIRED)
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public IIdType storeNewCodeSystemVersion(CodeSystem theCodeSystemResource, TermCodeSystemVersion theCodeSystemVersion, RequestDetails theRequestDetails, List<ValueSet> theValueSets, List<ConceptMap> theConceptMaps) {
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@ -1088,42 +1129,10 @@ public abstract class BaseHapiTerminologySvcImpl implements IHapiTerminologySvc,
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termConceptMap.setResource(theResourceTable);
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termConceptMap.setUrl(theConceptMap.getUrl());
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// Get existing entity so it can be deleted.
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Optional<TermConceptMap> optionalExistingTermConceptMapById = myConceptMapDao.findTermConceptMapByResourcePid(theResourceTable.getId());
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/*
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* For now we always delete old versions. At some point, it would be nice to allow configuration to keep old versions.
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*/
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if (optionalExistingTermConceptMapById.isPresent()) {
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TermConceptMap existingTermConceptMap = optionalExistingTermConceptMapById.get();
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ourLog.info("Deleting existing TermConceptMap {} and its children...", existingTermConceptMap.getId());
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for (TermConceptMapGroup group : existingTermConceptMap.getConceptMapGroups()) {
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for (TermConceptMapGroupElement element : group.getConceptMapGroupElements()) {
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for (TermConceptMapGroupElementTarget target : element.getConceptMapGroupElementTargets()) {
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myConceptMapGroupElementTargetDao.deleteTermConceptMapGroupElementTargetById(target.getId());
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}
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myConceptMapGroupElementDao.deleteTermConceptMapGroupElementById(element.getId());
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}
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myConceptMapGroupDao.deleteTermConceptMapGroupById(group.getId());
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}
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myConceptMapDao.deleteTermConceptMapById(existingTermConceptMap.getId());
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ourLog.info("Done deleting existing TermConceptMap {} and its children.", existingTermConceptMap.getId());
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ourLog.info("Flushing...");
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myConceptMapGroupElementTargetDao.flush();
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myConceptMapGroupElementDao.flush();
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myConceptMapGroupDao.flush();
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myConceptMapDao.flush();
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ourLog.info("Done flushing.");
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}
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deleteConceptMap(theResourceTable);
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/*
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* Do the upload.
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@ -68,6 +68,8 @@ public interface IHapiTerminologySvc {
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*/
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IIdType storeNewCodeSystemVersion(org.hl7.fhir.r4.model.CodeSystem theCodeSystemResource, TermCodeSystemVersion theCodeSystemVersion, RequestDetails theRequestDetails, List<org.hl7.fhir.r4.model.ValueSet> theValueSets, List<org.hl7.fhir.r4.model.ConceptMap> theConceptMaps);
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void deleteConceptMapAndChildren(ResourceTable theResourceTable);
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void storeTermConceptMapAndChildren(ResourceTable theResourceTable, ConceptMap theConceptMap);
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boolean supportsSystem(String theCodeSystem);
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@ -288,6 +288,13 @@ public class TerminologyLoaderSvcImpl implements IHapiTerminologyLoaderSvc {
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handler = new LoincAnswerListLinkHandler(code2concept, valueSets);
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iterateOverZipFile(theDescriptors, LOINC_ANSWERLIST_LINK_FILE, handler, ',', QuoteMode.NON_NUMERIC, false);
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// RSNA Playbook file
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// Note that this should come before the "Part Related Code Mapping"
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// file because there are some duplicate mappings between these
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// two files, and the RSNA Playbook file has more metadata
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handler = new LoincRsnaPlaybookHandler(code2concept, valueSets, conceptMaps, uploadProperties);
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iterateOverZipFile(theDescriptors, LOINC_RSNA_PLAYBOOK_FILE, handler, ',', QuoteMode.NON_NUMERIC, false);
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// Part link file
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handler = new LoincPartLinkHandler(codeSystemVersion, code2concept);
|
||||
iterateOverZipFile(theDescriptors, LOINC_PART_LINK_FILE, handler, ',', QuoteMode.NON_NUMERIC, false);
|
||||
|
|
@ -300,10 +307,6 @@ public class TerminologyLoaderSvcImpl implements IHapiTerminologyLoaderSvc {
|
|||
handler = new LoincDocumentOntologyHandler(code2concept, propertyNamesToTypes, valueSets, conceptMaps, uploadProperties);
|
||||
iterateOverZipFile(theDescriptors, LOINC_DOCUMENT_ONTOLOGY_FILE, handler, ',', QuoteMode.NON_NUMERIC, false);
|
||||
|
||||
// RSNA Playbook file
|
||||
handler = new LoincRsnaPlaybookHandler(code2concept, valueSets, conceptMaps, uploadProperties);
|
||||
iterateOverZipFile(theDescriptors, LOINC_RSNA_PLAYBOOK_FILE, handler, ',', QuoteMode.NON_NUMERIC, false);
|
||||
|
||||
// Top 2000 Codes - US
|
||||
handler = new LoincTop2000LabResultsUsHandler(code2concept, valueSets, conceptMaps, uploadProperties);
|
||||
iterateOverZipFile(theDescriptors, LOINC_TOP2000_COMMON_LAB_RESULTS_US_FILE, handler, ',', QuoteMode.NON_NUMERIC, false);
|
||||
|
|
|
|||
|
|
@ -26,6 +26,8 @@ import org.hl7.fhir.r4.model.ConceptMap;
|
|||
import org.hl7.fhir.r4.model.ContactPoint;
|
||||
import org.hl7.fhir.r4.model.Enumerations;
|
||||
import org.hl7.fhir.r4.model.ValueSet;
|
||||
import org.slf4j.Logger;
|
||||
import org.slf4j.LoggerFactory;
|
||||
|
||||
import java.util.HashMap;
|
||||
import java.util.List;
|
||||
|
|
@ -35,8 +37,9 @@ import java.util.Properties;
|
|||
import static org.apache.commons.lang3.StringUtils.*;
|
||||
|
||||
public abstract class BaseLoincHandler implements IRecordHandler {
|
||||
|
||||
private static final Logger ourLog = LoggerFactory.getLogger(BaseLoincHandler.class);
|
||||
public static final String LOINC_COPYRIGHT_STATEMENT = "This content from LOINC® is copyright © 1995 Regenstrief Institute, Inc. and the LOINC Committee, and available at no cost under the license at https://loinc.org/license/";
|
||||
|
||||
/**
|
||||
* This is <b>NOT</b> the LOINC CodeSystem URI! It is just
|
||||
* the website URL to LOINC.
