Examples with SnomedOWLRelationshipDocument com.b2international.snowowl.snomed.datastore.index.entry.SnomedOWLRelationshipDocument used on opensource projects

Example 1 with SnomedOWLRelationshipDocument

use of com.b2international.snowowl.snomed.datastore.index.entry.SnomedOWLRelationshipDocument in project snow-owl by b2ihealthcare.

the class Taxonomies method updateEdge.

private static void updateEdge(SnomedRefSetMemberIndexEntry member, TaxonomyGraph graphToUpdate, SnomedOWLExpressionConverter expressionConverter) {
    if (member.isActive()) {
        SnomedOWLExpressionConverterResult result = expressionConverter.toSnomedOWLRelationships(member.getReferencedComponentId(), member.getOwlExpression());
        if (!CompareUtils.isEmpty(result.getClassAxiomRelationships())) {
            /*
				 * XXX: IS A relationships are expected to have a destination ID, not a value,
				 * but we do not check this explicitly here -- Long#parseLong will throw a
				 * NumberFormatException if it encounters a null value.
				 */
            final long[] destinationIds = result.getClassAxiomRelationships().stream().filter(r -> Concepts.IS_A.equals(r.getTypeId())).map(SnomedOWLRelationshipDocument::getDestinationId).mapToLong(Long::parseLong).toArray();
            graphToUpdate.addEdge(member.getId(), Long.parseLong(member.getReferencedComponentId()), destinationIds);
        } else {
            graphToUpdate.removeEdge(member.getId());
        }
    } else {
        graphToUpdate.removeEdge(member.getId());
    }
}

Example 2 with SnomedOWLRelationshipDocument

use of com.b2international.snowowl.snomed.datastore.index.entry.SnomedOWLRelationshipDocument in project snow-owl by b2ihealthcare.

the class Taxonomies method getStatements.

private static Collection<Object[]> getStatements(RevisionSearcher searcher, LongCollection conceptIds, String characteristicTypeId, boolean filterByConceptIds) throws IOException {
    // merge stated relationships and OWL axiom relationships into a single array
    ImmutableList.Builder<Object[]> isaStatementsBuilder = ImmutableList.builder();
    final Set<String> concepts = LongSets.toStringSet(conceptIds);
    ExpressionBuilder activeIsaRelationshipQuery = Expressions.builder().filter(active()).filter(typeId(Concepts.IS_A)).filter(characteristicTypeId(characteristicTypeId));
    if (filterByConceptIds) {
        activeIsaRelationshipQuery.filter(sourceIds(concepts)).filter(destinationIds(concepts));
    }
    final Query<String[]> activeStatedISARelationshipsQuery = Query.select(String[].class).from(SnomedRelationshipIndexEntry.class).fields(SnomedRelationshipIndexEntry.Fields.ID, SnomedRelationshipIndexEntry.Fields.SOURCE_ID, SnomedRelationshipIndexEntry.Fields.DESTINATION_ID).where(activeIsaRelationshipQuery.build()).limit(Integer.MAX_VALUE).build();
    Hits<String[]> activeIsaRelationships = searcher.search(activeStatedISARelationshipsQuery);
    activeIsaRelationships.forEach(activeIsaRelationship -> {
        isaStatementsBuilder.add(new Object[] { activeIsaRelationship[0], Long.parseLong(activeIsaRelationship[1]), new long[] { Long.parseLong(activeIsaRelationship[2]) } });
    });
    activeIsaRelationships = null;
    if (Concepts.STATED_RELATIONSHIP.equals(characteristicTypeId)) {
        // search existing axioms defined for the given set of conceptIds
        ExpressionBuilder activeOwlAxiomMemberQuery = Expressions.builder().filter(active());
        if (filterByConceptIds) {
            activeOwlAxiomMemberQuery.filter(SnomedRefSetMemberIndexEntry.Expressions.referencedComponentIds(concepts)).filter(Expressions.nestedMatch(SnomedRefSetMemberIndexEntry.Fields.CLASS_AXIOM_RELATIONSHIP, Expressions.builder().filter(typeId(Concepts.IS_A)).filter(destinationIds(concepts)).build()));
        } else {
            activeOwlAxiomMemberQuery.filter(Expressions.nestedMatch(SnomedRefSetMemberIndexEntry.Fields.CLASS_AXIOM_RELATIONSHIP, Expressions.builder().filter(typeId(Concepts.IS_A)).build()));
        }
        final Query<SnomedRefSetMemberIndexEntry> activeAxiomISARelationshipsQuery = Query.select(SnomedRefSetMemberIndexEntry.class).where(activeOwlAxiomMemberQuery.build()).limit(Integer.MAX_VALUE).build();
        Hits<SnomedRefSetMemberIndexEntry> activeAxiomISARelationships = searcher.search(activeAxiomISARelationshipsQuery);
        activeAxiomISARelationships.forEach(owlMember -> {
            if (!CompareUtils.isEmpty(owlMember.getClassAxiomRelationships())) {
                // XXX: breaks with a NumberFormatException if any of the IS A relationships has a value
                long[] destinationIds = owlMember.getClassAxiomRelationships().stream().filter(classAxiom -> Concepts.IS_A.equals(classAxiom.getTypeId())).map(SnomedOWLRelationshipDocument::getDestinationId).mapToLong(Long::parseLong).toArray();
                isaStatementsBuilder.add(new Object[] { owlMember.getId(), Long.parseLong(owlMember.getReferencedComponentId()), destinationIds });
            }
        });
        activeAxiomISARelationships = null;
    }
    return isaStatementsBuilder.build();
}

