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

Example 1 with RevisionSearcher

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

the class RevisionIndexReadRequest method execute.

@Override
public B execute(final BranchContext context) {
    final String branchPath = context.path();
    RevisionIndex index = context.service(RevisionIndex.class);
    if (snapshot) {
        return index.read(branchPath, searcher -> {
            try {
                return next(context.inject().bind(RevisionSearcher.class, searcher).build());
            } catch (QueryParseException e) {
                throw new IllegalQueryParameterException(e.getMessage());
            }
        });
    } else {
        return next(context.inject().bind(RevisionSearcher.class, new RevisionSearcher() {

            @Override
            public <T> Aggregation<T> aggregate(AggregationBuilder<T> aggregation) throws IOException {
                return index.read(branchPath, searcher -> searcher.aggregate(aggregation));
            }

            @Override
            public Searcher searcher() {
                return index.read(branchPath, searcher -> searcher.searcher());
            }

            @Override
            public <T> Hits<T> search(Query<T> query) throws IOException {
                return index.read(branchPath, searcher -> searcher.search(query));
            }

            @Override
            public <T> Iterable<T> get(Class<T> type, Iterable<String> keys) throws IOException {
                return index.read(branchPath, searcher -> searcher.get(type, keys));
            }

            @Override
            public <T> T get(Class<T> type, String key) throws IOException {
                return index.read(branchPath, searcher -> searcher.get(type, key));
            }

            @Override
            public String branch() {
                return branchPath;
            }
        }).build());
    }
}

Example 2 with RevisionSearcher

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

the class Taxonomies method updateTaxonomy.

private static TaxonomyGraphStatus updateTaxonomy(RevisionSearcher searcher, SnomedOWLExpressionConverter expressionConverter, StagingArea staging, TaxonomyGraph graphToUpdate, String characteristicTypeId) throws IOException {
    LOGGER.trace("Processing changes taxonomic information.");
    staging.getNewObjects(SnomedRelationshipIndexEntry.class).filter(relationship -> characteristicTypeId.equals(relationship.getCharacteristicTypeId())).forEach(newRelationship -> updateEdge(newRelationship, graphToUpdate));
    final Set<String> relationshipsToExcludeFromReactivatedConcepts = newHashSet();
    staging.getChangedRevisions(SnomedRelationshipIndexEntry.class).map(diff -> (SnomedRelationshipIndexEntry) diff.newRevision).filter(relationship -> characteristicTypeId.equals(relationship.getCharacteristicTypeId())).forEach(dirtyRelationship -> {
        relationshipsToExcludeFromReactivatedConcepts.add(dirtyRelationship.getId());
        updateEdge(dirtyRelationship, graphToUpdate);
    });
    staging.getRemovedObjects(SnomedRelationshipIndexEntry.class).filter(relationship -> characteristicTypeId.equals(relationship.getCharacteristicTypeId())).forEach(relationship -> {
        relationshipsToExcludeFromReactivatedConcepts.add(relationship.getId());
        graphToUpdate.removeEdge(relationship.getId());
    });
    if (Concepts.STATED_RELATIONSHIP.equals(characteristicTypeId)) {
        staging.getNewObjects(SnomedRefSetMemberIndexEntry.class).filter(member -> SnomedRefSetType.OWL_AXIOM == member.getReferenceSetType()).forEach(member -> updateEdge(member, graphToUpdate, expressionConverter));
        staging.getChangedRevisions(SnomedRefSetMemberIndexEntry.class).map(diff -> (SnomedRefSetMemberIndexEntry) diff.newRevision).filter(member -> SnomedRefSetType.OWL_AXIOM == member.getReferenceSetType()).forEach(member -> updateEdge(member, graphToUpdate, expressionConverter));
        staging.getRemovedObjects(SnomedRefSetMemberIndexEntry.class).filter(member -> SnomedRefSetType.OWL_AXIOM == member.getReferenceSetType()).map(SnomedRefSetMemberIndexEntry::getId).forEach(graphToUpdate::removeEdge);
    }
    staging.getNewObjects(SnomedConceptDocument.class).forEach(newConcept -> updateConcept(newConcept, graphToUpdate));
    staging.getRemovedObjects(SnomedConceptDocument.class).forEach(concept -> graphToUpdate.removeNode(concept.getId()));
    final Set<String> conceptWithPossibleMissingRelationships = newHashSet();
    staging.getChangedRevisions(SnomedConceptDocument.class, Collections.singleton(SnomedConceptDocument.Fields.ACTIVE)).forEach(diff -> {
        final RevisionPropertyDiff propDiff = diff.getRevisionPropertyDiff(SnomedConceptDocument.Fields.ACTIVE);
        final boolean oldValue = Boolean.parseBoolean(propDiff.getOldValue());
        final boolean newValue = Boolean.parseBoolean(propDiff.getNewValue());
        final String conceptId = diff.newRevision.getId();
        if (!oldValue && newValue) {
            // make sure the node is part of the new tree
            graphToUpdate.addNode(conceptId);
            conceptWithPossibleMissingRelationships.add(conceptId);
        }
    });
    if (!conceptWithPossibleMissingRelationships.isEmpty()) {
        Hits<String[]> possibleMissingRelationships = searcher.search(Query.select(String[].class).from(SnomedRelationshipIndexEntry.class).fields(SnomedRelationshipIndexEntry.Fields.ID, SnomedRelationshipIndexEntry.Fields.SOURCE_ID, SnomedRelationshipIndexEntry.Fields.DESTINATION_ID).where(Expressions.builder().filter(SnomedRelationshipIndexEntry.Expressions.active()).filter(SnomedRelationshipIndexEntry.Expressions.characteristicTypeId(characteristicTypeId)).filter(SnomedRelationshipIndexEntry.Expressions.typeId(Concepts.IS_A)).filter(SnomedRelationshipIndexEntry.Expressions.sourceIds(conceptWithPossibleMissingRelationships)).mustNot(SnomedRelationshipIndexEntry.Expressions.ids(relationshipsToExcludeFromReactivatedConcepts)).build()).limit(Integer.MAX_VALUE).build());
        for (String[] relationship : possibleMissingRelationships) {
            graphToUpdate.addNode(relationship[2]);
            graphToUpdate.addEdge(relationship[0], Long.parseLong(relationship[1]), new long[] { Long.parseLong(relationship[2]) });
        }
    }
    LOGGER.trace("Rebuilding taxonomic information based on the changes.");
    return graphToUpdate.update();
}

