Examples with SnomedReferenceSetMember com.b2international.snowowl.snomed.core.domain.refset.SnomedReferenceSetMember used on opensource projects

Example 26 with SnomedReferenceSetMember

use of com.b2international.snowowl.snomed.core.domain.refset.SnomedReferenceSetMember in project snow-owl by b2ihealthcare.

the class SnomedReferenceSetMemberConverter method expandTargetComponent.

private void expandTargetComponent(List<SnomedReferenceSetMember> results) {
    if (expand().containsKey(SnomedReferenceSetMember.Expand.TARGET_COMPONENT)) {
        final Options expandOptions = expand().get(SnomedReferenceSetMember.Expand.TARGET_COMPONENT, Options.class);
        final Multimap<String, SnomedReferenceSetMember> membersByTargetComponent = HashMultimap.create();
        for (SnomedReferenceSetMember member : results) {
            final Map<String, Object> props = member.getProperties();
            if (props.containsKey(SnomedRf2Headers.FIELD_TARGET_COMPONENT_ID)) {
                membersByTargetComponent.put(((String) props.get(SnomedRf2Headers.FIELD_TARGET_COMPONENT_ID)), member);
            }
        }
        final Multimap<ComponentCategory, String> targetComponentIdsByCategory = Multimaps.index(membersByTargetComponent.keySet(), new Function<String, ComponentCategory>() {

            @Override
            public ComponentCategory apply(String id) {
                return SnomedIdentifiers.getComponentCategory(id);
            }
        });
        for (ComponentCategory category : targetComponentIdsByCategory.keySet()) {
            final Collection<String> targetComponentIds = targetComponentIdsByCategory.get(category);
            final Map<String, ? extends SnomedCoreComponent> componentsById = Maps.uniqueIndex(getComponents(category, targetComponentIds, expandOptions.get("expand", Options.class)), IComponent::getId);
            for (String targetComponentId : targetComponentIds) {
                final SnomedCoreComponent targetComponent = componentsById.get(targetComponentId);
                if (targetComponent != null) {
                    for (SnomedReferenceSetMember member : membersByTargetComponent.get(targetComponentId)) {
                        final Map<String, Object> newProps = newHashMap(member.getProperties());
                        newProps.put(SnomedReferenceSetMember.Expand.TARGET_COMPONENT, targetComponent);
                        ((SnomedReferenceSetMember) member).setProperties(newProps);
                    }
                }
            }
        }
    }
}

Example 27 with SnomedReferenceSetMember

use of com.b2international.snowowl.snomed.core.domain.refset.SnomedReferenceSetMember 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);
        }
    }
}

Example 28 with SnomedReferenceSetMember

use of com.b2international.snowowl.snomed.core.domain.refset.SnomedReferenceSetMember in project snow-owl by b2ihealthcare.

the class ReasonerTaxonomyBuilder method addActiveConcreteDomainMembers.

