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

Example 6 with StagingArea

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

the class SnomedEclEvaluationRequestTest method generateDrugsWithGroups.

/**
 * Generates the following test fixtures:
 * <ul>
 * 	<li>Substances (children of SUBSTANCE):
 * 		<ul>
 * 			<li>INGREDIENT5 (ingredient with two inbound HAI from ASPIRIN_TABLET and ALGOFLEX_TABLET, one inbound HAS_BOSS from ALGOFLEX_TABLET)</li>
 * 			<li>INGREDIENT6 (ingredient with two inbound HAS_BOSS from ASPIRIN_TABLET and ALGOFLEX_TABLET, one inbound HAI from ALGOFLEX_TABLET)</li>
 * 		</ul>
 * 	</li>
 * 	<li>Drugs (children of DRUG_ROOT):
 * 		<ul>
 * 			<li>EPOX_TABLET (drug with one ungrouped HAI relationship to INGREDIENT5)</li>
 * 			<li>ASPIRIN_TABLET (drug with one HAI relationship to INGREDIENT5 in group 1 and one HAS_BOSS to INGREDIENT6 in group 1)</li>
 * 			<li>ALGOFLEX_TABLET (drug with two HAI relationship to INGREDIENT5,INGREDIENT6 in group 1 and 2 and two HAS_BOSS to INGREDIENT6 and 5 in group 1 and 2)</li>
 * 			<li>TRIPLEX_TABLET (drug with one HAI relationship to INGREDIENT5 in group 1 and one HAS_BOSS to ING6 in group 2)</li>
 * 		</ul>
 * 	</li>
 * </ul>
 */
private void generateDrugsWithGroups() {
    StagingArea staging = index().prepareCommit(MAIN);
    staging.stageNew(concept(INGREDIENT5).parents(SUBSTANCEL).statedParents(SUBSTANCEL).build()).stageNew(concept(INGREDIENT6).parents(SUBSTANCEL).statedParents(SUBSTANCEL).build()).stageNew(concept(EPOX_TABLET).parents(DRUG_ROOTL).statedParents(DRUG_ROOTL).build()).stageNew(concept(ASPIRIN_TABLET).parents(DRUG_ROOTL).statedParents(DRUG_ROOTL).build()).stageNew(concept(ALGOFLEX_TABLET).parents(DRUG_ROOTL).statedParents(DRUG_ROOTL).build()).stageNew(concept(TRIPLEX_TABLET).parents(DRUG_ROOTL).statedParents(DRUG_ROOTL).build());
    if (isAxiom()) {
        staging.stageNew(classAxioms(EPOX_TABLET, HAS_ACTIVE_INGREDIENT, INGREDIENT5, 0).build()).stageNew(classAxioms(ASPIRIN_TABLET, HAS_ACTIVE_INGREDIENT, INGREDIENT5, 1, HAS_BOSS, INGREDIENT6, 1).build()).stageNew(classAxioms(ALGOFLEX_TABLET, HAS_ACTIVE_INGREDIENT, INGREDIENT5, 1, HAS_BOSS, INGREDIENT6, 1, HAS_ACTIVE_INGREDIENT, INGREDIENT6, 2, HAS_BOSS, INGREDIENT5, 2).build()).stageNew(classAxioms(TRIPLEX_TABLET, HAS_ACTIVE_INGREDIENT, INGREDIENT5, 1, HAS_BOSS, INGREDIENT6, 2).build());
    } else {
        staging.stageNew(relationship(EPOX_TABLET, HAS_ACTIVE_INGREDIENT, INGREDIENT5, getCharacteristicType()).relationshipGroup(0).build()).stageNew(relationship(ASPIRIN_TABLET, HAS_ACTIVE_INGREDIENT, INGREDIENT5, getCharacteristicType()).relationshipGroup(1).build()).stageNew(relationship(ASPIRIN_TABLET, HAS_BOSS, INGREDIENT6, getCharacteristicType()).relationshipGroup(1).build()).stageNew(relationship(ALGOFLEX_TABLET, HAS_ACTIVE_INGREDIENT, INGREDIENT5, getCharacteristicType()).relationshipGroup(1).build()).stageNew(relationship(ALGOFLEX_TABLET, HAS_BOSS, INGREDIENT6, getCharacteristicType()).relationshipGroup(1).build()).stageNew(relationship(ALGOFLEX_TABLET, HAS_ACTIVE_INGREDIENT, INGREDIENT6, getCharacteristicType()).relationshipGroup(2).build()).stageNew(relationship(ALGOFLEX_TABLET, HAS_BOSS, INGREDIENT5, getCharacteristicType()).relationshipGroup(2).build()).stageNew(relationship(TRIPLEX_TABLET, HAS_ACTIVE_INGREDIENT, INGREDIENT5, getCharacteristicType()).relationshipGroup(1).build()).stageNew(relationship(TRIPLEX_TABLET, HAS_BOSS, INGREDIENT6, getCharacteristicType()).relationshipGroup(2).build());
    }
    staging.commit(currentTime(), UUID.randomUUID().toString(), "Initialize Drugs with groups");
}

