use of com.b2international.snowowl.core.terminology.ComponentCategory in project snow-owl by b2ihealthcare.
the class SnomedReferenceSetMemberConverter method expandReferencedComponent.
private void expandReferencedComponent(List<SnomedReferenceSetMember> results) {
if (expand().containsKey(SnomedReferenceSetMember.Expand.REFERENCED_COMPONENT)) {
Options expandOptions = expand().get(SnomedReferenceSetMember.Expand.REFERENCED_COMPONENT, Options.class);
final Multimap<String, SnomedReferenceSetMember> referencedComponentIdToMemberMap = collectReferencedComponentIds(results);
final Multimap<ComponentCategory, String> componentCategoryToIdMap = collectReferencedComponentCategories(referencedComponentIdToMemberMap);
for (ComponentCategory category : componentCategoryToIdMap.keySet()) {
expandComponentCategory(expandOptions, referencedComponentIdToMemberMap, componentCategoryToIdMap, category);
}
}
}
use of com.b2international.snowowl.core.terminology.ComponentCategory in project snow-owl by b2ihealthcare.
the class IdRequest method execute.
@Override
public R execute(final C context) {
final IdActionRecorder recorder = new IdActionRecorder(context);
try {
final Multimap<ComponentCategory, SnomedComponentCreateRequest> componentCreateRequests = getComponentCreateRequests(next());
if (!componentCreateRequests.isEmpty()) {
try {
for (final ComponentCategory category : componentCreateRequests.keySet()) {
final Class<? extends SnomedDocument> documentClass = getDocumentClass(category);
final Collection<SnomedComponentCreateRequest> categoryRequests = componentCreateRequests.get(category);
final Set<String> coreComponentIds = FluentIterable.from(categoryRequests).filter(SnomedCoreComponentCreateRequest.class).filter(request -> request.getIdGenerationStrategy() instanceof ConstantIdStrategy).transform(request -> ((ConstantIdStrategy) request.getIdGenerationStrategy()).getId()).toSet();
final Set<String> refsetMemberIds = FluentIterable.from(categoryRequests).filter(SnomedRefSetMemberCreateRequest.class).transform(request -> request.getId()).toSet();
final Set<String> userRequestedIds = Sets.newHashSet(Iterables.concat(coreComponentIds, refsetMemberIds));
final Set<String> existingIds = getExistingIds(context, userRequestedIds, documentClass);
if (!existingIds.isEmpty()) {
// TODO: Report all existing identifiers
throw new AlreadyExistsException(category.getDisplayName(), Iterables.getFirst(existingIds, null));
} else {
if (!coreComponentIds.isEmpty()) {
recorder.register(coreComponentIds);
}
}
final Multimap<String, BaseSnomedComponentCreateRequest> requestsByNamespace = HashMultimap.create();
// index requests where an explicit namespace identifier is specified (use it directly)
categoryRequests.stream().filter(BaseSnomedComponentCreateRequest.class::isInstance).map(BaseSnomedComponentCreateRequest.class::cast).filter(request -> request.getIdGenerationStrategy() instanceof NamespaceIdStrategy).forEach(request -> {
requestsByNamespace.put(getNamespaceKey(request), request);
});
// convert requests that define a namespaceConceptId by extracting the namespaceId from the namespaceConcept's FSN
final Multimap<String, BaseSnomedComponentCreateRequest> requestsByNamespaceConceptId = HashMultimap.create();
categoryRequests.stream().filter(BaseSnomedComponentCreateRequest.class::isInstance).map(BaseSnomedComponentCreateRequest.class::cast).filter(request -> request.getIdGenerationStrategy() instanceof NamespaceConceptIdStrategy).forEach(request -> {
requestsByNamespaceConceptId.put(request.getIdGenerationStrategy().getNamespace(), request);
});
if (!requestsByNamespaceConceptId.isEmpty()) {
final Map<String, String> namespacesByNamespaceConceptId = context.service(NamespaceIdProvider.class).extractNamespaceIds(context, requestsByNamespaceConceptId.keySet(), false);
for (String namespaceConceptId : Set.copyOf(requestsByNamespaceConceptId.keySet())) {
Collection<BaseSnomedComponentCreateRequest> requests = requestsByNamespaceConceptId.removeAll(namespaceConceptId);