/*
	 * XXX: sortedMembers should be sorted by referenced component ID; we can not verify this in advance
	 */
public ReasonerTaxonomyBuilder addActiveConcreteDomainMembers(final Stream<SnomedReferenceSetMember> sortedMembers) {
    entering("Registering active concrete domain members using stream");
    final List<ConcreteDomainFragment> statedFragments = new ArrayList<>(SCROLL_LIMIT);
    final List<ConcreteDomainFragment> inferredFragments = new ArrayList<>(SCROLL_LIMIT);
    final List<ConcreteDomainFragment> additionalGroupedFragments = new ArrayList<>(SCROLL_LIMIT);
    String lastReferencedComponentId = "";
    for (final List<SnomedReferenceSetMember> chunk : Iterables.partition(sortedMembers::iterator, SCROLL_LIMIT)) {
        for (final SnomedReferenceSetMember member : chunk) {
            final String characteristicTypeId = (String) member.getProperties().get(SnomedRf2Headers.FIELD_CHARACTERISTIC_TYPE_ID);
            if (member.isActive() && SnomedRefSetUtil.getConcreteDomainRefSetMap().containsValue(member.getRefsetId()) && CD_CHARACTERISTIC_TYPE_IDS.contains(characteristicTypeId) && !excludedModuleIds.contains(member.getModuleId())) {
                final String referencedComponentId = member.getReferencedComponent().getId();
                if (lastReferencedComponentId.isEmpty()) {
                    lastReferencedComponentId = referencedComponentId;
                } else if (!lastReferencedComponentId.equals(referencedComponentId)) {
                    if (conceptMap.containsKey(lastReferencedComponentId)) {
                        statedConcreteDomainMembers.putAll(lastReferencedComponentId, statedFragments);
                        inferredConcreteDomainMembers.putAll(lastReferencedComponentId, inferredFragments);
                        additionalGroupedConcreteDomainMembers.putAll(lastReferencedComponentId, additionalGroupedFragments);
                    } else {
                        LOGGER.debug("Not registering CD members for concept {} as it is inactive.", lastReferencedComponentId);
                    }
                    statedFragments.clear();
                    inferredFragments.clear();
                    additionalGroupedFragments.clear();
                    lastReferencedComponentId = referencedComponentId;
                }
                final String memberId = member.getId();
                final long refsetId = Long.parseLong(member.getRefsetId());
                final String serializedValue = (String) member.getProperties().get(SnomedRf2Headers.FIELD_VALUE);
                final Integer group = (Integer) member.getProperties().get(SnomedRf2Headers.FIELD_RELATIONSHIP_GROUP);
                final long typeId = Long.parseLong((String) member.getProperties().get(SnomedRf2Headers.FIELD_TYPE_ID));
                final ConcreteDomainFragment fragment = new ConcreteDomainFragment(memberId, refsetId, group, serializedValue, typeId, // XXX: "injected" CD members will not set this flag correctly, but they should only be used in equivalence checks
                false);
                if (Concepts.STATED_RELATIONSHIP.equals(characteristicTypeId)) {
                    statedFragments.add(fragment);
                } else if (Concepts.ADDITIONAL_RELATIONSHIP.equals(characteristicTypeId) && group > 0) {
                    additionalGroupedFragments.add(fragment);
                } else if (Concepts.INFERRED_RELATIONSHIP.equals(characteristicTypeId)) {
                    inferredFragments.add(fragment);
                }
            }
        }
    }
    if (!lastReferencedComponentId.isEmpty()) {
        if (conceptMap.containsKey(lastReferencedComponentId)) {
            statedConcreteDomainMembers.putAll(lastReferencedComponentId, statedFragments);
            inferredConcreteDomainMembers.putAll(lastReferencedComponentId, inferredFragments);
            additionalGroupedConcreteDomainMembers.putAll(lastReferencedComponentId, additionalGroupedFragments);
        } else {
            LOGGER.debug("Not registering CD members for concept {} as it is inactive.", lastReferencedComponentId);
        }
        statedFragments.clear();
        inferredFragments.clear();
        additionalGroupedFragments.clear();
    }
    leaving("Registering active concrete domain members using stream");
    return this;
}

Example 29 with SnomedReferenceSetMember

use of com.b2international.snowowl.snomed.core.domain.refset.SnomedReferenceSetMember in project snow-owl by b2ihealthcare.

the class SnomedDescriptionAcceptabilityUpdateRequest method doExecute.