|
||||
|
|
@ -177,6 +180,8 @@ public abstract class BaseLoincHandler implements IRecordHandler {
|
|||
.setCode(theMapping.getTargetCode())
|
||||
.setDisplay(theMapping.getTargetDisplay())
|
||||
.setEquivalence(theMapping.getEquivalence());
|
||||
} else {
|
||||
ourLog.info("Not going to add a mapping from [{}/{}] to [{}/{}] because one already exists", theMapping.getSourceCodeSystem(), theMapping.getSourceCode(), theMapping.getTargetCodeSystem(), theMapping.getTargetCode());
|
||||
}
|
||||
}
|
||||
|
||||
|
|
|
|||
|
|
@ -37,7 +37,7 @@ import static org.apache.commons.lang3.StringUtils.trim;
|
|||
public class LoincIeeeMedicalDeviceCodeHandler extends BaseLoincHandler implements IRecordHandler {
|
||||
|
||||
public static final String LOINC_IEEE_CM_ID = "LOINC-IEEE-MEDICAL-DEVICE-CM";
|
||||
public static final String LOINC_IEEE_CM_URI = "http://loinc.org/fhir/loinc-ieee-device-code-mappings";
|
||||
public static final String LOINC_IEEE_CM_URI = "http://loinc.org/cm/loinc-to-ieee-device-codes";
|
||||
public static final String LOINC_IEEE_CM_NAME = "LOINC/IEEE Device Code Mappings";
|
||||
private static final String CM_COPYRIGHT = "This content from LOINC® is copyright © 1995 Regenstrief Institute, Inc. and the LOINC Committee, and available at no cost under the license at https://loinc.org/license/. The LOINC/IEEE Medical Device Code Mapping Table contains content from IEEE (http://ieee.org), copyright © 2017 IEEE.";
|
||||
|
||||
|
|
|
|||
|
|
@ -36,7 +36,7 @@ import static org.apache.commons.lang3.StringUtils.trim;
|
|||
public class LoincImagingDocumentCodeHandler extends BaseLoincHandler implements IRecordHandler {
|
||||
|
||||
public static final String VS_ID = "loinc-imaging-document-codes";
|
||||
public static final String VS_URI = "http://loinc.org/fhir/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";
|
||||
|
||||
public LoincImagingDocumentCodeHandler(Map<String, TermConcept> theCode2concept, List<ValueSet> theValueSets, List<ConceptMap> theConceptMaps, Properties theUploadProperties) {
|
||||
|
|
|
|||
|
|
@ -9,9 +9,9 @@ package ca.uhn.fhir.jpa.term.loinc;
|
|||
* Licensed under the Apache License, Version 2.0 (the "License");
|
||||
* you may not use this file except in compliance with the License.
|
||||
* You may obtain a copy of the License at
|
||||
*
|
||||
*
|
||||
* http://www.apache.org/licenses/LICENSE-2.0
|
||||
*
|
||||
*
|
||||
* Unless required by applicable law or agreed to in writing, software
|
||||
* distributed under the License is distributed on an "AS IS" BASIS,
|
||||
* WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
|
||||
|
|
@ -40,13 +40,13 @@ public class LoincPartRelatedCodeMappingHandler extends BaseLoincHandler impleme
|
|||
|
||||
public static final String LOINC_SCT_PART_MAP_ID = "loinc-parts-to-snomed-ct";
|
||||
public static final String LOINC_SCT_PART_MAP_URI = "http://loinc.org/cm/loinc-parts-to-snomed-ct";
|
||||
static final String LOINC_RADLEX_PART_MAP_ID = "loinc-parts-to-radlex";
|
||||
static final String LOINC_RADLEX_PART_MAP_URI = "http://loinc.org/cm/loinc-parts-to-radlex";
|
||||
static final String LOINC_RADLEX_PART_MAP_NAME = "LOINC Part Map to RADLEX";
|
||||
private static final String LOINC_SCT_PART_MAP_NAME = "LOINC Part Map to SNOMED CT";
|
||||
private static final String LOINC_RXNORM_PART_MAP_ID = "loinc-parts-to-rxnorm";
|
||||
private static final String LOINC_RXNORM_PART_MAP_URI = "http://loinc.org/cm/loinc-parts-to-rxnorm";
|
||||
private static final String LOINC_RXNORM_PART_MAP_NAME = "LOINC Part Map to RxNORM";
|
||||
private static final String LOINC_RADLEX_PART_MAP_ID = "loinc-parts-to-radlex";
|
||||
private static final String LOINC_RADLEX_PART_MAP_URI = "http://loinc.org/cm/loinc-parts-to-radlex";
|
||||
private static final String LOINC_RADLEX_PART_MAP_NAME = "LOINC Part Map to RADLEX";
|
||||
private static final String CM_COPYRIGHT = "This content from LOINC® is copyright © 1995 Regenstrief Institute, Inc. and the LOINC Committee, and available at no cost under the license at https://loinc.org/license/. The LOINC Part File, LOINC/SNOMED CT Expression Association and Map Sets File, RELMA database and associated search index files include SNOMED Clinical Terms (SNOMED CT®) which is used by permission of the International Health Terminology Standards Development Organisation (IHTSDO) under license. All rights are reserved. SNOMED CT® was originally created by The College of American Pathologists. “SNOMED” and “SNOMED CT” are registered trademarks of the IHTSDO. Use of SNOMED CT content is subject to the terms and conditions set forth in the