Examples with TransactionContext com.b2international.snowowl.core.domain.TransactionContext used on opensource projects

Example 6 with TransactionContext

use of com.b2international.snowowl.core.domain.TransactionContext in project snow-owl by b2ihealthcare.

the class EvaluateQueryRefSetMemberRequest method execute.

@Override
public QueryRefSetMemberEvaluation execute(BranchContext context) {
    // TODO support pre-population???
    final boolean active;
    final String query;
    final String targetReferenceSet;
    if (context instanceof TransactionContext) {
        SnomedRefSetMemberIndexEntry member = ((TransactionContext) context).lookup(memberId, SnomedRefSetMemberIndexEntry.class);
        query = member.getQuery();
        targetReferenceSet = member.getReferencedComponentId();
        active = member.isActive();
    } else {
        final SnomedReferenceSetMember member = SnomedRequests.prepareGetMember(memberId).build().execute(context);
        query = (String) member.getProperties().get(SnomedRf2Headers.FIELD_QUERY);
        targetReferenceSet = member.getReferencedComponent().getId();
        active = member.isActive();
    }
    if (!active) {
        return new QueryRefSetMemberEvaluationImpl(memberId, targetReferenceSet, Collections.emptyList());
    }
    if (Strings.isNullOrEmpty(query)) {
        return new QueryRefSetMemberEvaluationImpl(memberId, targetReferenceSet, Collections.emptyList());
    }
    // add all matching first
    final Map<String, SnomedConcept> conceptsToAdd = newHashMap();
    // GET matching members of a query
    SnomedRequests.prepareSearchConcept().filterByEcl(query).setLimit(10_000).stream(context).flatMap(SnomedConcepts::stream).forEach(match -> conceptsToAdd.put(match.getId(), match));
    final Collection<SnomedReferenceSetMember> membersToRemove = newHashSet();
    final Collection<SnomedReferenceSetMember> conceptsToActivate = newHashSet();
    // then re-evaluate all current members of the target simple type reference set
    SnomedRequests.prepareSearchMember().filterByRefSet(targetReferenceSet).setLimit(10_000).stream(context).flatMap(SnomedReferenceSetMembers::stream).forEach(member -> {
        final String referencedComponentId = member.getReferencedComponent().getId();
        if (conceptsToAdd.containsKey(referencedComponentId)) {
            if (!member.isActive()) {
                conceptsToAdd.remove(referencedComponentId);
                conceptsToActivate.add(member);
            } else {
                conceptsToAdd.remove(referencedComponentId);
            }
        } else {
            if (member.isActive()) {
                membersToRemove.add(member);
            }
        }
    });
    // fetch all referenced components
    final Set<String> referencedConceptIds = newHashSet();
    referencedConceptIds.addAll(conceptsToAdd.keySet());
    referencedConceptIds.addAll(FluentIterable.from(membersToRemove).transform(SnomedReferenceSetMember::getReferencedComponent).transform(IComponent::getId).toSet());
    referencedConceptIds.addAll(FluentIterable.from(conceptsToActivate).transform(SnomedReferenceSetMember::getReferencedComponent).transform(IComponent::getId).toSet());
    final Map<String, SnomedConcept> concepts;
    if (expand().containsKey("referencedComponent")) {
        final Options expandOptions = expand().getOptions("referencedComponent");
        concepts = Maps.uniqueIndex(SnomedRequests.prepareSearchConcept().filterByIds(referencedConceptIds).setLimit(referencedConceptIds.size()).setExpand(expandOptions.getOptions("expand")).setLocales(locales()).build().execute(context), IComponent::getId);
    } else {
        // initialize with empty SnomedConcept resources
        concepts = newHashMap();
        for (String referencedConceptId : referencedConceptIds) {
            concepts.put(referencedConceptId, new SnomedConcept(referencedConceptId));
        }
    }
    final Collection<MemberChange> changes = newArrayList();
    for (String id : conceptsToAdd.keySet()) {
        changes.add(MemberChangeImpl.added(concepts.get(id)));
    }
    for (SnomedReferenceSetMember memberToRemove : membersToRemove) {
        changes.add(MemberChangeImpl.removed(concepts.get(memberToRemove.getReferencedComponent().getId()), memberToRemove.getId()));
    }
    for (SnomedReferenceSetMember conceptToActivate : conceptsToActivate) {
        changes.add(MemberChangeImpl.changed(concepts.get(conceptToActivate.getReferencedComponent().getId()), conceptToActivate.getId()));
    }
    return new QueryRefSetMemberEvaluationImpl(memberId, targetReferenceSet, changes);
}

