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

Example 21 with SnomedDescription

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

the class SnomedSimpleTypeRefSetDSVExporter method writeValues.

private void writeValues(BufferedWriter writer, SnomedConcepts chunk) throws IOException {
    List<String> dataRow = newArrayList();
    for (SnomedConcept concept : chunk) {
        dataRow.clear();
        for (AbstractSnomedDsvExportItem exportItem : exportItems) {
            switch(exportItem.getType()) {
                case DESCRIPTION:
                    {
                        final ComponentIdSnomedDsvExportItem descriptionItem = (ComponentIdSnomedDsvExportItem) exportItem;
                        final String typeId = descriptionItem.getComponentId();
                        int occurrences = descriptionCount.get(typeId);
                        final Map<String, String> termsById = concept.getDescriptions().stream().filter(d -> typeId.equals(d.getTypeId())).collect(Collectors.toMap(SnomedDescription::getId, SnomedDescription::getTerm));
                        addCells(dataRow, occurrences, includeDescriptionId, termsById);
                        break;
                    }
                case RELATIONSHIP:
                    {
                        final ComponentIdSnomedDsvExportItem relationshipItem = (ComponentIdSnomedDsvExportItem) exportItem;
                        for (Integer propertyGroup : propertyCountByGroup.keySet()) {
                            final String typeId = relationshipItem.getComponentId();
                            final Map<String, Integer> groupOccurrences = propertyCountByGroup.getOrDefault(propertyGroup, NO_OCCURRENCES);
                            final int occurrences = groupOccurrences.getOrDefault(typeId, 0);
                            concept.getRelationships().stream().filter(r -> typeId.equals(r.getTypeId()) && Objects.equals(r.getRelationshipGroup(), propertyGroup) && (Concepts.INFERRED_RELATIONSHIP.equals(r.getCharacteristicTypeId()) || Concepts.ADDITIONAL_RELATIONSHIP.equals(r.getCharacteristicTypeId()))).forEach(relationship -> {
                                if (relationship.hasValue()) {
                                    addCells(dataRow, occurrences, includeRelationshipId, ImmutableMap.of(relationship.getValue(), ""));
                                } else {
                                    addCells(dataRow, occurrences, includeRelationshipId, ImmutableMap.of(relationship.getDestinationId(), getPreferredTerm(relationship.getDestination())));
                                }
                            });
                        }
                        break;
                    }
                case DATAYPE:
                    {
                        final DatatypeSnomedDsvExportItem datatypeItem = (DatatypeSnomedDsvExportItem) exportItem;
                        for (Integer propertyGroup : propertyCountByGroup.keySet()) {
                            Map<String, Integer> groupedOccurrences = propertyCountByGroup.getOrDefault(propertyGroup, NO_OCCURRENCES);
                            final String typeId = datatypeItem.getComponentId();
                            int occurrences = groupedOccurrences.getOrDefault(typeId, 0);
                            if (occurrences < 1) {
                                break;
                            }
                            final List<String> properties = concept.getMembers().stream().filter(m -> SnomedRefSetType.CONCRETE_DATA_TYPE.equals(m.type()) && m.isActive() && typeId.equals(m.getProperties().get(SnomedRf2Headers.FIELD_TYPE_ID)) && Objects.equals(m.getProperties().get(SnomedRf2Headers.FIELD_RELATIONSHIP_GROUP), propertyGroup) && (Concepts.INFERRED_RELATIONSHIP.equals(m.getProperties().get(SnomedRf2Headers.FIELD_CHARACTERISTIC_TYPE_ID)) || Concepts.ADDITIONAL_RELATIONSHIP.equals(m.getProperties().get(SnomedRf2Headers.FIELD_CHARACTERISTIC_TYPE_ID)))).map(m -> m.getProperties().get(SnomedRf2Headers.FIELD_VALUE)).map(p -> {
                                if (datatypeItem.isBooleanDatatype()) {
                                    return "1".equals(p) ? "Yes" : "No";
                                } else {
                                    return p.toString();
                                }
                            }).sorted().collect(Collectors.toList());
                            for (String value : properties) {
                                dataRow.add(value);
                                occurrences--;
                            }
                            while (occurrences > 0) {
                                dataRow.add("");
                                occurrences--;
                            }
                        }
                        break;
                    }
                case PREFERRED_TERM:
                    if (includeDescriptionId) {
                        dataRow.add(getPreferredTermId(concept));
                        dataRow.add(getPreferredTerm(concept));
                    } else {
                        dataRow.add(getPreferredTerm(concept));
                    }
                    break;
                case CONCEPT_ID:
                    dataRow.add(concept.getId());
                    break;
                case MODULE:
                    dataRow.add(concept.getModuleId());
                    break;
                case EFFECTIVE_TIME:
                    dataRow.add(EffectiveTimes.format(concept.getEffectiveTime()));
                    break;
                case STATUS_LABEL:
                    dataRow.add(concept.isActive() ? "Active" : "Inactive");
                    break;
                case DEFINITION_STATUS:
                    dataRow.add(concept.getDefinitionStatusId());
                    break;
                default:
                    break;
            }
        }
        writer.write(joiner.join(dataRow));
        writer.write(lineSeparator);
    }
}

