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

Example 31 with SnomedConceptDocument

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

the class SnomedDescendantsExpander method expand.

@Override
protected void expand(List<SnomedConcept> results, final Set<String> conceptIds, Options descendantExpandOptions, boolean direct) {
    try {
        final int limit = getLimit(descendantExpandOptions);
        final ExpressionBuilder expression = Expressions.builder();
        expression.filter(active());
        final ExpressionBuilder descendantFilter = Expressions.builder();
        if (stated) {
            descendantFilter.should(statedParents(conceptIds));
            if (!direct) {
                descendantFilter.should(statedAncestors(conceptIds));
            }
        } else {
            descendantFilter.should(parents(conceptIds));
            if (!direct) {
                descendantFilter.should(ancestors(conceptIds));
            }
        }
        expression.filter(descendantFilter.build());
        final Query<SnomedConceptDocument> query = Query.select(SnomedConceptDocument.class).where(expression.build()).limit((conceptIds.size() == 1 && limit == 0) ? limit : Integer.MAX_VALUE).build();
        final RevisionSearcher searcher = context().service(RevisionSearcher.class);
        final Hits<SnomedConceptDocument> hits = searcher.search(query);
        if (hits.getTotal() < 1) {
            final SnomedConcepts descendants = new SnomedConcepts(0, 0);
            for (SnomedConcept concept : results) {
                if (stated) {
                    concept.setStatedDescendants(descendants);
                } else {
                    concept.setDescendants(descendants);
                }
            }
            return;
        }
        // XXX won't work if number of results is greater than one, either use custom ConceptSearch or figure out how to expand descendants effectively
        if (conceptIds.size() == 1 && limit == 0) {
            for (SnomedConcept concept : results) {
                final SnomedConcepts descendants = new SnomedConcepts(0, hits.getTotal());
                if (stated) {
                    concept.setStatedDescendants(descendants);
                } else {
                    concept.setDescendants(descendants);
                }
            }
            return;
        }
        final Multimap<String, String> descendantsByAncestor = TreeMultimap.create();
        for (SnomedConceptDocument hit : hits) {
            final Set<String> parentsAndAncestors = newHashSet();
            if (stated) {
                parentsAndAncestors.addAll(LongSets.toStringSet(hit.getStatedParents()));
                if (!direct) {
                    parentsAndAncestors.addAll(LongSets.toStringSet(hit.getStatedAncestors()));
                }
            } else {
                parentsAndAncestors.addAll(LongSets.toStringSet(hit.getParents()));
                if (!direct) {
                    parentsAndAncestors.addAll(LongSets.toStringSet(hit.getAncestors()));
                }
            }
            parentsAndAncestors.retainAll(conceptIds);
            for (String ancestor : parentsAndAncestors) {
                descendantsByAncestor.put(ancestor, hit.getId());
            }
        }
        final Collection<String> componentIds = newHashSet(descendantsByAncestor.values());
        if (limit > 0 && !componentIds.isEmpty()) {
            // query descendants again
            final SnomedConcepts descendants = SnomedRequests.prepareSearchConcept().all().filterByIds(componentIds).setLocales(locales()).setExpand(descendantExpandOptions.get("expand", Options.class)).build().execute(context());
            final Map<String, SnomedConcept> descendantsById = newHashMap();
            descendantsById.putAll(Maps.uniqueIndex(descendants, SnomedConcept::getId));
            for (SnomedConcept concept : results) {
                final Collection<String> descendantIds = descendantsByAncestor.get(concept.getId());
                final List<SnomedConcept> currentDescendants = FluentIterable.from(descendantIds).limit(limit).transform(Functions.forMap(descendantsById)).toList();
                final SnomedConcepts descendantConcepts = new SnomedConcepts(currentDescendants, null, limit, descendantIds.size());
                if (stated) {
                    concept.setStatedDescendants(descendantConcepts);
                } else {
                    concept.setDescendants(descendantConcepts);
                }
            }
        } else {
            for (SnomedConcept concept : results) {
                final Collection<String> descendantIds = descendantsByAncestor.get(concept.getId());
                final SnomedConcepts descendants = new SnomedConcepts(limit, descendantIds.size());
                if (stated) {
                    concept.setStatedDescendants(descendants);
                } else {
                    concept.setDescendants(descendants);
                }
            }
        }
    } catch (IOException e) {
        throw SnowowlRuntimeException.wrap(e);
    }
}

Example 32 with SnomedConceptDocument

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

the class DetachedContainerChangeProcessor method process.

@Override
public void process(StagingArea staging, RevisionSearcher searcher) throws IOException {
    final Set<String> deletedCoreComponentIds = newHashSet();
    final Set<String> deletedConceptIds = newHashSet();
    staging.getRemovedObjects().forEach(detachedObject -> {
        if (detachedObject instanceof SnomedComponentDocument) {
            String id = ((SnomedComponentDocument) detachedObject).getId();
            deletedCoreComponentIds.add(id);
            if (detachedObject instanceof SnomedConceptDocument) {
                deletedConceptIds.add(id);
            }
        }
    });
    if (deletedCoreComponentIds.isEmpty() && deletedConceptIds.isEmpty()) {
        return;
    }
    // deleting concepts should delete all of its descriptions, relationships, and inbound relationships
    Query.select(SnomedDescriptionIndexEntry.class).where(SnomedDescriptionIndexEntry.Expressions.concepts(deletedConceptIds)).limit(PAGE_SIZE).build().stream(searcher).flatMap(Hits::stream).forEachOrdered(description -> {
        deletedCoreComponentIds.add(description.getId());
        stageRemove(description);
    });
    Query.select(SnomedRelationshipIndexEntry.class).where(Expressions.builder().should(SnomedRelationshipIndexEntry.Expressions.sourceIds(deletedConceptIds)).should(SnomedRelationshipIndexEntry.Expressions.destinationIds(deletedConceptIds)).build()).limit(PAGE_SIZE).build().stream(searcher).flatMap(Hits::stream).forEachOrdered(relationship -> {
        deletedCoreComponentIds.add(relationship.getId());
        stageRemove(relationship);
    });
    // deleting core components should delete all referring members as well
    ExpressionBuilder referringMembersQuery = Expressions.builder().should(SnomedRefSetMemberIndexEntry.Expressions.referencedComponentIds(deletedCoreComponentIds)).should(SnomedRefSetMemberIndexEntry.Expressions.refsetIds(deletedConceptIds));
    SnomedRf2Headers.MEMBER_FIELDS_WITH_COMPONENT_ID.forEach(memberField -> {
        referringMembersQuery.should(Expressions.matchAny(memberField, deletedCoreComponentIds));
    });
    Query.select(SnomedRefSetMemberIndexEntry.class).where(referringMembersQuery.build()).limit(PAGE_SIZE).build().stream(searcher).flatMap(Hits::stream).forEachOrdered(member -> stageRemove(member));
}