SNOMED CT Affiliate License Agreement. It is the responsibility of those implementing this product to ensure they are appropriately licensed and for more information on the license, including how to register as an Affiliate Licensee, please refer to http://www.snomed.org/snomed-ct/get-snomed-ct or info@snomed.org. Under the terms of the Affiliate License, use of SNOMED CT in countries that are not IHTSDO Members is subject to reporting and fee payment obligations. However, IHTSDO agrees to waive the requirements to report and pay fees for use of SNOMED CT content included in the LOINC Part Mapping and LOINC Term Associations for purposes that support or enable more effective use of LOINC. This material includes content from the US Edition to SNOMED CT, which is developed and maintained by the U.S. National Library of Medicine and is available to authorized UMLS Metathesaurus Licensees from the UTS Downloads site at https://uts.nlm.nih.gov.";
|
||||
private static final String LOINC_PUBCHEM_PART_MAP_URI = "http://loinc.org/cm/loinc-parts-to-pubchem";
|
||||
private static final String LOINC_PUBCHEM_PART_MAP_ID = "loinc-parts-to-pubchem";
|
||||
|
|
|
|||
|
|
@ -39,21 +39,19 @@ public class LoincRsnaPlaybookHandler extends BaseLoincHandler implements IRecor
|
|||
public static final String RSNA_CODES_VS_ID = "loinc-rsna-radiology-playbook";
|
||||
public static final String RSNA_CODES_VS_URI = "http://loinc.org/vs/loinc-rsna-radiology-playbook";
|
||||
public static final String RSNA_CODES_VS_NAME = "LOINC/RSNA Radiology Playbook";
|
||||
public static final String RID_MAPPING_CM_ID = "LOINC-TO-RID-CODES-CM";
|
||||
public static final String RID_MAPPING_CM_URI = "http://loinc.org/rid-codes";
|
||||
public static final String RID_MAPPING_CM_NAME = "RSNA Playbook RID Codes Mapping";
|
||||
public static final String RADLEX_MAPPING_CM_ID = LoincPartRelatedCodeMappingHandler.LOINC_RADLEX_PART_MAP_ID;
|
||||
public static final String RADLEX_MAPPING_CM_URI = LoincPartRelatedCodeMappingHandler.LOINC_RADLEX_PART_MAP_URI;
|
||||
public static final String RADLEX_MAPPING_CM_NAME = LoincPartRelatedCodeMappingHandler.LOINC_RADLEX_PART_MAP_NAME;
|
||||
public static final String RID_CS_URI = "http://www.radlex.org";
|
||||
public static final String RPID_MAPPING_CM_ID = "LOINC-TO-RPID-CODES-CM";
|
||||
public static final String RPID_MAPPING_CM_URI = "http://loinc.org/rpid-codes";
|
||||
public static final String RPID_MAPPING_CM_NAME = "RSNA Playbook RPID Codes Mapping";
|
||||
/*
|
||||
* About these being the same - Per Dan:
|
||||
* About these being the same - Per Dan Vreeman:
|
||||
* We had some discussion about this, and both
|
||||
* RIDs (RadLex clinical terms) and RPIDs (Radlex Playbook Ids)
|
||||
* RIDs (RadLex clinical terms) and RPIDs (Radlex Playbook Ids)
|
||||
* belong to the same "code system" since they will never collide.
|
||||
* The codesystem uri is "http://www.radlex.org". FYI, that's
|
||||
* now listed on the FHIR page:
|
||||
* https://www.hl7.org/fhir/terminologies-systems.html
|
||||
* -ja
|
||||
*/
|
||||
public static final String RPID_CS_URI = RID_CS_URI;
|
||||
private static final String CM_COPYRIGHT = "This content from LOINC® is copyright © 1995 Regenstrief Institute, Inc. and the LOINC Committee, and available at no cost under the license at https://loinc.org/license/. The LOINC/RSNA Radiology Playbook and the LOINC Part File contain content from RadLex® (http://rsna.org/RadLex.aspx), copyright © 2005-2017, The Radiological Society of North America, Inc., available at no cost under the license at http://www.rsna.org/uploadedFiles/RSNA/Content/Informatics/RadLex_License_Agreement_and_Terms_of_Use_V2_Final.pdf.";
|
||||
|
|
@ -179,9 +177,9 @@ public class LoincRsnaPlaybookHandler extends BaseLoincHandler implements IRecor
|
|||
if (isNotBlank(rid)) {
|
||||
addConceptMapEntry(
|
||||
new ConceptMapping()
|
||||
.setConceptMapId(RID_MAPPING_CM_ID)
|
||||
.setConceptMapUri(RID_MAPPING_CM_URI)
|
||||
.setConceptMapName(RID_MAPPING_CM_NAME)
|
||||
.setConceptMapId(RADLEX_MAPPING_CM_ID)
|
||||
.setConceptMapUri(RADLEX_MAPPING_CM_URI)
|
||||
.setConceptMapName(RADLEX_MAPPING_CM_NAME)
|
||||
.setSourceCodeSystem(IHapiTerminologyLoaderSvc.LOINC_URI)
|
||||
.setSourceCode(partNumber)
|
||||
.setSourceDisplay(partName)
|
||||
|
|
@ -196,9 +194,9 @@ public class LoincRsnaPlaybookHandler extends BaseLoincHandler implements IRecor
|
|||
if (isNotBlank(rpid)) {
|
||||
addConceptMapEntry(
|
||||
new ConceptMapping()
|
||||
.setConceptMapId(RPID_MAPPING_CM_ID)
|
||||
.setConceptMapUri(RPID_MAPPING_CM_URI)
|
||||
.setConceptMapName(RPID_MAPPING_CM_NAME)