Example 7 with TransactionContext

use of com.b2international.snowowl.core.domain.TransactionContext in project snow-owl by b2ihealthcare.

the class SnomedVersioningRequest method adjustDependencyRefSetMembers.

private void adjustDependencyRefSetMembers(TransactionContext context, Multimap<String, String> moduleDependencies, Map<String, Long> moduleToLatestEffectiveTime, long effectiveTime) {
    // Update existing, add new members to moduleDependencyRefSet
    if (!CompareUtils.isEmpty(moduleDependencies)) {
        moduleDependencies.entries().forEach((entry) -> {
            final String source = entry.getKey();
            final String target = entry.getValue();
            final SnomedReferenceSetMember existingLatestMember = SnomedRequests.prepareSearchMember().all().filterByModule(source).filterByReferencedComponent(target).filterByRefSet(Concepts.REFSET_MODULE_DEPENDENCY_TYPE).build().execute(context).stream().sorted((o1, o2) -> {
                if (null == o1.getEffectiveTime() && null == o2.getEffectiveTime()) {
                    return 0;
                } else if (null == o1.getEffectiveTime() && null != o2.getEffectiveTime()) {
                    return 1;
                } else if (null != o1.getEffectiveTime() && null == o2.getEffectiveTime()) {
                    return -1;
                }
                return o1.getEffectiveTime().compareTo(o2.getEffectiveTime());
            }).reduce((first, second) -> second).orElse(null);
            final SnomedRefSetMemberIndexEntry.Builder updatedMember;
            if (existingLatestMember == null) {
                updatedMember = SnomedRefSetMemberIndexEntry.builder().id(UUID.randomUUID().toString()).active(true).refsetId(Concepts.REFSET_MODULE_DEPENDENCY_TYPE).referenceSetType(SnomedRefSetType.MODULE_DEPENDENCY).moduleId(source).referencedComponentId(target);
            } else {
                updatedMember = SnomedRefSetMemberIndexEntry.builder(existingLatestMember);
            }
            final long targetEffectiveTime = moduleToLatestEffectiveTime.get(target) == EffectiveTimes.UNSET_EFFECTIVE_TIME ? effectiveTime : moduleToLatestEffectiveTime.get(target);
            updatedMember.released(true).effectiveTime(effectiveTime).field(SnomedRf2Headers.FIELD_SOURCE_EFFECTIVE_TIME, effectiveTime).field(SnomedRf2Headers.FIELD_TARGET_EFFECTIVE_TIME, targetEffectiveTime);
            if (existingLatestMember == null) {
                context.add(updatedMember.build());
            } else {
                context.update(SnomedRefSetMemberIndexEntry.builder(existingLatestMember).build(), updatedMember.build());
            }
        });
    }
}

Example 8 with TransactionContext

use of com.b2international.snowowl.core.domain.TransactionContext in project snow-owl by b2ihealthcare.

the class SnomedBulkRequest method execute.

@Override
public R execute(TransactionContext context) {
    ImmutableList.Builder<SnomedComponentRequest<?>> requests = ImmutableList.builder();
    ImmutableList.Builder<DeleteRequest> deletions = ImmutableList.builder();
    collectNestedRequests(next(), requests, deletions);
    // Prefetch all component IDs mentioned in reference set member creation requests, abort if any of them can not be found
    final Set<String> requiredComponentIds = requests.build().stream().flatMap(request -> request.getRequiredComponentIds(context).stream()).filter(// just in case filter out invalid component IDs
    componentId -> SnomedComponent.getTypeSafe(componentId) != null || isMember(componentId)).collect(Collectors.toSet());
    final Multimap<Class<? extends SnomedDocument>, String> componentIdsByType = HashMultimap.create();
    for (String requiredComponentId : requiredComponentIds) {
        if (!Strings.isNullOrEmpty(requiredComponentId)) {
            componentIdsByType.put(this.getDocType(requiredComponentId), requiredComponentId);
        }
    }
    // collect all deleted IDs as well
    deletions.build().stream().map(DeleteRequest::getComponentId).forEach(componentId -> componentIdsByType.put(getDocType(componentId), componentId));
    try {
        for (final Entry<Class<? extends SnomedDocument>, Collection<String>> idsForType : componentIdsByType.asMap().entrySet()) {
            context.lookup(idsForType.getValue(), idsForType.getKey());
        }
    } catch (final ComponentNotFoundException e) {
        throw e.toBadRequestException();
    }
    // bind additional caches to the context
    TransactionContext newContext = context.inject().bind(SnomedOWLExpressionConverter.class, new SnomedOWLExpressionConverter(context)).build();
    return next(newContext);
}

Example 9 with TransactionContext

use of com.b2international.snowowl.core.domain.TransactionContext in project snow-owl by b2ihealthcare.