Example 33 with SnomedConceptDocument

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

the class ConceptChangeProcessorAxiomTest method deleteEmpty.

@Test
public void deleteEmpty() throws Exception {
    final SnomedConceptDocument concept = concept().activeMemberOf(Collections.singleton(Concepts.REFSET_OWL_AXIOM)).memberOf(Collections.singleton(Concepts.REFSET_OWL_AXIOM)).build();
    final SnomedRefSetMemberIndexEntry member = createOwlAxiom(concept.getId(), "").build();
    indexRevision(MAIN, concept, member);
    stageRemove(member);
    final ConceptChangeProcessor processor = process();
    assertEquals(1, processor.getChangedMappings().size());
    final SnomedConceptDocument expected = docWithDefaults(concept).build();
    final Revision actual = Iterables.getOnlyElement(processor.getChangedMappings().values()).getNewRevision();
    assertDocEquals(expected, actual);
    assertEquals(0, processor.getNewMappings().size());
    assertEquals(0, processor.getDeletions().size());
}

Example 34 with SnomedConceptDocument

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

the class ConceptChangeProcessorAxiomTest method newSubClassOfAxiom_TwoTargets.

@Test
public void newSubClassOfAxiom_TwoTargets() throws Exception {
    SnomedConceptDocument concept = concept().build();
    SnomedConceptDocument parentConcept = concept().build();
    SnomedConceptDocument parentConcept2 = concept().build();
    indexRevision(MAIN, concept, parentConcept, parentConcept2);
    statedChangedConceptIds.add(Long.parseLong(concept.getId()));
    statedChangedConceptIds.add(Long.parseLong(parentConcept.getId()));
    statedChangedConceptIds.add(Long.parseLong(parentConcept2.getId()));
    SnomedRefSetMemberIndexEntry member = createOwlAxiom(concept.getId(), String.format("SubClassOf(:%s ObjectIntersectionOf(:%s :%s))", concept.getId(), parentConcept.getId(), parentConcept2.getId())).build();
    stageNew(member);
    final ConceptChangeProcessor processor = process();
    assertEquals(1, processor.getChangedMappings().size());
    final SnomedConceptDocument expected = docWithDefaults(concept).statedParents(Long.parseLong(parentConcept.getId()), Long.parseLong(parentConcept2.getId())).statedAncestors(IComponent.ROOT_IDL).activeMemberOf(Collections.singleton(Concepts.REFSET_OWL_AXIOM)).memberOf(Collections.singleton(Concepts.REFSET_OWL_AXIOM)).build();
    final Revision actual = Iterables.getOnlyElement(processor.getChangedMappings().values()).getNewRevision();
    assertDocEquals(expected, actual);
    assertEquals(0, processor.getNewMappings().size());
    assertEquals(0, processor.getDeletions().size());
}

Example 35 with SnomedConceptDocument

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

the class ConceptChangeProcessorAxiomTest method updateEmptyAxiom.

@Test
public void updateEmptyAxiom() throws Exception {
    SnomedConceptDocument concept = concept().activeMemberOf(Collections.singleton(Concepts.REFSET_OWL_AXIOM)).memberOf(Collections.singleton(Concepts.REFSET_OWL_AXIOM)).build();
    SnomedConceptDocument parentConcept = concept().build();
    SnomedRefSetMemberIndexEntry member = createOwlAxiom(concept.getId(), "").build();
    indexRevision(MAIN, concept, parentConcept, member);
    statedChangedConceptIds.add(Long.parseLong(concept.getId()));
    statedChangedConceptIds.add(Long.parseLong(parentConcept.getId()));
    // update axiom
    stageChange(member, SnomedRefSetMemberIndexEntry.builder(member).owlExpression(String.format("SubClassOf(:%s :%s)", concept.getId(), parentConcept.getId())).build());
    final ConceptChangeProcessor processor = process();
    assertEquals(1, processor.getChangedMappings().size());
    final SnomedConceptDocument expected = docWithDefaults(concept).statedParents(Long.parseLong(parentConcept.getId())).statedAncestors(IComponent.ROOT_IDL).activeMemberOf(Collections.singleton(Concepts.REFSET_OWL_AXIOM)).memberOf(Collections.singleton(Concepts.REFSET_OWL_AXIOM)).build();
    final Revision actual = Iterables.getOnlyElement(processor.getChangedMappings().values()).getNewRevision();
    assertDocEquals(expected, actual);
    assertEquals(0, processor.getNewMappings().size());
    assertEquals(0, processor.getDeletions().size());
}