Example 7 with StagingArea

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

the class SnomedEclEvaluationRequestTest method generateTisselKit.

/**
 * Generates the following test fixtures:
 * <ul>
 * 	<li>Substances (children of SUBSTANCE):
 * 		<ul>
 * 			<li>INGREDIENT4 (ingredient with one inbound HAI from TISSEL_KIT)</li>
 * 		</ul>
 * 	</li>
 * 	<li>Drugs (children of DRUG_ROOT):
 * 		<ul>
 * 			<li>TISSEL_KIT (drug with one outgoing inferred HAI relationship to INGREDIENT4)</li>
 * 		</ul>
 * 	</li>
 * </ul>
 */
private void generateTisselKit() {
    StagingArea staging = index().prepareCommit(MAIN);
    staging.stageNew(concept(INGREDIENT4).parents(SUBSTANCEL).statedParents(SUBSTANCEL).build());
    staging.stageNew(concept(TISSEL_KIT).parents(DRUG_ROOTL).statedParents(DRUG_ROOTL).build());
    if (isAxiom()) {
        staging.stageNew(classAxioms(TISSEL_KIT, HAS_ACTIVE_INGREDIENT, INGREDIENT4, 0).build());
    } else {
        staging.stageNew(relationship(TISSEL_KIT, HAS_ACTIVE_INGREDIENT, INGREDIENT4, getCharacteristicType()).relationshipGroup(0).build());
    }
    staging.commit(currentTime(), "test", "Generate TISSEL Kit");
}

Example 8 with StagingArea

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

the class ConceptChangeProcessor method processNewConcepts.

private void processNewConcepts(StagingArea staging) {
    final Multimap<String, SnomedDescriptionFragment> newDescriptionFragmentsByConcept = HashMultimap.create();
    // changed descriptions are coming from potential merges/rebases
    Streams.concat(staging.getNewObjects(SnomedDescriptionIndexEntry.class), staging.getChangedObjects(SnomedDescriptionIndexEntry.class)).filter(SnomedDescriptionIndexEntry::isActive).filter(description -> !Concepts.TEXT_DEFINITION.equals(description.getTypeId())).filter(description -> !getPreferredLanguageMembers(description).isEmpty()).forEach(description -> newDescriptionFragmentsByConcept.put(description.getConceptId(), toDescriptionFragment(description)));
    // index new concepts
    staging.getNewObjects(SnomedConceptDocument.class).forEach(concept -> {
        final String id = concept.getId();
        final Builder doc = SnomedConceptDocument.builder().id(id);
        // in case of a new concept, all of its descriptions should be part of the staging area as well
        final List<SnomedDescriptionFragment> preferredDescriptions = newDescriptionFragmentsByConcept.removeAll(id).stream().sorted(DESCRIPTION_FRAGMENT_ORDER).collect(Collectors.toList());
        update(doc, preferredDescriptions, concept, null);
        stageNew(doc.build());
    });
}

Example 9 with StagingArea

use of com.b2international.index.revision.StagingArea 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 10 with StagingArea

use of com.b2international.index.revision.StagingArea 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());
        }
    }
}