the class SaveJobRequest method mergeEquivalentConcepts.

private Set<String> mergeEquivalentConcepts(final BranchContext context, final BulkRequestBuilder<TransactionContext> bulkRequestBuilder, final SnomedNamespaceAndModuleAssigner assigner) {
    if (!fixEquivalences) {
        return Collections.emptySet();
    }
    // XXX: Restrict merging to active components only
    final String expand = "equivalentConcepts(expand(" + "descriptions(active:true)," + "relationships(active:true)," + "inboundRelationships(active:true)," + "members(active:true)))";
    final Multimap<SnomedConcept, SnomedConcept> equivalentConcepts = HashMultimap.create();
    ClassificationRequests.prepareSearchEquivalentConceptSet().setLimit(SCROLL_LIMIT).setExpand(expand).filterByClassificationId(classificationId).stream(context).flatMap(EquivalentConceptSets::stream).filter(equivalentSet -> !equivalentSet.isUnsatisfiable()).forEach(equivalentSet -> {
        final List<SnomedConcept> conceptsToRemove = newArrayList(equivalentSet.getEquivalentConcepts());
        final SnomedConcept conceptToKeep = conceptsToRemove.remove(0);
        equivalentConcepts.putAll(conceptToKeep, conceptsToRemove);
    });
    // Are there any equivalent concepts present? or Were all equivalent concepts unsatisfiable?
    if (equivalentConcepts.isEmpty()) {
        return Collections.emptySet();
    }
    IEquivalentConceptMerger merger = Extensions.getFirstPriorityExtension(IEquivalentConceptMerger.EXTENSION_POINT, IEquivalentConceptMerger.class);
    if (merger == null) {
        merger = new IEquivalentConceptMerger.Default();
    }
    final String mergerName = merger.getClass().getSimpleName();
    LOG.info("Reasoner service will use {} for equivalent concept merging.", mergerName);
    final Set<String> conceptIdsToSkip = merger.merge(equivalentConcepts);
    final Set<String> conceptIdsToKeep = equivalentConcepts.keySet().stream().map(SnomedConcept::getId).collect(Collectors.toSet());
    // Prepare to provide namespace-module for inbound relationship source concepts as well
    final Set<String> relationshipChangeConceptIds = newHashSet(conceptIdsToKeep);
    // Add source concepts on new/about to be inactivated inbound relationships, pointing to "kept" concepts
    for (final SnomedConcept conceptToKeep : equivalentConcepts.keySet()) {
        for (final SnomedRelationship relationship : conceptToKeep.getInboundRelationships()) {
            if (relationship.getId().startsWith(IEquivalentConceptMerger.PREFIX_NEW)) {
                relationshipChangeConceptIds.add(relationship.getSourceId());
            } else if (!relationship.isActive()) {
                relationshipChangeConceptIds.add(relationship.getSourceId());
            }
        }
    }
    assigner.collectRelationshipNamespacesAndModules(relationshipChangeConceptIds, context);
    for (final SnomedConcept conceptToKeep : equivalentConcepts.keySet()) {
        for (final SnomedRelationship relationship : conceptToKeep.getInboundRelationships()) {
            // Already handled as another concept's outbound relationship
            if (relationship.getId() == null) {
                continue;
            }
            if (relationship.getId().startsWith(IEquivalentConceptMerger.PREFIX_NEW)) {
                relationship.setId(null);
                addComponent(bulkRequestBuilder, assigner, relationship);
            } else if (!relationship.isActive()) {
                removeOrDeactivate(bulkRequestBuilder, assigner, relationship);
            }
        }
        for (final SnomedRelationship relationship : conceptToKeep.getRelationships()) {
            // Already handled as another concept's inbound relationship
            if (relationship.getId() == null) {
                continue;
            }
            if (relationship.getId().startsWith(IEquivalentConceptMerger.PREFIX_NEW)) {
                relationship.setId(null);
                addComponent(bulkRequestBuilder, assigner, relationship);
            } else if (!relationship.isActive()) {
                removeOrDeactivate(bulkRequestBuilder, assigner, relationship);
            }
        }
    }
    // CD members are always "outbound", however, so the concept SCTID set can be reduced
    assigner.clear();
    assigner.collectConcreteDomainModules(conceptIdsToKeep, context);
    for (final SnomedConcept conceptToKeep : equivalentConcepts.keySet()) {
        for (final SnomedReferenceSetMember member : conceptToKeep.getMembers()) {
            if (member.getId().startsWith(IEquivalentConceptMerger.PREFIX_NEW)) {
                member.setId(null);
                addComponent(bulkRequestBuilder, assigner, member);
            } else if (member.getId().startsWith(IEquivalentConceptMerger.PREFIX_UPDATED)) {
                // Trim the prefix from the ID to restore its original form
                member.setId(member.getId().substring(IEquivalentConceptMerger.PREFIX_UPDATED.length()));
                bulkRequestBuilder.add(member.toUpdateRequest());
            } else if (!member.isActive()) {
                removeOrDeactivate(bulkRequestBuilder, assigner, member);
            }
        }
    }
    // Descriptions are also "outbound"
    assigner.clear();
    assigner.collectRelationshipNamespacesAndModules(conceptIdsToKeep, context);
    for (final SnomedConcept conceptToKeep : equivalentConcepts.keySet()) {
        for (final SnomedDescription description : conceptToKeep.getDescriptions()) {
            if (description.getId().startsWith(IEquivalentConceptMerger.PREFIX_NEW)) {
                description.setId(null);
                addComponent(bulkRequestBuilder, assigner, description);
            } else if (description.getId().startsWith(IEquivalentConceptMerger.PREFIX_UPDATED)) {
                // Trim the prefix from the ID to restore its original form
                description.setId(description.getId().substring(IEquivalentConceptMerger.PREFIX_UPDATED.length()));
                bulkRequestBuilder.add(description.toUpdateRequest());
            } else if (!description.isActive()) {
                removeOrDeactivate(bulkRequestBuilder, assigner, description);
            }
        }
    }
    // Inactivation of "removed" concepts also requires modules to be collected according to the assigner rules
    assigner.clear();
    assigner.collectRelationshipNamespacesAndModules(conceptIdsToSkip, context);
    for (final SnomedConcept conceptToRemove : equivalentConcepts.values()) {
        // Check if the concept needs to be removed or deactivated
        if (!conceptToRemove.isActive()) {
            removeOrDeactivate(bulkRequestBuilder, assigner, conceptToRemove);
        }
    }
    assigner.clear();
    return conceptIdsToSkip;
}

