Examples with SnomedNamespaceAndModuleAssigner com.b2international.snowowl.snomed.datastore.id.assigner.SnomedNamespaceAndModuleAssigner used on opensource projects

Example 1 with SnomedNamespaceAndModuleAssigner

use of com.b2international.snowowl.snomed.datastore.id.assigner.SnomedNamespaceAndModuleAssigner in project snow-owl by b2ihealthcare.

the class SaveJobRequest method createNamespaceAndModuleAssigner.

private SnomedNamespaceAndModuleAssigner createNamespaceAndModuleAssigner(final BranchContext context) {
    // Override assigner type if given
    final String selectedType;
    if (assignerType != null) {
        selectedType = assignerType;
    } else {
        final TerminologyResource resource = context.service(TerminologyResource.class);
        selectedType = (String) resource.getSettings().getOrDefault(NAMESPACE_AND_MODULE_ASSIGNER, DEFAULT_NAMESPACE_AND_MODULE_ASSIGNER);
    }
    final SnomedNamespaceAndModuleAssigner assigner = SnomedNamespaceAndModuleAssigner.create(context, selectedType, moduleId, namespace);
    LOG.info("Reasoner service will use {} for relationship/concrete domain namespace and module assignment.", assigner);
    return assigner;
}

Example 2 with SnomedNamespaceAndModuleAssigner

use of com.b2international.snowowl.snomed.datastore.id.assigner.SnomedNamespaceAndModuleAssigner in project snow-owl by b2ihealthcare.

the class SaveJobRequest method applyChanges.

private void applyChanges(final SubMonitor subMonitor, final BranchContext context, final BulkRequestBuilder<TransactionContext> bulkRequestBuilder) {
    final SnomedNamespaceAndModuleAssigner assigner = createNamespaceAndModuleAssigner(context);
    final Set<String> conceptIdsToSkip = mergeEquivalentConcepts(context, bulkRequestBuilder, assigner);
    applyRelationshipChanges(context, bulkRequestBuilder, assigner, conceptIdsToSkip);
    if (handleConcreteDomains) {
        // CD member support in configuration overrides the flag on the save request
        final SnomedCoreConfiguration snomedCoreConfiguration = context.service(SnomedCoreConfiguration.class);
        if (snomedCoreConfiguration.isConcreteDomainSupported()) {
            applyConcreteDomainChanges(context, bulkRequestBuilder, assigner, conceptIdsToSkip);
        }
    }
}

Example 3 with SnomedNamespaceAndModuleAssigner

use of com.b2international.snowowl.snomed.datastore.id.assigner.SnomedNamespaceAndModuleAssigner 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;
}