Example 3 with SnomedOWLRelationshipDocument

use of com.b2international.snowowl.snomed.datastore.index.entry.SnomedOWLRelationshipDocument in project snow-owl by b2ihealthcare.

the class SnomedOWLExpressionConverter method toSnomedOWLRelationships.

public SnomedOWLExpressionConverterResult toSnomedOWLRelationships(String conceptId, String axiomExpression) {
    // Only attempt to convert axioms which the OWL toolkit supports
    if (Strings.isNullOrEmpty(axiomExpression) || !isAxiomSupported(axiomExpression)) {
        return SnomedOWLExpressionConverterResult.EMPTY;
    }
    try {
        final Long conceptIdLong = Long.valueOf(conceptId);
        final AxiomRepresentation axiomRepresentation = convertAxiom(conceptId, axiomExpression);
        if (axiomRepresentation == null) {
            return SnomedOWLExpressionConverterResult.EMPTY;
        }
        boolean gci = false;
        Map<Integer, List<Relationship>> relationships = null;
        if (conceptIdLong.equals(axiomRepresentation.getLeftHandSideNamedConcept())) {
            relationships = axiomRepresentation.getRightHandSideRelationships();
        } else if (conceptIdLong.equals(axiomRepresentation.getRightHandSideNamedConcept())) {
            /*
				 * XXX: EquivalentClasses axioms are not ordered in any meaningful way, so it
				 * can happen that the class expression representing relationships falls on the left-hand side
				 */
            gci = axiomRepresentation.isPrimitive();
            relationships = axiomRepresentation.getLeftHandSideRelationships();
        } else {
            LOG.warn("Illegal assignment of referenced component id ('{}') was detected for the OWL expression: '{}'", conceptId, axiomExpression);
        }
        if (relationships == null) {
            return SnomedOWLExpressionConverterResult.EMPTY;
        }
        final List<SnomedOWLRelationshipDocument> convertedRelationships = relationships.values().stream().flatMap(List::stream).map(relationship -> {
            if (relationship.isConcrete()) {
                return SnomedOWLRelationshipDocument.createValue(Long.toString(relationship.getTypeId()), toRelationshipValue(relationship.getValue()), relationship.getGroup());
            } else {
                return SnomedOWLRelationshipDocument.create(Long.toString(relationship.getTypeId()), Long.toString(relationship.getDestinationId()), relationship.getGroup());
            }
        }).collect(Collectors.toList());
        return new SnomedOWLExpressionConverterResult(gci ? null : convertedRelationships, gci ? convertedRelationships : null);
    } catch (ApiException e) {
        throw e;
    } catch (Exception e) {
        LOG.error("Failed to convert OWL axiom '{}' to relationship representations for concept '{}'", axiomExpression, conceptId, e);
        return SnomedOWLExpressionConverterResult.EMPTY;
    }
}

Example 4 with SnomedOWLRelationshipDocument

use of com.b2international.snowowl.snomed.datastore.index.entry.SnomedOWLRelationshipDocument in project snow-owl by b2ihealthcare.

the class SnomedOWLRelationshipConverter method fromSnomedOwlRelationships.

public String fromSnomedOwlRelationships(final boolean gci, final boolean isPrimitive, final String conceptId, final List<SnomedOWLRelationshipDocument> owlRelationships) {
    final AxiomRepresentation axiomRepresentation = new AxiomRepresentation();
    final Long conceptIdLong = Long.valueOf(conceptId);
    final ListMultimap<Integer, Relationship> relationships = ArrayListMultimap.create();
    for (final SnomedOWLRelationshipDocument owlRelationship : owlRelationships) {
        final Relationship relationship;
        if (owlRelationship.hasValue()) {
            relationship = new Relationship(owlRelationship.getRelationshipGroup(), Long.valueOf(owlRelationship.getTypeId()), toConcreteValue(owlRelationship.getValueAsObject()));
        } else {
            relationship = new Relationship(owlRelationship.getRelationshipGroup(), Long.valueOf(owlRelationship.getTypeId()), Long.valueOf(owlRelationship.getDestinationId()));
        }
        relationships.put(relationship.getGroup(), relationship);
    }
    final Map<Integer, List<Relationship>> relationshipsMap = Multimaps.asMap(relationships);
    if (gci) {
        axiomRepresentation.setLeftHandSideRelationships(relationshipsMap);
        axiomRepresentation.setRightHandSideNamedConcept(conceptIdLong);
    } else {
        axiomRepresentation.setLeftHandSideNamedConcept(conceptIdLong);
        axiomRepresentation.setRightHandSideRelationships(relationshipsMap);
    }
    axiomRepresentation.setPrimitive(isPrimitive);
    return convertRelationshipToAxiom(conceptId, axiomRepresentation);
}