Example 10 with TransactionContext

use of com.b2international.snowowl.core.domain.TransactionContext in project snow-owl by b2ihealthcare.

the class SaveJobRequest method persistChanges.

private Boolean persistChanges(final BranchContext context, final IProgressMonitor monitor) {
    // Repeat the same checks as in ClassificationSaveRequest, now within the lock
    final ClassificationTask classification = ClassificationRequests.prepareGetClassification(classificationId).build().execute(context);
    final String branchPath = classification.getBranch();
    final Branch branch = RepositoryRequests.branching().prepareGet(branchPath).build().execute(context);
    if (!ClassificationSaveRequest.SAVEABLE_STATUSES.contains(classification.getStatus())) {
        throw new BadRequestException("Classification '%s' is not in the expected state to start saving changes.", classificationId);
    }
    if (classification.getTimestamp() < branch.headTimestamp()) {
        throw new BadRequestException("Classification '%s' on branch '%s' is stale (classification timestamp: %s, head timestamp: %s).", classificationId, branchPath, classification.getTimestamp(), branch.headTimestamp());
    }
    final ClassificationTracker classificationTracker = context.service(ClassificationTracker.class);
    // Signal the state change
    classificationTracker.classificationSaving(classificationId);
    final SubMonitor subMonitor = SubMonitor.convert(monitor, "Persisting changes", 6);
    final BulkRequestBuilder<TransactionContext> bulkRequestBuilder = BulkRequest.create();
    applyChanges(subMonitor, context, bulkRequestBuilder);
    long resultTimeStamp = Commit.NO_COMMIT_TIMESTAMP;
    for (List<Request<TransactionContext, ?>> partition : Iterables.partition(bulkRequestBuilder.build().getRequests(), getCommitLimit(context))) {
        final BulkRequestBuilder<TransactionContext> batchRequest = BulkRequest.create();
        partition.forEach(request -> batchRequest.add(request));
        final Request<BranchContext, CommitResult> commitRequest = SnomedRequests.prepareCommit().setBody(batchRequest.build()).setCommitComment(commitComment).setParentContextDescription(DatastoreLockContextDescriptions.SAVE_CLASSIFICATION_RESULTS).setAuthor(userId).build();
        final CommitResult commitResult = new IdRequest<>(commitRequest).execute(context);
        resultTimeStamp = commitResult.getCommitTimestamp();
    }
    if (Commit.NO_COMMIT_TIMESTAMP == resultTimeStamp) {
        classificationTracker.classificationSaveFailed(classificationId);
        return Boolean.FALSE;
    } else {
        classificationTracker.classificationSaved(classificationId, resultTimeStamp);
        return Boolean.TRUE;
    }
}