Examples with StatementFragment com.b2international.snowowl.snomed.datastore.StatementFragment used on opensource projects

Example 1 with StatementFragment

use of com.b2international.snowowl.snomed.datastore.StatementFragment in project snow-owl by b2ihealthcare.

the class NormalFormGenerator method computeChanges.

@Override
public final void computeChanges(final IProgressMonitor monitor, final OntologyChangeProcessor<StatementFragment> statementProcessor, final OntologyChangeProcessor<ConcreteDomainFragment> concreteDomainProcessor) {
    final Stopwatch stopwatch = Stopwatch.createStarted();
    LOGGER.info(">>> Distribution normal form generation");
    final LongList entries = reasonerTaxonomy.getIterationOrder();
    final SubMonitor subMonitor = SubMonitor.convert(monitor, "Generating distribution normal form...", entries.size() * 2);
    try {
        LongSet previousLayer = null;
        LongSet currentLayer = PrimitiveSets.newLongOpenHashSet();
        final Set<Long> graphTypeIds = reasonerTaxonomy.getPropertyChains().stream().map(PropertyChain::getDestinationType).collect(Collectors.toSet());
        // The first round can be skipped entirely, if no type IDs participate in a property chain
        final boolean propertyChainsPresent = !graphTypeIds.isEmpty();
        if (propertyChainsPresent) {
            // Initialize node graphs for properties we need to traverse
            LOGGER.info("--- Initializing node graphs for types: {}", graphTypeIds);
            graphTypeIds.forEach(id -> transitiveNodeGraphs.put(id, new NodeGraph()));
            // Round 1: build alternative hierarchies
            for (final LongIterator itr = entries.iterator(); itr.hasNext(); ) /* empty */
            {
                final long conceptId = itr.next();
                if (conceptId == ReasonerTaxonomyInferrer.DEPTH_CHANGE) {
                    if (previousLayer != null) {
                        invalidate(previousLayer);
                    }
                    previousLayer = currentLayer;
                    currentLayer = PrimitiveSets.newLongOpenHashSet();
                    continue;
                }
                precomputeProperties(conceptId, false);
                final Collection<StatementFragment> inferredNonIsAFragments = statementCache.get(conceptId);
                inferredNonIsAFragments.stream().filter(r -> transitiveNodeGraphs.keySet().contains(r.getTypeId())).filter(StatementFragmentWithDestination.class::isInstance).map(StatementFragmentWithDestination.class::cast).forEachOrdered(r -> transitiveNodeGraphs.get(r.getTypeId()).addParent(conceptId, r.getDestinationId()));
            }
            // Clear the last layer of concepts
            previousLayer = null;
            currentLayer = PrimitiveSets.newLongOpenHashSet();
            statementCache.clear();
            concreteDomainCache.clear();
        } else {
            LOGGER.info("--- Node graphs computation skipped, no types used for property chaining");
        }
        LOGGER.info("--- Use node graphs for hierarchy computation");
        // Round 2: record changes using the hierarchies
        for (final LongIterator itr = entries.iterator(); itr.hasNext(); ) /* empty */
        {
            final long conceptId = itr.next();
            if (conceptId == ReasonerTaxonomyInferrer.DEPTH_CHANGE) {
                if (previousLayer != null) {
                    invalidate(previousLayer);
                }
                previousLayer = currentLayer;
                currentLayer = PrimitiveSets.newLongOpenHashSet();
                continue;
            }
            // Run costly comparison of property chain hierarchies only if there are any
            precomputeProperties(conceptId, propertyChainsPresent);
            final Collection<StatementFragment> existingStatements = reasonerTaxonomy.getExistingInferredRelationships().get(conceptId);
            final Collection<StatementFragment> targetStatements = getTargetRelationships(conceptId);
            statementProcessor.apply(conceptId, existingStatements, targetStatements, StatementFragmentOrdering.INSTANCE, subMonitor.newChild(1));
            final Collection<ConcreteDomainFragment> existingMembers = reasonerTaxonomy.getInferredConcreteDomainMembers().get(Long.toString(conceptId));
            final Collection<ConcreteDomainFragment> targetMembers = getTargetMembers(conceptId);
            concreteDomainProcessor.apply(conceptId, existingMembers, targetMembers, ConcreteDomainChangeOrdering.INSTANCE, subMonitor.newChild(1));
        }
    } finally {
        subMonitor.done();
        LOGGER.info("<<< Distribution normal form generation [{}]", stopwatch.toString());
    }
}

Example 2 with StatementFragment

use of com.b2international.snowowl.snomed.datastore.StatementFragment in project snow-owl by b2ihealthcare.

the class NormalFormGenerator method toZeroUnionGroups.