|
||||
.setConceptMapId(RADLEX_MAPPING_CM_ID)
|
||||
.setConceptMapUri(RADLEX_MAPPING_CM_URI)
|
||||
.setConceptMapName(RADLEX_MAPPING_CM_NAME)
|
||||
.setSourceCodeSystem(IHapiTerminologyLoaderSvc.LOINC_URI)
|
||||
.setSourceCode(loincNumber)
|
||||
.setSourceDisplay(longCommonName)
|
||||
|
|
|
|||
|
|
@ -34,7 +34,7 @@ import static org.apache.commons.lang3.StringUtils.trim;
|
|||
public class LoincUniversalOrderSetHandler extends BaseLoincHandler implements IRecordHandler {
|
||||
|
||||
public static final String VS_ID = "loinc-universal-order-set-vs";
|
||||
public static final String VS_URI = "http://loinc.org/fhir/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";
|
||||
|
||||
public LoincUniversalOrderSetHandler(Map<String, TermConcept> theCode2concept, List<ValueSet> theValueSets, List<ConceptMap> theConceptMaps, Properties theUploadProperties) {
|
||||
|
|
|
|||
|
|
@ -24,17 +24,33 @@ public class FhirResourceDaoDstu3ConceptMapTest extends BaseJpaDstu3Test {
|
|||
|
||||
private IIdType myConceptMapId;
|
||||
|
||||
@AfterClass
|
||||
public static void afterClassClearContext() {
|
||||
TestUtil.clearAllStaticFieldsForUnitTest();
|
||||
}
|
||||
|
||||
@Before
|
||||
@Transactional
|
||||
public void before02() {
|
||||
myConceptMapId = myConceptMapDao.create(createConceptMap(), mySrd).getId().toUnqualifiedVersionless();
|
||||
}
|
||||
|
||||
@Test
|
||||
public void testDeleteConceptMap() {
|
||||
myConceptMapDao.delete(myConceptMapId);
|
||||
|
||||
new TransactionTemplate(myTxManager).execute(new TransactionCallbackWithoutResult() {
|
||||
@Override
|
||||
protected void doInTransactionWithoutResult(TransactionStatus theStatus) {
|
||||
TranslationRequest translationRequest = new TranslationRequest();
|
||||
translationRequest.getCodeableConcept().addCoding()
|
||||
.setSystem(CS_URL)
|
||||
.setCode("12345");
|
||||
translationRequest.setTargetSystem(new UriType(CS_URL_3));
|
||||
|
||||
TranslationResult translationResult = myConceptMapDao.translate(translationRequest, null);
|
||||
|
||||
assertFalse(translationResult.getResult().booleanValue());
|
||||
}
|
||||
});
|
||||
|
||||
}
|
||||
|
||||
@Test
|
||||
public void testTranslateByCodeSystemsAndSourceCodeOneToMany() {
|
||||
ConceptMap conceptMap = myConceptMapDao.read(myConceptMapId);
|
||||
|
|
@ -81,4 +97,9 @@ public class FhirResourceDaoDstu3ConceptMapTest extends BaseJpaDstu3Test {
|
|||
}
|
||||
});
|
||||
}
|
||||
|
||||
@AfterClass
|
||||
public static void afterClassClearContext() {
|
||||
TestUtil.clearAllStaticFieldsForUnitTest();
|
||||
}
|
||||
}
|
||||
|
|
|
|||
|
|
@ -26,17 +26,33 @@ public class FhirResourceDaoR4ConceptMapTest extends BaseJpaR4Test {
|
|||
|
||||
private IIdType myConceptMapId;
|
||||
|
||||
@AfterClass
|
||||
public static void afterClassClearContext() {
|
||||
TestUtil.clearAllStaticFieldsForUnitTest();
|
||||
}
|
||||
|
||||
@Before
|
||||
@Transactional
|
||||
public void before02() {
|
||||
myConceptMapId = myConceptMapDao.create(createConceptMap(), mySrd).getId().toUnqualifiedVersionless();
|
||||
}
|
||||
|
||||
@Test
|
||||
public void testDeleteConceptMap() {
|
||||
myConceptMapDao.delete(myConceptMapId);
|
||||
|
||||
new TransactionTemplate(myTxManager).execute(new TransactionCallbackWithoutResult() {
|
||||
@Override
|
||||
protected void doInTransactionWithoutResult(TransactionStatus theStatus) {
|
||||
TranslationRequest translationRequest = new TranslationRequest();
|
||||
translationRequest.getCodeableConcept().addCoding()
|
||||
.setSystem(CS_URL)
|
||||
.setCode("12345");
|
||||
translationRequest.setTargetSystem(new UriType(CS_URL_3));
|
||||
|
||||
TranslationResult translationResult = myConceptMapDao.translate(translationRequest, null);
|
||||
|
||||
assertFalse(translationResult.getResult().booleanValue());
|
||||
}
|
||||
});
|
||||
|
||||
}
|
||||
|
||||
@Test
|
||||
public void testTranslateByCodeSystemsAndSourceCodeOneToMany() {
|
||||
ConceptMap conceptMap = myConceptMapDao.read(myConceptMapId);
|
||||
|
|
@ -205,6 +221,98 @@ public class FhirResourceDaoR4ConceptMapTest extends BaseJpaR4Test {
|
|||
});
|
||||
}
|
||||
|
||||
@Test
|
||||
public void testTranslateUsingPredicatesWithSourceAndTargetSystem2() {
|
||||
ConceptMap conceptMap = myConceptMapDao.read(myConceptMapId);
|
||||
|
||||
ourLog.info("ConceptMap:\n" + myFhirCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(conceptMap));
|
||||
|
||||
new TransactionTemplate(myTxManager).execute(new TransactionCallbackWithoutResult() {
|
||||
@Override
|
||||
protected void doInTransactionWithoutResult(TransactionStatus theStatus) {
|
||||
