Examples with RevisionSearcher com.b2international.index.revision.RevisionSearcher used on opensource projects

Example 11 with RevisionSearcher

use of com.b2international.index.revision.RevisionSearcher 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 12 with RevisionSearcher

use of com.b2international.index.revision.RevisionSearcher in project snow-owl by b2ihealthcare.

the class EclExpression method resolve.

public Promise<Set<String>> resolve(final BranchContext context) {
    if (promise == null) {
        RevisionSearcher searcher = context.service(RevisionSearcher.class);
        boolean cached = context.optionalService(PathWithVersion.class).isPresent();
        promise = resolveToExpression(context).then(expression -> {
            // shortcut to extract IDs from the query itself if possible
            if (SnomedEclEvaluationRequest.canExtractIds(expression)) {
                return SnomedEclEvaluationRequest.extractIds(expression);
            }
            try {
                return newHashSet(searcher.search(Query.select(String.class).from(SnomedConceptDocument.class).fields(SnomedConceptDocument.Fields.ID).where(expression).limit(Integer.MAX_VALUE).cached(cached).build()));
            } catch (IOException e) {
                throw new SnowowlRuntimeException(e);
            }
        });
    }
    return promise;
}

Example 13 with RevisionSearcher

use of com.b2international.index.revision.RevisionSearcher in project snow-owl by b2ihealthcare.

the class ConceptChangeProcessor method process.

@Override
public void process(StagingArea staging, RevisionSearcher searcher) throws IOException {
    // collect member changes
    this.referringRefSets = HashMultimap.create(memberChangeProcessor.process(staging, searcher));
    processNewConcepts(staging);
    // collect dirty concepts that require additional properties to be set for index
    final Map<String, RevisionDiff> dirtyConceptDiffsById = Maps.uniqueIndex(staging.getChangedRevisions(SnomedConceptDocument.class).iterator(), diff -> diff.newRevision.getId());
    final Set<String> dirtyConceptIds = collectDirtyConceptIds(staging);
    // remaining new/dirty/detached descriptions should be properly processed for preferredDescriptions field
    final Map<String, SnomedDescriptionIndexEntry> affectedDescriptionsById = getDescriptionDocuments(staging, searcher);
    final Multimap<String, SnomedDescriptionIndexEntry> affectedDescriptionsByConcept = Multimaps.index(affectedDescriptionsById.values(), SnomedDescriptionIndexEntry::getConceptId);
    dirtyConceptIds.addAll(affectedDescriptionsByConcept.keySet());
    // remove all new/detached concept IDs, we've already processed them
    staging.getRemovedObjects(SnomedConceptDocument.class).map(SnomedConceptDocument::getId).forEach(dirtyConceptIds::remove);
    staging.getNewObjects(SnomedConceptDocument.class).map(SnomedConceptDocument::getId).forEach(dirtyConceptIds::remove);
    if (!dirtyConceptIds.isEmpty()) {
        final Map<ObjectId, RevisionDiff> changedRevisions = staging.getChangedRevisions();