Example 3 with RevisionSearcher

use of com.b2international.index.revision.RevisionSearcher 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 4 with RevisionSearcher

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

the class SnomedValidationIssueDetailExtension method extendIssueDetails.

private void extendIssueDetails(BranchContext context, Collection<ValidationIssue> issues) {
    final RevisionSearcher searcher = context.service(RevisionSearcher.class);
    final Multimap<String, ValidationIssue> issuesByComponentId = Multimaps.index(issues, issue -> issue.getAffectedComponent().getComponentId());
    final Multimap<ComponentCategory, String> issueComponentIdsByComponentCategory = HashMultimap.create();
    issues.stream().forEach(issue -> {
        final ComponentCategory componentCategory = getComponentCategory(issue.getAffectedComponent().getComponentType());
        issueComponentIdsByComponentCategory.put(componentCategory, issue.getAffectedComponent().getComponentId());
    });
    final Multimap<String, String> issueIdsByConceptIds = HashMultimap.create();
    final Set<String> alreadyFetchedConceptIds = Sets.newHashSet();
    for (ComponentCategory category : issueComponentIdsByComponentCategory.keySet()) {
        final Query<String[]> query = buildQuery(category, issueComponentIdsByComponentCategory.get(category));
        query.stream(searcher).forEachOrdered(hits -> {
            for (String[] hit : hits) {
                String id = hit[0];
                String status = hit[1];
                String moduleId = hit[2];
                issuesByComponentId.get(id).forEach(validationIssue -> {
                    validationIssue.setDetails(COMPONENT_STATUS, status);
                    validationIssue.setDetails(COMPONENT_MODULE_ID, moduleId);
                    if (CONCEPT == category) {
                        validationIssue.setDetails(CONCEPT_STATUS, status);
                        validationIssue.setDetails(SnomedDocument.Fields.EFFECTIVE_TIME, Long.parseLong(hit[3]));
                        alreadyFetchedConceptIds.add(id);
                    } else if (DESCRIPTION == category || RELATIONSHIP == category || SET_MEMBER == category) {
                        validationIssue.setDetails(SnomedDocument.Fields.EFFECTIVE_TIME, Long.parseLong(hit[3]));
                        final String containerConceptId = hit[4];
                        if (!Strings.isNullOrEmpty(containerConceptId) && (!issueIdsByConceptIds.containsKey(containerConceptId) || !alreadyFetchedConceptIds.contains(containerConceptId))) {
                            issueIdsByConceptIds.put(containerConceptId, id);
                        }
                        // in case of description just add the already fetched term as label to the issue, concepts and relationship will get their
                        if (DESCRIPTION == category) {
                            validationIssue.setAffectedComponentLabels(Collections.singletonList(hit[5]));
                        }
                    }
                });
            }
        });
    }
    if (!issueIdsByConceptIds.isEmpty()) {
        final Query<String[]> conceptStatusQuery = Query.select(String[].class).from(SnomedConceptDocument.class).fields(SnomedConceptDocument.Fields.ID, SnomedConceptDocument.Fields.ACTIVE).where(SnomedConceptDocument.Expressions.ids(issueIdsByConceptIds.keySet())).limit(SCROLL_SIZE).build();
        conceptStatusQuery.stream(searcher).flatMap(Hits::stream).forEachOrdered(hit -> {
            Collection<String> issueIds = issueIdsByConceptIds.get(hit[0]);
            issueIds.stream().forEach(id -> {
                issuesByComponentId.get(id).forEach(validationIssue -> validationIssue.setDetails(CONCEPT_STATUS, hit[1]));
            });
        });
    }
}