Example 22 with SnomedDescription

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

the class SnomedDescriptionApiTest method updateInactivationIndicatorOnActiveReleasedDescription.

@Test
public void updateInactivationIndicatorOnActiveReleasedDescription() throws Exception {
    String descriptionToInactivate = createNewDescription(branchPath);
    assertInactivation(branchPath, descriptionToInactivate, new InactivationProperties(Concepts.PENDING_MOVE, Collections.emptyList()));
    // release component
    createCodeSystemAndVersion(branchPath, "SNOMEDCT-RELDESC-INACTIVATIONINDICATOR", "v1", LocalDate.parse("2018-07-01"));
    SnomedDescription description = assertInactivation(branchPath, descriptionToInactivate, new InactivationProperties(Concepts.CONCEPT_NON_CURRENT, Collections.emptyList())).extract().as(SnomedDescription.class);
    List<SnomedReferenceSetMember> inactivationIndicators = description.getMembers().stream().filter(member -> Concepts.REFSET_DESCRIPTION_INACTIVITY_INDICATOR.equals(member.getRefsetId())).collect(Collectors.toList());
    final SnomedReferenceSetMember inactivationIndicator = Iterables.getOnlyElement(inactivationIndicators);
    assertEquals(Concepts.CONCEPT_NON_CURRENT, inactivationIndicator.getProperties().get(SnomedRf2Headers.FIELD_VALUE_ID));
    assertNull(inactivationIndicator.getEffectiveTime());
}

Example 23 with SnomedDescription

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

the class SnomedDescriptionApiTest method testDuplicateMemberCleanupEmptiesAcceptabilityMap.