private Iterable<NormalFormUnionGroup> toZeroUnionGroups(final Collection<StatementFragment> unionGroupRelationships, final Collection<ConcreteDomainFragment> unionGroupMembers, final boolean useNodeGraphs) {
    final ImmutableList.Builder<NormalFormUnionGroup> zeroUnionGroups = ImmutableList.builder();
    for (final StatementFragment unionGroupRelationship : unionGroupRelationships) {
        final NormalFormProperty normalFormProperty = toProperty(unionGroupRelationship, useNodeGraphs);
        zeroUnionGroups.add(new NormalFormUnionGroup(normalFormProperty));
    }
    for (final ConcreteDomainFragment unionGroupMember : unionGroupMembers) {
        final NormalFormValue normalFormValue = new NormalFormValue(unionGroupMember, reasonerTaxonomy);
        zeroUnionGroups.add(new NormalFormUnionGroup(normalFormValue));
    }
    return zeroUnionGroups.build();
}

Example 3 with StatementFragment

use of com.b2international.snowowl.snomed.datastore.StatementFragment in project snow-owl by b2ihealthcare.

the class NormalFormGenerator method precomputeProperties.

private void precomputeProperties(final long conceptId, final boolean useNodeGraphs) {
    final LongSet parentIds = reasonerTaxonomy.getInferredAncestors().getDestinations(conceptId, true);
    /*
		 * Non IS-A relationships are fetched from ancestors; redundancy must be removed. Since we are working through the list
		 * of concepts in breadth-first order, we only need to look at cached results from the direct parents, and "distill"
		 * a non-redundant set of components out of them.
		 */
    final LongKeyMap<Collection<StatementFragment>> candidateNonIsARelationships = PrimitiveMaps.newLongKeyOpenHashMap();
    for (final LongIterator itr = parentIds.iterator(); itr.hasNext(); ) /* empty */
    {
        final long parentId = itr.next();
        candidateNonIsARelationships.put(parentId, statementCache.get(parentId));
    }
    // Stated axiom fragments are non-IS A, but any stated relationships need to be filtered (if they are still present)
    final Collection<StatementFragment> ownStatedRelationships = reasonerTaxonomy.getStatedRelationships().get(conceptId);
    final Collection<StatementFragment> ownStatedNonIsaRelationships = ownStatedRelationships.stream().filter(r -> r.getTypeId() != IS_A).collect(Collectors.toList());
    candidateNonIsARelationships.put(conceptId, ImmutableList.<StatementFragment>builder().addAll(ownStatedNonIsaRelationships).addAll(reasonerTaxonomy.getAxiomNonIsARelationships().get(conceptId)).addAll(reasonerTaxonomy.getAdditionalGroupedRelationships().get(conceptId)).build());
    // Collect existing inferred relationships for cross-referencing group numbers
    final Collection<StatementFragment> ownInferredRelationships = reasonerTaxonomy.getExistingInferredRelationships().get(conceptId);
    final Collection<StatementFragment> ownInferredNonIsaRelationships = ownInferredRelationships.stream().filter(r -> r.getTypeId() != IS_A).collect(Collectors.toList());
    /*
		 * Do the same as the above, but for CD members
		 */
    final LongKeyMap<Collection<ConcreteDomainFragment>> candidateMembers = PrimitiveMaps.newLongKeyOpenHashMap();
    for (final LongIterator itr = parentIds.iterator(); itr.hasNext(); ) /* empty */
    {
        final long parentId = itr.next();
        candidateMembers.put(parentId, concreteDomainCache.get(parentId));
    }
    final String referencedComponentId = Long.toString(conceptId);
    final Collection<ConcreteDomainFragment> ownStatedMembers = reasonerTaxonomy.getStatedConcreteDomainMembers().get(referencedComponentId);
    final Collection<ConcreteDomainFragment> ownAdditionalGroupedMembers = reasonerTaxonomy.getAdditionalGroupedConcreteDomainMembers().get(referencedComponentId);
    candidateMembers.put(conceptId, ImmutableList.<ConcreteDomainFragment>builder().addAll(ownStatedMembers).addAll(ownAdditionalGroupedMembers).build());
    final Collection<ConcreteDomainFragment> ownInferredMembers = reasonerTaxonomy.getInferredConcreteDomainMembers().get(referencedComponentId);
    // Remove redundancy
    final NormalFormGroupSet targetGroupSet = getTargetGroupSet(conceptId, parentIds, ownInferredNonIsaRelationships, ownInferredMembers, candidateNonIsARelationships, candidateMembers, useNodeGraphs);
    // Extract results; place them in the cache, so following concepts can re-use it
    statementCache.put(conceptId, ImmutableList.copyOf(relationshipsFromGroupSet(targetGroupSet)));
    concreteDomainCache.put(conceptId, ImmutableList.copyOf(membersFromGroupSet(targetGroupSet)));
}