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MAINT-2621 Address SonarQube feedback
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@QuyenLy87
QuyenLy87 committed Oct 15, 2024
1 parent 5d758a8 commit ee9d18c
Showing 1 changed file with 86 additions and 66 deletions.
152 changes: 86 additions & 66 deletions ...o/otf/transformationandtemplate/service/componenttransform/HighLevelAuthoringService.java
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Original file line number Diff line number Diff line change
Expand Up @@ -10,6 +10,7 @@
import org.ihtsdo.otf.transformationandtemplate.domain.TransformationRecipe;
import org.ihtsdo.otf.transformationandtemplate.service.ConstantStrings;
import org.ihtsdo.otf.transformationandtemplate.service.client.*;
import org.jetbrains.annotations.NotNull;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import org.springframework.web.reactive.function.client.WebClientException;
Expand Down Expand Up @@ -353,69 +354,15 @@ public List<ChangeResult<? extends SnomedComponent>> updateDescriptions(Transfor
List<String> optionalLanguageRefsets = snowstormClient.getOptionalLanguageRefsets(request.getBranchPath());

// retrieve all concepts before processing update
List<ConceptPojo> concepts = new ArrayList <>();
for (List<DescriptionPojo> descriptionProcessingBatch : Iterables.partition(descriptions, processingBatchMaxSize)) {
if (ChangeType.INACTIVATE.equals(recipe.getChangeType())) {
Set<DescriptionPojo> descriptionsWithTermOnly = descriptionProcessingBatch.stream().filter(item -> item.getDescriptionId() == null && item.getTerm() != null).collect(Collectors.toSet());
for (DescriptionPojo description : descriptionsWithTermOnly) {
SnowstormClient.ConceptPage conceptPage = snowstormClient.fetchConceptPage(projectBranchPath, true, null, null, null, description.getTerm(), null).block();
if (conceptPage != null) {
boolean found = false;
for (Concept concept : conceptPage.getItems()) {
ConceptPojo fullConcept = snowstormClient.getFullConcept(projectBranchPath, concept.getConceptId());
for (DescriptionPojo des : fullConcept.getDescriptions()) {
if (des.isActive() && des.isReleased() && des.getTerm().equalsIgnoreCase(description.getTerm()) && des.getLang().equals(description.getLang())) {
description.setDescriptionId(des.getDescriptionId());
found = true;
logger.info("Found description ID {} for term '{}'", des.getDescriptionId(), description.getTerm());
break;
}
}
if (found) break;
}
if (!found) {
getChangeResult(changes, description, DESCRIPTION_WITHOUT_ID_COMPARATOR).fail(format("Description term '%s' not found.", description.getTerm()));
}
} else {
getChangeResult(changes, description, DESCRIPTION_WITHOUT_ID_COMPARATOR).fail(format("Description term '%s' not found.", description.getTerm()));
}
}
}

Set<String> descriptionIds = descriptionProcessingBatch.stream().map(DescriptionPojo::getDescriptionId).filter(Objects::nonNull).collect(Collectors.toSet());
List<ConceptPojo> fullConcepts = snowstormClient.getFullConcepts(SnowstormClient.ConceptBulkLoadRequest.byDescriptionId(descriptionIds), projectBranchPath);
concepts.addAll(fullConcepts.stream()
.filter(c1 -> concepts.stream().noneMatch(c1::equals))
.toList()
);
}
List<ConceptPojo> concepts = retrieveAllConcepts(recipe, descriptions, changes, projectBranchPath);

Map<String, ConceptPojo> conceptMap = concepts.stream().collect(Collectors.toMap(ConceptPojo::getConceptId, Function.identity()));
Map<String, DescriptionPojo> descriptionIdMap = descriptions.stream().filter(des -> des.getId() != null).collect(Collectors.toMap(DescriptionPojo::getDescriptionId, Function.identity()));