if (!namespacesByNamespaceConceptId.containsKey(namespaceConceptId)) {
throw new BadRequestException("There is no namespace value associated with the '%s' namespaceConcept's FSN.", namespaceConceptId);
}
requestsByNamespace.putAll(namespacesByNamespaceConceptId.get(namespaceConceptId), requests);
}
}
for (final String namespace : requestsByNamespace.keySet()) {
final String convertedNamespace = SnomedIdentifiers.INT_NAMESPACE.equals(namespace) ? null : namespace;
final Collection<BaseSnomedComponentCreateRequest> namespaceRequests = requestsByNamespace.get(namespace);
final int count = namespaceRequests.size();
final Set<String> uniqueIds = getUniqueIds(context, recorder, category, documentClass, count, convertedNamespace);
final Iterator<String> idsToUse = Iterators.consumingIterator(uniqueIds.iterator());
for (final BaseSnomedComponentCreateRequest createRequest : namespaceRequests) {
createRequest.setIdGenerationStrategy(new ConstantIdStrategy(idsToUse.next()));
}
checkState(!idsToUse.hasNext(), "More SNOMED CT ids have been requested than used.");
}
}
} finally {
// idGenerationSample.stop(registry.timer("idGenerationTime"));
}
}
final R commitInfo = next(context);
recorder.commit();
return commitInfo;
} catch (final Exception e) {
recorder.rollback();
throw e;
}
}
use of com.b2international.snowowl.core.terminology.ComponentCategory in project snow-owl by b2ihealthcare.
the class ConcreteDomainChangeConverter method expand.
@Override
public void expand(final List<ConcreteDomainChange> results) {
if (!expand().containsKey(ConcreteDomainChange.Expand.CONCRETE_DOMAIN_MEMBER)) {
return;
}
/*
* Depending on the CD member change search request, we might need to issue
* SNOMED CT searches against multiple branches; find out which ones we have.
*/
final Multimap<String, ConcreteDomainChange> itemsByBranch = getItemsByBranch(results);
// Check if we only need to load inferred CD members in their entirety
final Options expandOptions = expand().getOptions(ConcreteDomainChange.Expand.CONCRETE_DOMAIN_MEMBER);
final boolean inferredOnly = expandOptions.getBoolean("inferredOnly");
final Options cdMemberExpandOptions = expandOptions.getOptions("expand");
final Options referencedComponentOptions = cdMemberExpandOptions.getOptions(SnomedReferenceSetMember.Expand.REFERENCED_COMPONENT);
/*
* Remove this option from the member expand options map, so that member search
* does not expand the referenced component again
*/
final boolean needsReferencedComponent = cdMemberExpandOptions.keySet().remove(SnomedReferenceSetMember.Expand.REFERENCED_COMPONENT);
for (final String branch : itemsByBranch.keySet()) {
final Collection<ConcreteDomainChange> itemsForCurrentBranch = itemsByBranch.get(branch);
/*
* Expand referenced component on members via a separate search request, as they
* can be different from the referenced component on the "origin" member
*/
if (needsReferencedComponent) {
final List<ReasonerConcreteDomainMember> blankMembers = itemsForCurrentBranch.stream().filter(c -> !inferredOnly || ChangeNature.NEW.equals(c.getChangeNature())).map(ConcreteDomainChange::getConcreteDomainMember).collect(Collectors.toList());
final Multimap<String, ReasonerConcreteDomainMember> membersByReferencedComponent = Multimaps.index(blankMembers, ReasonerConcreteDomainMember::getReferencedComponentId);
final Multimap<ComponentCategory, String> referencedComponentsByCategory = Multimaps.index(membersByReferencedComponent.keySet(), SnomedIdentifiers::getComponentCategory);
for (final Entry<ComponentCategory, Collection<String>> categoryEntry : referencedComponentsByCategory.asMap().entrySet()) {
expandComponentCategory(branch, categoryEntry.getKey(), categoryEntry.getValue(), referencedComponentOptions, membersByReferencedComponent);
}
}
/*
* Then fetch all the required members (these will have a referenced component
* ID that should no longer be copied on inferred members). Note that the same "origin"
* member might be used for multiple eg. "new" counterparts.