@Override
protected void doExecute(TransactionContext context, SnomedComponentDocument componentToUpdate) {
    final Iterable<SnomedReferenceSetMember> existingMembers = create ? Collections.emptySet() : SnomedRequests.prepareSearchMember().all().filterByReferencedComponent(componentToUpdate.getId()).filterByRefSetType(Collections.singleton(SnomedRefSetType.LANGUAGE)).build().execute(context);
    final Map<String, Acceptability> newLanguageMembersToCreate = newHashMap(newAcceptabilityMap);
    final ModuleIdProvider moduleIdSupplier = context.service(ModuleIdProvider.class);
    // check if there are existing matches
    for (SnomedReferenceSetMember existingMember : existingMembers) {
        final String acceptabilityId = (String) existingMember.getProperties().get(SnomedRf2Headers.FIELD_ACCEPTABILITY_ID);
        final Acceptability acceptability = Acceptability.getByConceptId(acceptabilityId);
        final String languageReferenceSetId = existingMember.getRefsetId();
        if (null == acceptability) {
            continue;
        }
        final SnomedRefSetMemberIndexEntry.Builder updatedMember = SnomedRefSetMemberIndexEntry.builder(existingMember);
        final SnomedRefSetMemberIndexEntry oldRevision = updatedMember.build();
        if (acceptability.equals(newLanguageMembersToCreate.get(languageReferenceSetId))) {
            // Exact match: make sure that the member is active
            if (ensureMemberActive(context, existingMember, updatedMember)) {
                context.update(oldRevision, updatedMember.build());
            }
            // Remove it from the working list, as we have found a match
            newLanguageMembersToCreate.remove(languageReferenceSetId);
        } else if (newLanguageMembersToCreate.containsKey(languageReferenceSetId)) {
            // Change acceptability, set status to active if required, place it in the supplied module
            final Acceptability newAcceptability = newLanguageMembersToCreate.get(languageReferenceSetId);
            updatedMember.field(SnomedRf2Headers.FIELD_ACCEPTABILITY_ID, newAcceptability.getConceptId());
            ensureMemberActive(context, existingMember, updatedMember);
            updateModule(context, existingMember, updatedMember, moduleIdSupplier.apply(componentToUpdate));
            unsetEffectiveTime(existingMember, updatedMember);
            context.update(oldRevision, updatedMember.build());
            newLanguageMembersToCreate.remove(languageReferenceSetId);
        } else {
            // Not acceptable in this language reference set, remove or inactivate if already released
            if (removeOrDeactivate(context, existingMember, updatedMember)) {
                context.update(oldRevision, updatedMember.build());
            }
        }
    }
    for (final Entry<String, Acceptability> languageMemberEntry : newLanguageMembersToCreate.entrySet()) {
        SnomedComponents.newLanguageMember().withAcceptability(languageMemberEntry.getValue()).withRefSet(languageMemberEntry.getKey()).withModuleId(moduleIdSupplier.apply(componentToUpdate)).withReferencedComponent(componentToUpdate.getId()).addTo(context);
    }
}

Example 30 with SnomedReferenceSetMember

use of com.b2international.snowowl.snomed.core.domain.refset.SnomedReferenceSetMember in project snow-owl by b2ihealthcare.

the class SaveJobRequest method mergeEquivalentConcepts.