Example 5 with RevisionSearcher

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

the class SnomedValidationIssueDetailExtension method extendRelationshipIssueLabels.

private void extendRelationshipIssueLabels(BranchContext context, Collection<ValidationIssue> issues, Map<String, Object> ruleParameters) {
    final RevisionSearcher searcher = context.service(RevisionSearcher.class);
    final List<ValidationIssue> relationshipIssues = issues.stream().filter(issue -> SnomedRelationship.TYPE == issue.getAffectedComponent().getComponentType()).collect(Collectors.toList());
    if (relationshipIssues.isEmpty()) {
        return;
    }
    final Multimap<String, ValidationIssue> issuesByRelationshipId = Multimaps.index(relationshipIssues, issue -> issue.getAffectedComponent().getComponentId());
    final Set<String> conceptsToFetch = newHashSet();
    final Map<String, String> relationshipFragmentsByRelationshipId = Maps.newHashMap();
    searcher.stream(Query.select(String[].class).from(SnomedRelationshipIndexEntry.class).fields(SnomedRelationshipIndexEntry.Fields.ID, SnomedRelationshipIndexEntry.Fields.SOURCE_ID, SnomedRelationshipIndexEntry.Fields.TYPE_ID, SnomedRelationshipIndexEntry.Fields.DESTINATION_ID, SnomedRelationshipIndexEntry.Fields.VALUE_TYPE, SnomedRelationshipIndexEntry.Fields.NUMERIC_VALUE, SnomedRelationshipIndexEntry.Fields.STRING_VALUE).where(SnomedRelationshipIndexEntry.Expressions.ids(issuesByRelationshipId.keySet())).limit(SCROLL_SIZE).build()).forEach(hits -> {
        for (String[] hit : hits) {
            final String id = hit[0];
            final String sourceId = hit[1];
            final String typeId = hit[2];
            final String destinationId = hit[3];
            final String valueType = hit[4];
            final String numericValue = hit[5];
            final String stringValue = hit[6];
            String destination = "";
            conceptsToFetch.add(sourceId);
            conceptsToFetch.add(typeId);
            if (!Strings.isNullOrEmpty(destinationId)) {
                conceptsToFetch.add(destinationId);
                destination = destinationId;
            } else {
                if (RelationshipValueType.DECIMAL.name().equals(valueType) || RelationshipValueType.INTEGER.name().equals(valueType)) {
                    destination = DecimalUtils.decode(numericValue).toString();
                } else if (RelationshipValueType.STRING.name().equals(valueType)) {
                    destination = stringValue;
                }
            }
            relationshipFragmentsByRelationshipId.put(id, String.format("%s|%s|%s", sourceId, typeId, destination));
        }
    });
    Map<String, String> affectedComponentLabelsByConcept = getAffectedComponentLabels(context, ruleParameters, conceptsToFetch);
    if (!affectedComponentLabelsByConcept.isEmpty()) {
        issuesByRelationshipId.values().forEach(issue -> {
            final String[] relationshipFragments = relationshipFragmentsByRelationshipId.get(issue.getAffectedComponent().getComponentId()).split("[|]");
            final String sourceId = relationshipFragments[0];
            final String typeId = relationshipFragments[1];
            final String destinationIdOrValue = relationshipFragments[2];
            final String sourceTerm = affectedComponentLabelsByConcept.getOrDefault(sourceId, sourceId);
            final String typeTerm = affectedComponentLabelsByConcept.getOrDefault(typeId, typeId);
            final String destinationTerm = affectedComponentLabelsByConcept.getOrDefault(destinationIdOrValue, destinationIdOrValue);
            issue.setAffectedComponentLabels(ImmutableList.of(String.format("%s - %s - %s", sourceTerm, typeTerm, destinationTerm)));
        });
    }
}