/*
|
||||
* Provided:
|
||||
* source code
|
||||
* source code system
|
||||
* target code system #2
|
||||
*/
|
||||
TranslationRequest translationRequest = new TranslationRequest();
|
||||
translationRequest.getCodeableConcept().addCoding()
|
||||
.setSystem(CS_URL)
|
||||
.setCode("12345");
|
||||
translationRequest.setTargetSystem(new UriType(CS_URL_2));
|
||||
|
||||
TranslationResult translationResult = myConceptMapDao.translate(translationRequest, null);
|
||||
|
||||
assertTrue(translationResult.getResult().booleanValue());
|
||||
assertEquals("Matches found!", translationResult.getMessage().getValueAsString());
|
||||
|
||||
assertEquals(1, translationResult.getMatches().size());
|
||||
|
||||
TranslationMatch translationMatch = translationResult.getMatches().get(0);
|
||||
assertEquals(ConceptMapEquivalence.EQUAL.toCode(), translationMatch.getEquivalence().getCode());
|
||||
Coding concept = translationMatch.getConcept();
|
||||
assertEquals("34567", concept.getCode());
|
||||
assertEquals("Target Code 34567", concept.getDisplay());
|
||||
assertEquals(CS_URL_2, concept.getSystem());
|
||||
assertEquals("Version 2", concept.getVersion());
|
||||
assertFalse(concept.getUserSelected());
|
||||
assertEquals(CM_URL, translationMatch.getSource().getValueAsString());
|
||||
}
|
||||
});
|
||||
}
|
||||
|
||||
@Test
|
||||
public void testTranslateUsingPredicatesWithSourceAndTargetSystem3() {
|
||||
ConceptMap conceptMap = myConceptMapDao.read(myConceptMapId);
|
||||
|
||||
ourLog.info("ConceptMap:\n" + myFhirCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(conceptMap));
|
||||
|
||||
new TransactionTemplate(myTxManager).execute(new TransactionCallbackWithoutResult() {
|
||||
@Override
|
||||
protected void doInTransactionWithoutResult(TransactionStatus theStatus) {
|
||||
/*
|
||||
* Provided:
|
||||
* source code
|
||||
* source code system
|
||||
* target code system #3
|
||||
*/
|
||||
TranslationRequest translationRequest = new TranslationRequest();
|
||||
translationRequest.getCodeableConcept().addCoding()
|
||||
.setSystem(CS_URL)
|
||||
.setCode("12345");
|
||||
translationRequest.setTargetSystem(new UriType(CS_URL_3));
|
||||
|
||||
TranslationResult translationResult = myConceptMapDao.translate(translationRequest, null);
|
||||
|
||||
assertTrue(translationResult.getResult().booleanValue());
|
||||
assertEquals("Matches found!", translationResult.getMessage().getValueAsString());
|
||||
|
||||
assertEquals(2, translationResult.getMatches().size());
|
||||
|
||||
TranslationMatch translationMatch = translationResult.getMatches().get(0);
|
||||
assertEquals(ConceptMapEquivalence.EQUAL.toCode(), translationMatch.getEquivalence().getCode());
|
||||
Coding concept = translationMatch.getConcept();
|
||||
assertEquals("56789", concept.getCode());
|
||||
assertEquals("Target Code 56789", concept.getDisplay());
|
||||
assertEquals(CS_URL_3, concept.getSystem());
|
||||
assertEquals("Version 4", concept.getVersion());
|
||||
assertFalse(concept.getUserSelected());
|
||||
assertEquals(CM_URL, translationMatch.getSource().getValueAsString());
|
||||
|
||||
translationMatch = translationResult.getMatches().get(1);
|
||||
assertEquals(ConceptMapEquivalence.WIDER.toCode(), translationMatch.getEquivalence().getCode());
|
||||
concept = translationMatch.getConcept();
|
||||
assertEquals("67890", concept.getCode());
|
||||
assertEquals("Target Code 67890", concept.getDisplay());
|
||||
assertEquals(CS_URL_3, concept.getSystem());
|
||||
assertEquals("Version 4", concept.getVersion());
|
||||
assertFalse(concept.getUserSelected());
|
||||
assertEquals(CM_URL, translationMatch.getSource().getValueAsString());
|
||||
}
|
||||
});
|
||||
}
|
||||
|
||||
@Test
|
||||
public void testTranslateUsingPredicatesWithSourceSystem() {
|
||||
ConceptMap conceptMap = myConceptMapDao.read(myConceptMapId);
|
||||
|
|
@ -356,98 +464,6 @@ public class FhirResourceDaoR4ConceptMapTest extends BaseJpaR4Test {
|
|||
});
|
||||
}
|
||||
|
||||
@Test
|
||||
public void testTranslateUsingPredicatesWithSourceAndTargetSystem2() {
|
||||
ConceptMap conceptMap = myConceptMapDao.read(myConceptMapId);
|
||||
|
||||
ourLog.info("ConceptMap:\n" + myFhirCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(conceptMap));
|
||||
|
||||
new TransactionTemplate(myTxManager).execute(new TransactionCallbackWithoutResult() {
|
||||
@Override
|
||||
protected void doInTransactionWithoutResult(TransactionStatus theStatus) {
|
||||
/*
|
||||
* Provided:
|
||||
* source code
|
||||
* source code system
|
||||
* target code system #2
|
||||
*/
|
||||
TranslationRequest translationRequest = new TranslationRequest();