        // fetch all dirty concept documents by their ID
        final Set<String> missingCurrentConceptIds = dirtyConceptIds.stream().filter(id -> !changedRevisions.containsKey(ObjectId.of(SnomedConcept.TYPE, id))).collect(Collectors.toSet());
        final Map<String, SnomedConceptDocument> currentConceptDocumentsById = newHashMap(Maps.uniqueIndex(searcher.get(SnomedConceptDocument.class, missingCurrentConceptIds), Revision::getId));
        dirtyConceptIds.stream().map(id -> ObjectId.of(SnomedConcept.TYPE, id)).filter(changedRevisions::containsKey).map(changedRevisions::get).map(diff -> (SnomedConceptDocument) diff.oldRevision).forEach(doc -> currentConceptDocumentsById.put(doc.getId(), doc));
        // update dirty concepts
        for (final String id : dirtyConceptIds) {
            final SnomedConceptDocument concept = dirtyConceptDiffsById.containsKey(id) ? (SnomedConceptDocument) dirtyConceptDiffsById.get(id).newRevision : null;
            final SnomedConceptDocument currentDoc = currentConceptDocumentsById.get(id);
            if (currentDoc == null) {
                throw new IllegalStateException("Current concept revision should not be null for: " + id);
            }
            final Builder doc = SnomedConceptDocument.builder(currentDoc);
            final Collection<SnomedDescriptionIndexEntry> affectedDescriptions = affectedDescriptionsByConcept.get(id);
            if (!affectedDescriptions.isEmpty()) {
                final Map<String, SnomedDescriptionFragment> updatedPreferredDescriptions = newHashMap(Maps.uniqueIndex(currentDoc.getPreferredDescriptions(), SnomedDescriptionFragment::getId));
                // add new/dirty fragments if they are preferred and active terms
                for (SnomedDescriptionIndexEntry affectedDescription : affectedDescriptions) {
                    if (staging.isNew(affectedDescription) || staging.isChanged(affectedDescription)) {
                        updatedPreferredDescriptions.remove(affectedDescription.getId());
                        if (affectedDescription.isActive() && !getPreferredLanguageMembers(affectedDescription).isEmpty()) {
                            updatedPreferredDescriptions.put(affectedDescription.getId(), toDescriptionFragment(affectedDescription));
                        }
                    }
                }
                // remove deleted descriptions
                for (SnomedDescriptionIndexEntry affectedDescription : affectedDescriptions) {
                    if (staging.isRemoved(affectedDescription)) {
                        updatedPreferredDescriptions.remove(affectedDescription.getId());
                    }
                }
                final List<SnomedDescriptionFragment> preferredDescriptions = updatedPreferredDescriptions.values().stream().sorted(DESCRIPTION_FRAGMENT_ORDER).collect(Collectors.toList());
                update(doc, preferredDescriptions, concept, currentDoc);
            } else {
                update(doc, currentDoc.getPreferredDescriptions(), concept, currentDoc);
            }
            stageChange(currentDoc, doc.build());
        }
    }
}