private Set<String> mergeEquivalentConcepts(final BranchContext context, final BulkRequestBuilder<TransactionContext> bulkRequestBuilder, final SnomedNamespaceAndModuleAssigner assigner) {
    if (!fixEquivalences) {
        return Collections.emptySet();
    }
    // XXX: Restrict merging to active components only
    final String expand = "equivalentConcepts(expand(" + "descriptions(active:true)," + "relationships(active:true)," + "inboundRelationships(active:true)," + "members(active:true)))";
    final Multimap<SnomedConcept, SnomedConcept> equivalentConcepts = HashMultimap.create();
    ClassificationRequests.prepareSearchEquivalentConceptSet().setLimit(SCROLL_LIMIT).setExpand(expand).filterByClassificationId(classificationId).stream(context).flatMap(EquivalentConceptSets::stream).filter(equivalentSet -> !equivalentSet.isUnsatisfiable()).forEach(equivalentSet -> {
        final List<SnomedConcept> conceptsToRemove = newArrayList(equivalentSet.getEquivalentConcepts());
        final SnomedConcept conceptToKeep = conceptsToRemove.remove(0);
        equivalentConcepts.putAll(conceptToKeep, conceptsToRemove);
    });
    // Are there any equivalent concepts present? or Were all equivalent concepts unsatisfiable?
    if (equivalentConcepts.isEmpty()) {
        return Collections.emptySet();
    }
    IEquivalentConceptMerger merger = Extensions.getFirstPriorityExtension(IEquivalentConceptMerger.EXTENSION_POINT, IEquivalentConceptMerger.class);
    if (merger == null) {
        merger = new IEquivalentConceptMerger.Default();
    }
    final String mergerName = merger.getClass().getSimpleName();
    LOG.info("Reasoner service will use {} for equivalent concept merging.", mergerName);
    final Set<String> conceptIdsToSkip = merger.merge(equivalentConcepts);
    final Set<String> conceptIdsToKeep = equivalentConcepts.keySet().stream().map(SnomedConcept::getId).collect(Collectors.toSet());
    // Prepare to provide namespace-module for inbound relationship source concepts as well
    final Set<String> relationshipChangeConceptIds = newHashSet(conceptIdsToKeep);
    // Add source concepts on new/about to be inactivated inbound relationships, pointing to "kept" concepts
    for (final SnomedConcept conceptToKeep : equivalentConcepts.keySet()) {
        for (final SnomedRelationship relationship : conceptToKeep.getInboundRelationships()) {
            if (relationship.getId().startsWith(IEquivalentConceptMerger.PREFIX_NEW)) {
                relationshipChangeConceptIds.add(relationship.getSourceId());
            } else if (!relationship.isActive()) {
                relationshipChangeConceptIds.add(relationship.getSourceId());
            }
        }
    }
    assigner.collectRelationshipNamespacesAndModules(relationshipChangeConceptIds, context);
    for (final SnomedConcept conceptToKeep : equivalentConcepts.keySet()) {
        for (final SnomedRelationship relationship : conceptToKeep.getInboundRelationships()) {
            // Already handled as another concept's outbound relationship
            if (relationship.getId() == null) {
                continue;
            }
            if (relationship.getId().startsWith(IEquivalentConceptMerger.PREFIX_NEW)) {
                relationship.setId(null);
                addComponent(bulkRequestBuilder, assigner, relationship);
            } else if (!relationship.isActive()) {
                removeOrDeactivate(bulkRequestBuilder, assigner, relationship);
            }
        }
        for (final SnomedRelationship relationship : conceptToKeep.getRelationships()) {
            // Already handled as another concept's inbound relationship
            if (relationship.getId() == null) {
                continue;
            }
            if (relationship.getId().startsWith(IEquivalentConceptMerger.PREFIX_NEW)) {
                relationship.setId(null);
                addComponent(bulkRequestBuilder, assigner, relationship);
            } else if (!relationship.isActive()) {
                removeOrDeactivate(bulkRequestBuilder, assigner, relationship);
            }
        }
    }
    // CD members are always "outbound", however, so the concept SCTID set can be reduced
    assigner.clear();
    assigner.collectConcreteDomainModules(conceptIdsToKeep, context);
    for (final SnomedConcept conceptToKeep : equivalentConcepts.keySet()) {
        for (final SnomedReferenceSetMember member : conceptToKeep.getMembers()) {
            if (member.getId().startsWith(IEquivalentConceptMerger.PREFIX_NEW)) {
                member.setId(null);
                addComponent(bulkRequestBuilder, assigner, member);
            } else if (member.getId().startsWith(IEquivalentConceptMerger.PREFIX_UPDATED)) {
                // Trim the prefix from the ID to restore its original form
                member.setId(member.getId().substring(IEquivalentConceptMerger.PREFIX_UPDATED.length()));
                bulkRequestBuilder.add(member.toUpdateRequest());
            } else if (!member.isActive()) {
                removeOrDeactivate(bulkRequestBuilder, assigner, member);
            }
        }
    }
    // Descriptions are also "outbound"
    assigner.clear();
    assigner.collectRelationshipNamespacesAndModules(conceptIdsToKeep, context);
    for (final SnomedConcept conceptToKeep : equivalentConcepts.keySet()) {
        for (final SnomedDescription description : conceptToKeep.getDescriptions()) {
            if (description.getId().startsWith(IEquivalentConceptMerger.PREFIX_NEW)) {
                description.setId(null);
                addComponent(bulkRequestBuilder, assigner, description);
            } else if (description.getId().startsWith(IEquivalentConceptMerger.PREFIX_UPDATED)) {
                // Trim the prefix from the ID to restore its original form
                description.setId(description.getId().substring(IEquivalentConceptMerger.PREFIX_UPDATED.length()));
                bulkRequestBuilder.add(description.toUpdateRequest());
            } else if (!description.isActive()) {
                removeOrDeactivate(bulkRequestBuilder, assigner, description);
            }
        }
    }
    // Inactivation of "removed" concepts also requires modules to be collected according to the assigner rules
    assigner.clear();
    assigner.collectRelationshipNamespacesAndModules(conceptIdsToSkip, context);
    for (final SnomedConcept conceptToRemove : equivalentConcepts.values()) {
        // Check if the concept needs to be removed or deactivated
        if (!conceptToRemove.isActive()) {
            removeOrDeactivate(bulkRequestBuilder, assigner, conceptToRemove);
        }
    }
    assigner.clear();
    return conceptIdsToSkip;
}