Map<String, String > descriptionsFound = new HashMap <>();
Map<String, String > invalidModuleDescriptions = new HashMap <>();
for (ConceptPojo loadedConcept : concepts) {
for (DescriptionPojo loadedDescription : loadedConcept.getDescriptions()) {
DescriptionPojo descriptionUpdate = descriptionIdMap.get(loadedDescription.getDescriptionId());
if (descriptionUpdate != null) {
if (defaultModuleId == null || defaultModuleId.equals(loadedDescription.getModuleId())) {
descriptionsFound.put(descriptionUpdate.getDescriptionId(), loadedDescription.getConceptId());
} else {
invalidModuleDescriptions.put(descriptionUpdate.getDescriptionId(), loadedDescription.getConceptId());
}

if (!optionalLanguageRefsets.isEmpty() && loadedDescription.isActive() && !descriptionUpdate.isActive()) {
Set<String> intersectedLanguageRefsets = optionalLanguageRefsets.stream()
.distinct()
.filter(loadedDescription.getAcceptabilityMap().keySet()::contains)
.collect(Collectors.toSet());
if (!intersectedLanguageRefsets.isEmpty()) {
getChangeResult(changes, descriptionUpdate, DESCRIPTION_WITH_ID_COMPARATOR).addWarning("The description is referenced in following context based language reference set " + intersectedLanguageRefsets);
}
}
}
}
detectMatchingDescriptions(changes, loadedConcept, descriptionIdMap, defaultModuleId, descriptionsFound, invalidModuleDescriptions, optionalLanguageRefsets);
}
Set<String> descriptionIdsFound = new HashSet <>();
descriptionIdsFound.addAll(descriptionsFound.keySet());
Expand Down Expand Up @@ -443,16 +390,7 @@ public List<ChangeResult<? extends SnomedComponent>> updateDescriptions(Transfor

if(!descriptionIdMap.keySet().isEmpty()) {
// Split into batches
int batchNumber = 0;
for (List<ConceptPojo> conceptTaskBatch : Iterables.partition(conceptMap.values(), request.getBatchSize())) {
batchNumber++;
String branchPath = getBatchBranch(request, batchNumber);

// Split into smaller batches if the number of per branch changes exceeds the number of concepts which should be processed at a time.
for (List<ConceptPojo> conceptProcessingBatch : Iterables.partition(conceptTaskBatch, processingBatchMaxSize)) {
updateDescriptionBatch(conceptProcessingBatch, descriptionIdMap, changes, branchPath);
}
}
processUpdateDescriptionBatch(request, changes, conceptMap, descriptionIdMap);
}

// Mark all changes which have not failed as successful
Expand All @@ -465,6 +403,88 @@ public List<ChangeResult<? extends SnomedComponent>> updateDescriptions(Transfor
return new ArrayList<>(changes);
}

private void processUpdateDescriptionBatch(ComponentTransformationRequest request, List<ChangeResult<DescriptionPojo>> changes, Map<String, ConceptPojo> conceptMap, Map<String, DescriptionPojo> descriptionIdMap) throws TimeoutException {
int batchNumber = 0;
for (List<ConceptPojo> conceptTaskBatch : Iterables.partition(conceptMap.values(), request.getBatchSize())) {
batchNumber++;
String branchPath = getBatchBranch(request, batchNumber);

// Split into smaller batches if the number of per branch changes exceeds the number of concepts which should be processed at a time.
for (List<ConceptPojo> conceptProcessingBatch : Iterables.partition(conceptTaskBatch, processingBatchMaxSize)) {
updateDescriptionBatch(conceptProcessingBatch, descriptionIdMap, changes, branchPath);
}
}
}

private void detectMatchingDescriptions(List<ChangeResult<DescriptionPojo>> changes, ConceptPojo loadedConcept, Map<String, DescriptionPojo> descriptionIdMap, String defaultModuleId, Map<String, String> descriptionsFound, Map<String, String> invalidModuleDescriptions, List<String> optionalLanguageRefsets) throws BusinessServiceException {
for (DescriptionPojo loadedDescription : loadedConcept.getDescriptions()) {
DescriptionPojo descriptionUpdate = descriptionIdMap.get(loadedDescription.getDescriptionId());
if (descriptionUpdate == null) continue;
if (defaultModuleId == null || defaultModuleId.equals(loadedDescription.getModuleId())) {
descriptionsFound.put(descriptionUpdate.getDescriptionId(), loadedDescription.getConceptId());
} else {
invalidModuleDescriptions.put(descriptionUpdate.getDescriptionId(), loadedDescription.getConceptId());
}