|
||||
translationRequest.getCodeableConcept().addCoding()
|
||||
.setSystem(CS_URL)
|
||||
.setCode("12345");
|
||||
translationRequest.setTargetSystem(new UriType(CS_URL_2));
|
||||
|
||||
TranslationResult translationResult = myConceptMapDao.translate(translationRequest, null);
|
||||
|
||||
assertTrue(translationResult.getResult().booleanValue());
|
||||
assertEquals("Matches found!", translationResult.getMessage().getValueAsString());
|
||||
|
||||
assertEquals(1, translationResult.getMatches().size());
|
||||
|
||||
TranslationMatch translationMatch = translationResult.getMatches().get(0);
|
||||
assertEquals(ConceptMapEquivalence.EQUAL.toCode(), translationMatch.getEquivalence().getCode());
|
||||
Coding concept = translationMatch.getConcept();
|
||||
assertEquals("34567", concept.getCode());
|
||||
assertEquals("Target Code 34567", concept.getDisplay());
|
||||
assertEquals(CS_URL_2, concept.getSystem());
|
||||
assertEquals("Version 2", concept.getVersion());
|
||||
assertFalse(concept.getUserSelected());
|
||||
assertEquals(CM_URL, translationMatch.getSource().getValueAsString());
|
||||
}
|
||||
});
|
||||
}
|
||||
|
||||
@Test
|
||||
public void testTranslateUsingPredicatesWithSourceAndTargetSystem3() {
|
||||
ConceptMap conceptMap = myConceptMapDao.read(myConceptMapId);
|
||||
|
||||
ourLog.info("ConceptMap:\n" + myFhirCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(conceptMap));
|
||||
|
||||
new TransactionTemplate(myTxManager).execute(new TransactionCallbackWithoutResult() {
|
||||
@Override
|
||||
protected void doInTransactionWithoutResult(TransactionStatus theStatus) {
|
||||
/*
|
||||
* Provided:
|
||||
* source code
|
||||
* source code system
|
||||
* target code system #3
|
||||
*/
|
||||
TranslationRequest translationRequest = new TranslationRequest();
|
||||
translationRequest.getCodeableConcept().addCoding()
|
||||
.setSystem(CS_URL)
|
||||
.setCode("12345");
|
||||
translationRequest.setTargetSystem(new UriType(CS_URL_3));
|
||||
|
||||
TranslationResult translationResult = myConceptMapDao.translate(translationRequest, null);
|
||||
|
||||
assertTrue(translationResult.getResult().booleanValue());
|
||||
assertEquals("Matches found!", translationResult.getMessage().getValueAsString());
|
||||
|
||||
assertEquals(2, translationResult.getMatches().size());
|
||||
|
||||
TranslationMatch translationMatch = translationResult.getMatches().get(0);
|
||||
assertEquals(ConceptMapEquivalence.EQUAL.toCode(), translationMatch.getEquivalence().getCode());
|
||||
Coding concept = translationMatch.getConcept();
|
||||
assertEquals("56789", concept.getCode());
|
||||
assertEquals("Target Code 56789", concept.getDisplay());
|
||||
assertEquals(CS_URL_3, concept.getSystem());
|
||||
assertEquals("Version 4", concept.getVersion());
|
||||
assertFalse(concept.getUserSelected());
|
||||
assertEquals(CM_URL, translationMatch.getSource().getValueAsString());
|
||||
|
||||
translationMatch = translationResult.getMatches().get(1);
|
||||
assertEquals(ConceptMapEquivalence.WIDER.toCode(), translationMatch.getEquivalence().getCode());
|
||||
concept = translationMatch.getConcept();
|
||||
assertEquals("67890", concept.getCode());
|
||||
assertEquals("Target Code 67890", concept.getDisplay());
|
||||
assertEquals(CS_URL_3, concept.getSystem());
|
||||
assertEquals("Version 4", concept.getVersion());
|
||||
assertFalse(concept.getUserSelected());
|
||||
assertEquals(CM_URL, translationMatch.getSource().getValueAsString());
|
||||
}
|
||||
});
|
||||
}
|
||||
|
||||
@Test
|
||||
public void testTranslateUsingPredicatesWithSourceValueSet() {
|
||||
ConceptMap conceptMap = myConceptMapDao.read(myConceptMapId);
|
||||
|
|
@ -686,6 +702,92 @@ public class FhirResourceDaoR4ConceptMapTest extends BaseJpaR4Test {
|
|||
});
|
||||
}
|
||||
|
||||
@Test
|
||||
public void testTranslateWithReverseUsingPredicatesWithSourceAndTargetSystem1() {
|
||||
ConceptMap conceptMap = myConceptMapDao.read(myConceptMapId);
|
||||
|
||||
ourLog.info("ConceptMap:\n" + myFhirCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(conceptMap));
|
||||
|
||||
new TransactionTemplate(myTxManager).execute(new TransactionCallbackWithoutResult() {
|
||||
@Override
|
||||
protected void doInTransactionWithoutResult(TransactionStatus theStatus) {
|
||||
/*
|
||||
* Provided:
|
||||
* source code
|
||||
* source code system
|
||||
* target code system #1
|
||||
* reverse = true
|
||||
*/
|
||||
TranslationRequest translationRequest = new TranslationRequest();
|
||||
translationRequest.getCodeableConcept().addCoding()
|
||||
.setSystem(CS_URL_2)
|