*/
final Set<String> cdMemberUuids = itemsForCurrentBranch.stream().filter(c -> !inferredOnly || ChangeNature.NEW.equals(c.getChangeNature())).map(c -> c.getConcreteDomainMember().getOriginMemberId()).collect(Collectors.toSet());
final Request<BranchContext, SnomedReferenceSetMembers> cdMemberSearchRequest = SnomedRequests.prepareSearchMember().filterByIds(cdMemberUuids).setLimit(cdMemberUuids.size()).setExpand(cdMemberExpandOptions).setLocales(locales()).build();
final SnomedReferenceSetMembers cdMembers = new BranchRequest<>(branch, new RevisionIndexReadRequest<>(cdMemberSearchRequest)).execute(context());
final Map<String, SnomedReferenceSetMember> cdMembersByUuid = Maps.uniqueIndex(cdMembers, SnomedReferenceSetMember::getId);
/*
* Finally, set the member on the change item, but preserve the properties that
* were already set in "toResource"
*/
for (final ConcreteDomainChange item : itemsForCurrentBranch) {
final ReasonerConcreteDomainMember reasonerMember = item.getConcreteDomainMember();
final String memberUuid = reasonerMember.getOriginMemberId();
switch(item.getChangeNature()) {
case NEW:
{
final SnomedReferenceSetMember expandedMember = cdMembersByUuid.get(memberUuid);
final Map<String, Object> expandedProperties = expandedMember.getProperties();
// reasonerMember.setCharacteristicTypeId(...) is already set
// reasonerMember.setGroup(...) is already set
// reasonerMember.setReferencedComponent(...) is already set (or expanded)
reasonerMember.setReferenceSetId(expandedMember.getRefsetId());
// reasonerMember.setReleased(...) is already set
reasonerMember.setSerializedValue((String) expandedProperties.get(SnomedRf2Headers.FIELD_VALUE));
reasonerMember.setTypeId((String) expandedProperties.get(SnomedRf2Headers.FIELD_TYPE_ID));
}
break;
case UPDATED:
if (!inferredOnly) {
final SnomedReferenceSetMember expandedMember = cdMembersByUuid.get(memberUuid);
final Map<String, Object> expandedProperties = expandedMember.getProperties();
reasonerMember.setCharacteristicTypeId((String) expandedProperties.get(SnomedRf2Headers.FIELD_CHARACTERISTIC_TYPE_ID));
reasonerMember.setGroup((Integer) expandedProperties.get(SnomedRf2Headers.FIELD_RELATIONSHIP_GROUP));
// reasonerMember.setReferencedComponent(...) is already set (or expanded)
reasonerMember.setReferenceSetId(expandedMember.getRefsetId());
// reasonerMember.setReleased(...) is already set
// reasonerMember.setSerializedValue(...) is already set
reasonerMember.setTypeId((String) expandedProperties.get(SnomedRf2Headers.FIELD_TYPE_ID));
}
break;
case REDUNDANT:
if (!inferredOnly) {
final SnomedReferenceSetMember expandedMember = cdMembersByUuid.get(memberUuid);
final Map<String, Object> expandedProperties = expandedMember.getProperties();
reasonerMember.setCharacteristicTypeId((String) expandedProperties.get(SnomedRf2Headers.FIELD_CHARACTERISTIC_TYPE_ID));
reasonerMember.setGroup((Integer) expandedProperties.get(SnomedRf2Headers.FIELD_RELATIONSHIP_GROUP));
// reasonerMember.setReferencedComponent(...) is already set (or expanded)
reasonerMember.setReferenceSetId(expandedMember.getRefsetId());
// reasonerMember.setReleased(...) is already set
reasonerMember.setSerializedValue((String) expandedProperties.get(SnomedRf2Headers.FIELD_VALUE));
reasonerMember.setTypeId((String) expandedProperties.get(SnomedRf2Headers.FIELD_TYPE_ID));
}
break;
default:
throw new IllegalStateException(String.format("Unexpected CD member change '%s' found with UUID '%s'.", item.getChangeNature(), item.getConcreteDomainMember().getOriginMemberId()));
}
}
}
}
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