if (!optionalLanguageRefsets.isEmpty() && loadedDescription.isActive() && !descriptionUpdate.isActive()) {
Set<String> intersectedLanguageRefsets = optionalLanguageRefsets.stream()
.distinct()
.filter(loadedDescription.getAcceptabilityMap().keySet()::contains)
.collect(Collectors.toSet());
if (!intersectedLanguageRefsets.isEmpty()) {
getChangeResult(changes, descriptionUpdate, DESCRIPTION_WITH_ID_COMPARATOR).addWarning("The description is referenced in following context based language reference set " + intersectedLanguageRefsets);
}
}
}
}

private List<ConceptPojo> retrieveAllConcepts(TransformationRecipe recipe, List<DescriptionPojo> descriptions, List<ChangeResult<DescriptionPojo>> changes, String projectBranchPath) throws BusinessServiceException {
List<ConceptPojo> concepts = new ArrayList <>();
for (List<DescriptionPojo> descriptionProcessingBatch : Iterables.partition(descriptions, processingBatchMaxSize)) {
findAndSetDescriptionIdForInactiveDescriptions(recipe, changes, descriptionProcessingBatch, projectBranchPath);

Set<String> descriptionIds = descriptionProcessingBatch.stream().map(DescriptionPojo::getDescriptionId).filter(Objects::nonNull).collect(Collectors.toSet());
List<ConceptPojo> fullConcepts = snowstormClient.getFullConcepts(SnowstormClient.ConceptBulkLoadRequest.byDescriptionId(descriptionIds), projectBranchPath);
concepts.addAll(fullConcepts.stream()
.filter(c1 -> concepts.stream().noneMatch(c1::equals))
.toList()
);
}
return concepts;
}

private void findAndSetDescriptionIdForInactiveDescriptions(TransformationRecipe recipe, List<ChangeResult<DescriptionPojo>> changes, List<DescriptionPojo> descriptionProcessingBatch, String projectBranchPath) throws BusinessServiceException {
if (ChangeType.INACTIVATE.equals(recipe.getChangeType())) {
Set<DescriptionPojo> descriptionsWithTermOnly = descriptionProcessingBatch.stream().filter(item -> item.getDescriptionId() == null && item.getTerm() != null).collect(Collectors.toSet());
for (DescriptionPojo description : descriptionsWithTermOnly) {
findAndSetDescriptionIdForInactiveDescription(changes, projectBranchPath, description);
}
}
}

private void findAndSetDescriptionIdForInactiveDescription(List<ChangeResult<DescriptionPojo>> changes, String projectBranchPath, DescriptionPojo description) throws BusinessServiceException {
SnowstormClient.ConceptPage conceptPage = snowstormClient.fetchConceptPage(projectBranchPath, true, null, null, null, description.getTerm(), null).block();
if (conceptPage == null) {
getChangeResult(changes, description, DESCRIPTION_WITHOUT_ID_COMPARATOR).fail(format("Description term '%s' not found.", description.getTerm()));
return;
}
boolean found = false;
for (Concept concept : conceptPage.getItems()) {
ConceptPojo fullConcept = snowstormClient.getFullConcept(projectBranchPath, concept.getConceptId());
for (DescriptionPojo des : fullConcept.getDescriptions()) {
if (des.isActive() && des.isReleased() && des.getTerm().equalsIgnoreCase(description.getTerm()) && des.getLang().equals(description.getLang())) {
description.setDescriptionId(des.getDescriptionId());
found = true;
break;
}
}
if (found) break;
}
if (!found) {
getChangeResult(changes, description, DESCRIPTION_WITHOUT_ID_COMPARATOR).fail(format("Description term '%s' not found.", description.getTerm()));
}
}

public List<ChangeResult<? extends SnomedComponent>> replaceDescriptions(
ComponentTransformationRequest request, List<DescriptionPojo> descriptions, List<ChangeResult<DescriptionReplacementPojo>> changes) throws BusinessServiceException {
if (descriptions.isEmpty()) {
Expand Down

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