||||
.setCode("34567");
|
||||
translationRequest.setTargetSystem(new UriType(CS_URL));
|
||||
translationRequest.setReverse(true);
|
||||
|
||||
TranslationResult translationResult = myConceptMapDao.translate(translationRequest, null);
|
||||
|
||||
assertTrue(translationResult.getResult().booleanValue());
|
||||
assertEquals("Matches found!", translationResult.getMessage().getValueAsString());
|
||||
|
||||
assertEquals(1, translationResult.getMatches().size());
|
||||
|
||||
TranslationMatch translationMatch = translationResult.getMatches().get(0);
|
||||
assertNull(translationMatch.getEquivalence());
|
||||
Coding concept = translationMatch.getConcept();
|
||||
assertEquals("12345", concept.getCode());
|
||||
assertEquals("Source Code 12345", concept.getDisplay());
|
||||
assertEquals(CS_URL, concept.getSystem());
|
||||
assertEquals("Version 1", concept.getVersion());
|
||||
assertFalse(concept.getUserSelected());
|
||||
assertEquals(CM_URL, translationMatch.getSource().getValueAsString());
|
||||
}
|
||||
});
|
||||
}
|
||||
|
||||
@Test
|
||||
public void testTranslateWithReverseUsingPredicatesWithSourceAndTargetSystem4() {
|
||||
ConceptMap conceptMap = myConceptMapDao.read(myConceptMapId);
|
||||
|
||||
ourLog.info("ConceptMap:\n" + myFhirCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(conceptMap));
|
||||
|
||||
new TransactionTemplate(myTxManager).execute(new TransactionCallbackWithoutResult() {
|
||||
@Override
|
||||
protected void doInTransactionWithoutResult(TransactionStatus theStatus) {
|
||||
/*
|
||||
* Provided:
|
||||
* source code
|
||||
* source code system
|
||||
* target code system #4
|
||||
* reverse = true
|
||||
*/
|
||||
TranslationRequest translationRequest = new TranslationRequest();
|
||||
translationRequest.getCodeableConcept().addCoding()
|
||||
.setSystem(CS_URL_2)
|
||||
.setCode("34567");
|
||||
translationRequest.setTargetSystem(new UriType(CS_URL_4));
|
||||
translationRequest.setReverse(true);
|
||||
|
||||
TranslationResult translationResult = myConceptMapDao.translate(translationRequest, null);
|
||||
|
||||
assertTrue(translationResult.getResult().booleanValue());
|
||||
assertEquals("Matches found!", translationResult.getMessage().getValueAsString());
|
||||
|
||||
assertEquals(1, translationResult.getMatches().size());
|
||||
|
||||
TranslationMatch translationMatch = translationResult.getMatches().get(0);
|
||||
assertNull(translationMatch.getEquivalence());
|
||||
Coding concept = translationMatch.getConcept();
|
||||
assertEquals("78901", concept.getCode());
|
||||
assertEquals("Source Code 78901", concept.getDisplay());
|
||||
assertEquals(CS_URL_4, concept.getSystem());
|
||||
assertEquals("Version 5", concept.getVersion());
|
||||
assertFalse(concept.getUserSelected());
|
||||
assertEquals(CM_URL, translationMatch.getSource().getValueAsString());
|
||||
}
|
||||
});
|
||||
}
|
||||
|
||||
@Test
|
||||
public void testTranslateWithReverseUsingPredicatesWithSourceSystem() {
|
||||
ConceptMap conceptMap = myConceptMapDao.read(myConceptMapId);
|
||||
|
|
@ -790,92 +892,6 @@ public class FhirResourceDaoR4ConceptMapTest extends BaseJpaR4Test {
|
|||
});
|
||||
}
|
||||
|
||||
@Test
|
||||
public void testTranslateWithReverseUsingPredicatesWithSourceAndTargetSystem1() {
|
||||
ConceptMap conceptMap = myConceptMapDao.read(myConceptMapId);
|
||||
|
||||
ourLog.info("ConceptMap:\n" + myFhirCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(conceptMap));
|
||||
|
||||
new TransactionTemplate(myTxManager).execute(new TransactionCallbackWithoutResult() {
|
||||
@Override
|
||||
protected void doInTransactionWithoutResult(TransactionStatus theStatus) {
|
||||
/*
|
||||
* Provided:
|
||||
* source code
|
||||
* source code system
|
||||
* target code system #1
|
||||
* reverse = true
|
||||
*/
|
||||
TranslationRequest translationRequest = new TranslationRequest();
|
||||
translationRequest.getCodeableConcept().addCoding()
|
||||
.setSystem(CS_URL_2)
|
||||
.setCode("34567");
|
||||
translationRequest.setTargetSystem(new UriType(CS_URL));
|
||||
translationRequest.setReverse(true);
|
||||
|
||||
TranslationResult translationResult = myConceptMapDao.translate(translationRequest, null);
|
||||
|
||||
assertTrue(translationResult.getResult().booleanValue());
|
||||
assertEquals("Matches found!", translationResult.getMessage().getValueAsString());
|
||||
|
||||
assertEquals(1, translationResult.getMatches().size());
|
||||
|
||||
TranslationMatch translationMatch = translationResult.getMatches().get(0);
|
||||
assertNull(translationMatch.getEquivalence());
|
||||
Coding concept = translationMatch.getConcept();