Example 14 with RevisionSearcher

use of com.b2international.index.revision.RevisionSearcher in project snow-owl by b2ihealthcare.

the class DescriptionChangeProcessor method process.

@Override
public void process(StagingArea staging, RevisionSearcher searcher) throws IOException {
    final Map<String, Multimap<Acceptability, RefSetMemberChange>> acceptabilityChangesByDescription = new DescriptionAcceptabilityChangeProcessor().process(staging, searcher);
    final Multimap<String, RefSetMemberChange> referringRefSets = HashMultimap.create(memberChangeProcessor.process(staging, searcher));
    // (re)index new and dirty descriptions
    final Map<String, SnomedDescriptionIndexEntry> newDescriptionsById = staging.getNewObjects(SnomedDescriptionIndexEntry.class).collect(Collectors.toMap(description -> description.getId(), description -> description));
    final Map<String, SnomedDescriptionIndexEntry> changedDescriptionsById = staging.getChangedRevisions(SnomedDescriptionIndexEntry.class).collect(Collectors.toMap(diff -> diff.newRevision.getId(), diff -> (SnomedDescriptionIndexEntry) diff.newRevision));
    final Set<String> changedDescriptionIds = newHashSet(changedDescriptionsById.keySet());
    final Set<String> referencedDescriptionIds = newHashSet(referringRefSets.keySet());
    referencedDescriptionIds.removeAll(newDescriptionsById.keySet());
    changedDescriptionIds.addAll(referencedDescriptionIds);
    // load the known descriptions
    final Iterable<SnomedDescriptionIndexEntry> changedDescriptionHits = searcher.get(SnomedDescriptionIndexEntry.class, changedDescriptionIds);
    final Map<String, SnomedDescriptionIndexEntry> changedDescriptionRevisionsById = Maps.uniqueIndex(changedDescriptionHits, Revision::getId);
    // load missing descriptions with only changed acceptability values
    final Set<String> descriptionsToBeLoaded = newHashSet();
    for (String descriptionWithAccepatibilityChange : acceptabilityChangesByDescription.keySet()) {
        if (!newDescriptionsById.containsKey(descriptionWithAccepatibilityChange) && !changedDescriptionIds.contains(descriptionWithAccepatibilityChange)) {
            descriptionsToBeLoaded.add(descriptionWithAccepatibilityChange);
        }
    }
    // process changes
    for (final String id : Iterables.concat(newDescriptionsById.keySet(), changedDescriptionIds)) {
        if (newDescriptionsById.containsKey(id)) {
            final SnomedDescriptionIndexEntry description = newDescriptionsById.get(id);
            final Builder doc = SnomedDescriptionIndexEntry.builder(description);
            processChanges(id, doc, null, acceptabilityChangesByDescription.get(id), referringRefSets);
            stageNew(doc.build());
        } else if (changedDescriptionIds.contains(id)) {
            final SnomedDescriptionIndexEntry currentDoc = changedDescriptionRevisionsById.get(id);
            if (currentDoc == null) {
                throw new IllegalStateException(String.format("Current description revision should not be null for: %s", id));
            }
            final SnomedDescriptionIndexEntry description = changedDescriptionsById.get(id);
            final Builder doc;
            if (description != null) {
                doc = SnomedDescriptionIndexEntry.builder(description);
            } else {
                doc = SnomedDescriptionIndexEntry.builder(currentDoc);
            }
            processChanges(id, doc, currentDoc, acceptabilityChangesByDescription.get(id), referringRefSets);
            stageChange(currentDoc, doc.build());
        } else {
            throw new IllegalStateException(String.format("Description %s is missing from new and dirty maps", id));
        }
    }
    // process cascading acceptability changes in unchanged docs
    if (!descriptionsToBeLoaded.isEmpty()) {
        for (SnomedDescriptionIndexEntry unchangedDescription : searcher.get(SnomedDescriptionIndexEntry.class, descriptionsToBeLoaded)) {
            final Builder doc = SnomedDescriptionIndexEntry.builder(unchangedDescription);
            processChanges(unchangedDescription.getId(), doc, unchangedDescription, acceptabilityChangesByDescription.get(unchangedDescription.getId()), HashMultimap.<String, RefSetMemberChange>create());
            stageChange(unchangedDescription, doc.build());
        }
    }
}

Example 15 with RevisionSearcher

use of com.b2international.index.revision.RevisionSearcher in project snow-owl by b2ihealthcare.

the class ReferringMemberChangeProcessor method process.

public Multimap<String, RefSetMemberChange> process(StagingArea staging, RevisionSearcher searcher) throws IOException {
    final Multimap<String, RefSetMemberChange> memberChanges = HashMultimap.create();
    // process new members
    staging.getNewObjects(SnomedRefSetMemberIndexEntry.class).filter(this::byReferencedComponentType).forEach((newMember) -> {
        addChange(memberChanges, newMember, MemberChangeKind.ADDED);
    });
    // process dirty members
    staging.getChangedRevisions(SnomedRefSetMemberIndexEntry.class).filter(diff -> byReferencedComponentType((SnomedRefSetMemberIndexEntry) diff.newRevision)).forEach((diff) -> {
        RevisionPropertyDiff propChange = diff.getRevisionPropertyDiff(SnomedRefSetMemberIndexEntry.Fields.ACTIVE);
        if (propChange != null) {
            addChange(memberChanges, (SnomedRefSetMemberIndexEntry) diff.newRevision, MemberChangeKind.CHANGED);
        }
    });
    // process detached members
    staging.getRemovedObjects(SnomedRefSetMemberIndexEntry.class).filter(this::byReferencedComponentType).forEach(doc -> {
        final String uuid = doc.getId();
        final String referencedComponentId = doc.getReferencedComponentId();
        final String refSetId = doc.getRefsetId();
        memberChanges.put(referencedComponentId, new RefSetMemberChange(uuid, refSetId, MemberChangeKind.REMOVED, doc.isActive()));
    });
    return memberChanges;
}