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

Example 46 with SnomedConceptDocument

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

the class PreferredDescriptionPreCommitHookTest method removeFsnFromExistingConcept.

@Test
public void removeFsnFromExistingConcept() throws Exception {
    final SnomedConceptDocument concept = concept().build();
    final SnomedDescriptionIndexEntry fsn = fsn(concept.getId(), Collections.singletonMap(Concepts.REFSET_LANGUAGE_TYPE_UK, Acceptability.PREFERRED));
    initRevisions(docWithDefaults(concept).preferredDescriptions(ImmutableList.of(new SnomedDescriptionFragment(fsn.getId(), fsn.getTypeId(), fsn.getTerm(), Concepts.REFSET_LANGUAGE_TYPE_UK))).build(), fsn);
    stageRemove(fsn);
    final ConceptChangeProcessor processor = process();
    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 47 with SnomedConceptDocument

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

the class TaxonomyPreCommitHookTest method indexOrphanConceptWithIconId_ShouldGetItsIconId.

@Test
public void indexOrphanConceptWithIconId_ShouldGetItsIconId() throws Exception {
    final SnomedConceptDocument concept = concept().build();
    availableImages.add(concept.getId());
    stageNew(concept);
    final ConceptChangeProcessor processor = process();
    final SnomedConceptDocument expected = docWithDefaults(concept).iconId(concept.getId()).build();
    final Revision actual = Iterables.getOnlyElement(processor.getNewMappings().values());
    assertDocEquals(expected, actual);
    assertEquals(0, processor.getChangedMappings().size());
    assertEquals(0, processor.getDeletions().size());
}

Example 48 with SnomedConceptDocument

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

the class TaxonomyPreCommitHookTest method indexOrphanConcept_ShouldFillDefaultsForDerivedFields.

@Test
public void indexOrphanConcept_ShouldFillDefaultsForDerivedFields() throws Exception {
    final SnomedConceptDocument concept = concept().build();
    stageNew(concept);
    final ConceptChangeProcessor processor = process();
    final SnomedConceptDocument expected = docWithDefaults(concept).build();
    final Revision actual = Iterables.getOnlyElement(processor.getNewMappings().values());
    assertDocEquals(expected, actual);
    assertEquals(0, processor.getChangedMappings().size());
    assertEquals(0, processor.getDeletions().size());
}

Example 49 with SnomedConceptDocument

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

the class ConceptChangeProcessor method update.

/*
	 * Updates already existing concept document with changes from concept and the current revision.
	 * New concepts does not have currentRevision and dirty concepts may not have a loaded Concept CDOObject, 
	 * therefore both can be null, but not at the same time.
	 * In case of new objects the Concept object should not be null, in case of dirty, the currentVersion should not be null, 
	 * but there can be a dirty concept if a property changed on it.
	 * We will use whatever we actually have locally to compute the new revision.
	 */
private void update(SnomedConceptDocument.Builder doc, List<SnomedDescriptionFragment> preferredDescriptions, @Nullable SnomedConceptDocument newOrDirtyRevision, SnomedConceptDocument cleanRevision) {
    checkArgument(newOrDirtyRevision != null || cleanRevision != null, "Either the newOrDirtyRevision is null or the cleanRevision but not both");
    final String id = newOrDirtyRevision != null ? newOrDirtyRevision.getId() : cleanRevision.getId();
    final long idLong = Long.parseLong(id);
    final boolean active = newOrDirtyRevision != null ? newOrDirtyRevision.isActive() : cleanRevision.isActive();
    if (newOrDirtyRevision != null) {
        doc.active(active).released(newOrDirtyRevision.isReleased()).effectiveTime(newOrDirtyRevision.getEffectiveTime()).moduleId(newOrDirtyRevision.getModuleId()).exhaustive(newOrDirtyRevision.isExhaustive()).definitionStatusId(newOrDirtyRevision.getDefinitionStatusId()).refSetType(newOrDirtyRevision.getRefSetType()).referencedComponentType(newOrDirtyRevision.getReferencedComponentType()).mapTargetComponentType(newOrDirtyRevision.getMapTargetComponentType()).doi(doiData.getDoiScore(idLong));
    } else {
        doc.active(active).released(cleanRevision.isReleased()).effectiveTime(cleanRevision.getEffectiveTime()).moduleId(cleanRevision.getModuleId()).exhaustive(cleanRevision.isExhaustive()).definitionStatusId(cleanRevision.getDefinitionStatusId()).refSetType(cleanRevision.getRefSetType()).referencedComponentType(cleanRevision.getReferencedComponentType()).mapTargetComponentType(cleanRevision.getMapTargetComponentType()).doi(doiData.getDoiScore(idLong));
    }
    /*
		 * Extract semantic tags from active FSNs received in preferredDescriptions (these are expected to be preferred in at 
		 * least one language reference set).
		 */
    final SortedSet<String> semanticTags = preferredDescriptions.stream().filter(f -> Concepts.FULLY_SPECIFIED_NAME.equals(f.getTypeId())).map(f -> SnomedDescriptionIndexEntry.extractSemanticTag(f.getTerm())).filter(semanticTag -> !semanticTag.isEmpty()).collect(Collectors.toCollection(TreeSet::new));
    final boolean inStated = statedTaxonomy.getNewTaxonomy().containsNode(idLong);
    final boolean inInferred = inferredTaxonomy.getNewTaxonomy().containsNode(idLong);
    if (inStated || inInferred) {
        iconId.update(id, Iterables.getFirst(semanticTags, ""), active, doc);
    }
    if (inStated) {
        stated.update(id, doc);
    }
    if (inInferred) {
        inferred.update(id, doc);
    }
    final Collection<String> currentMemberOf = cleanRevision == null ? Collections.emptySet() : cleanRevision.getMemberOf();
    final Collection<String> currentActiveMemberOf = cleanRevision == null ? Collections.emptySet() : cleanRevision.getActiveMemberOf();
    new ReferenceSetMembershipUpdater(referringRefSets.removeAll(id), currentMemberOf, currentActiveMemberOf).update(doc);
    doc.semanticTags(semanticTags);
    doc.preferredDescriptions(preferredDescriptions);
}

Example 50 with SnomedConceptDocument

use of com.b2international.snowowl.snomed.datastore.index.entry.SnomedConceptDocument 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());
        }
    }
}