|
||||
assertEquals("12345", concept.getCode());
|
||||
assertEquals("Source Code 12345", concept.getDisplay());
|
||||
assertEquals(CS_URL, concept.getSystem());
|
||||
assertEquals("Version 1", concept.getVersion());
|
||||
assertFalse(concept.getUserSelected());
|
||||
assertEquals(CM_URL, translationMatch.getSource().getValueAsString());
|
||||
}
|
||||
});
|
||||
}
|
||||
|
||||
@Test
|
||||
public void testTranslateWithReverseUsingPredicatesWithSourceAndTargetSystem4() {
|
||||
ConceptMap conceptMap = myConceptMapDao.read(myConceptMapId);
|
||||
|
||||
ourLog.info("ConceptMap:\n" + myFhirCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(conceptMap));
|
||||
|
||||
new TransactionTemplate(myTxManager).execute(new TransactionCallbackWithoutResult() {
|
||||
@Override
|
||||
protected void doInTransactionWithoutResult(TransactionStatus theStatus) {
|
||||
/*
|
||||
* Provided:
|
||||
* source code
|
||||
* source code system
|
||||
* target code system #4
|
||||
* reverse = true
|
||||
*/
|
||||
TranslationRequest translationRequest = new TranslationRequest();
|
||||
translationRequest.getCodeableConcept().addCoding()
|
||||
.setSystem(CS_URL_2)
|
||||
.setCode("34567");
|
||||
translationRequest.setTargetSystem(new UriType(CS_URL_4));
|
||||
translationRequest.setReverse(true);
|
||||
|
||||
TranslationResult translationResult = myConceptMapDao.translate(translationRequest, null);
|
||||
|
||||
assertTrue(translationResult.getResult().booleanValue());
|
||||
assertEquals("Matches found!", translationResult.getMessage().getValueAsString());
|
||||
|
||||
assertEquals(1, translationResult.getMatches().size());
|
||||
|
||||
TranslationMatch translationMatch = translationResult.getMatches().get(0);
|
||||
assertNull(translationMatch.getEquivalence());
|
||||
Coding concept = translationMatch.getConcept();
|
||||
assertEquals("78901", concept.getCode());
|
||||
assertEquals("Source Code 78901", concept.getDisplay());
|
||||
assertEquals(CS_URL_4, concept.getSystem());
|
||||
assertEquals("Version 5", concept.getVersion());
|
||||
assertFalse(concept.getUserSelected());
|
||||
assertEquals(CM_URL, translationMatch.getSource().getValueAsString());
|
||||
}
|
||||
});
|
||||
}
|
||||
|
||||
@Test
|
||||
public void testTranslateWithReverseUsingPredicatesWithSourceValueSet() {
|
||||
ConceptMap conceptMap = myConceptMapDao.read(myConceptMapId);
|
||||
|
|
@ -977,4 +993,9 @@ public class FhirResourceDaoR4ConceptMapTest extends BaseJpaR4Test {
|
|||
}
|
||||
});
|
||||
}
|
||||
|
||||
@AfterClass
|
||||
public static void afterClassClearContext() {
|
||||
TestUtil.clearAllStaticFieldsForUnitTest();
|
||||
}
|
||||
}
|
||||
|
|
|
|||
|
|
@ -222,9 +222,9 @@ public class TerminologyLoaderSvcLoincTest {
|
|||
assertEquals("NM", code.getCodingProperties(propertyName).get(0).getDisplay());
|
||||
|
||||
// RSNA Playbook - LOINC Part -> RadLex RID Mappings
|
||||
conceptMap = conceptMaps.get(LoincRsnaPlaybookHandler.RID_MAPPING_CM_ID);
|
||||
assertEquals(LoincRsnaPlaybookHandler.RID_MAPPING_CM_URI, conceptMap.getUrl());
|
||||
assertEquals(LoincRsnaPlaybookHandler.RID_MAPPING_CM_NAME, conceptMap.getName());
|
||||
conceptMap = conceptMaps.get(LoincRsnaPlaybookHandler.RADLEX_MAPPING_CM_ID);
|
||||
assertEquals(LoincRsnaPlaybookHandler.RADLEX_MAPPING_CM_URI, conceptMap.getUrl());
|
||||
assertEquals(LoincRsnaPlaybookHandler.RADLEX_MAPPING_CM_NAME, conceptMap.getName());
|
||||
assertEquals(1, conceptMap.getGroup().size());
|
||||
group = conceptMap.getGroupFirstRep();
|
||||
// all entries have the same source and target so these should be null
|
||||
|
|
@ -238,9 +238,9 @@ public class TerminologyLoaderSvcLoincTest {
|
|||
assertEquals(Enumerations.ConceptMapEquivalence.EQUAL, group.getElement().get(0).getTarget().get(0).getEquivalence());
|
||||
|
||||
// RSNA Playbook - LOINC Term -> RadLex RPID Mappings
|
||||
conceptMap = conceptMaps.get(LoincRsnaPlaybookHandler.RPID_MAPPING_CM_ID);
|
||||
assertEquals(LoincRsnaPlaybookHandler.RPID_MAPPING_CM_URI, conceptMap.getUrl());
|
||||
assertEquals(LoincRsnaPlaybookHandler.RPID_MAPPING_CM_NAME, conceptMap.getName());
|
||||
conceptMap = conceptMaps.get(LoincRsnaPlaybookHandler.RADLEX_MAPPING_CM_ID);
|
||||
assertEquals(LoincRsnaPlaybookHandler.RADLEX_MAPPING_CM_URI, conceptMap.getUrl());
|
||||
assertEquals(LoincRsnaPlaybookHandler.RADLEX_MAPPING_CM_URI, conceptMap.getName());
|
||||
assertEquals(1, conceptMap.getGroup().size());
|
||||
group = conceptMap.getGroupFirstRep();
|
||||
// all entries have the same source and target so these should be null
|
||||
|
|
|
|||
Loading…
Reference in New Issue