@Test
public void testDuplicateMemberCleanupEmptiesAcceptabilityMap() throws Exception {
    String descriptionId = createNewDescription(branchPath);
    // Inject inactive language member with different acceptability (API won't allow it)
    String memberIdToUpdate = UUID.randomUUID().toString();
    SnomedRefSetMemberIndexEntry member = SnomedRefSetMemberIndexEntry.builder().id(memberIdToUpdate).active(false).released(false).moduleId(Concepts.MODULE_SCT_CORE).refsetId(Concepts.REFSET_LANGUAGE_TYPE_UK).referencedComponentId(descriptionId).referenceSetType(SnomedRefSetType.LANGUAGE).field(SnomedRf2Headers.FIELD_ACCEPTABILITY_ID, Concepts.REFSET_DESCRIPTION_ACCEPTABILITY_PREFERRED).build();
    new RepositoryRequest<>(SnomedTerminologyComponentConstants.TOOLING_ID, context -> {
        ApplicationContext.getServiceForClass(RepositoryManager.class).get(SnomedTerminologyComponentConstants.TOOLING_ID).service(RevisionIndex.class).prepareCommit(branchPath.getPath()).stageNew(member).withContext(context.inject().bind(ModuleIdProvider.class, c -> c.getModuleId()).build()).commit(ApplicationContext.getServiceForClass(TimestampProvider.class).getTimestamp(), "test", "Added duplicate language reference set member to " + descriptionId);
        return null;
    }).execute(ApplicationContext.getServiceForClass(Environment.class));
    // Check the acceptability map; the description should be acceptable in the UK reference set
    SnomedDescription description = getComponent(branchPath, SnomedComponentType.DESCRIPTION, descriptionId, "members()").statusCode(200).extract().as(SnomedDescription.class);
    assertEquals(Acceptability.ACCEPTABLE, description.getAcceptabilityMap().get(Concepts.REFSET_LANGUAGE_TYPE_UK));
    assertEquals(2, description.getMembers().getTotal());
    String memberIdToDelete = null;
    for (SnomedReferenceSetMember descriptionMember : description.getMembers()) {
        if (Concepts.REFSET_DESCRIPTION_ACCEPTABILITY_ACCEPTABLE.equals(descriptionMember.getProperties().get(SnomedRf2Headers.FIELD_ACCEPTABILITY_ID))) {
            memberIdToDelete = descriptionMember.getId();
            break;
        }
    }
    assertNotNull(memberIdToDelete);
    // Using bulk update, remove the currently active member and activate the inactive one, also changing its acceptability
    Json bulkRequest = Json.object("requests", Json.array(Json.object("action", "delete", "memberId", memberIdToDelete), Json.object("action", "update", "memberId", memberIdToUpdate, "active", true, "acceptabilityId", Concepts.REFSET_DESCRIPTION_ACCEPTABILITY_ACCEPTABLE)), "commitComment", "Consolidated language reference set members");
    bulkUpdateMembers(branchPath, Concepts.REFSET_LANGUAGE_TYPE_UK, bulkRequest).statusCode(204);
    // Verify that description acceptability is still acceptable, but only one member remains
    SnomedDescription newDescription = getComponent(branchPath, SnomedComponentType.DESCRIPTION, descriptionId, "members()").statusCode(200).extract().as(SnomedDescription.class);
    assertEquals(Acceptability.ACCEPTABLE, newDescription.getAcceptabilityMap().get(Concepts.REFSET_LANGUAGE_TYPE_UK));
    assertEquals(1, newDescription.getMembers().getTotal());
    SnomedReferenceSetMember languageMember = Iterables.getOnlyElement(newDescription.getMembers());
    assertEquals(memberIdToUpdate, languageMember.getId());
    assertEquals(true, languageMember.isActive());
}

Example 24 with SnomedDescription

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

the class SnomedDescriptionConverter method toResource.

@Override
protected SnomedDescription toResource(final SnomedDescriptionIndexEntry input) {
    final SnomedDescription result = new SnomedDescription();
    result.setAcceptabilityMap(input.getAcceptabilityMap());
    result.setActive(input.isActive());
    result.setCaseSignificanceId(input.getCaseSignificanceId());
    result.setConceptId(input.getConceptId());
    result.setEffectiveTime(toEffectiveTime(input.getEffectiveTime()));
    result.setId(input.getId());
    result.setLanguageCode(input.getLanguageCode());
    result.setModuleId(input.getModuleId());
    result.setIconId(input.getIconId());
    result.setReleased(input.isReleased());
    result.setTerm(input.getTerm());
    result.setSemanticTag(input.getSemanticTag());
    result.setTypeId(input.getTypeId());
    result.setType(new SnomedConcept(input.getTypeId()));
    result.setScore(input.getScore());
    if (input.getMemberOf() != null) {
        result.setMemberOf(ImmutableSortedSet.copyOf(input.getMemberOf()));
    }
    if (input.getActiveMemberOf() != null) {
        result.setActiveMemberOf(ImmutableSortedSet.copyOf(input.getActiveMemberOf()));
    }
    return result;
}

Example 25 with SnomedDescription

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

the class SnomedDescriptionConverter method expandAcceptabilities.

private void expandAcceptabilities(List<SnomedDescription> results) {
    if (!expand().containsKey("acceptabilities")) {
        return;
    }
    // expand the acceptability objects first
    for (SnomedDescription result : results) {
        if (!CompareUtils.isEmpty(result.getAcceptabilityMap())) {
            List<AcceptabilityMembership> acceptabilities = result.getAcceptabilityMap().entrySet().stream().map(entry -> new AcceptabilityMembership(entry.getKey(), entry.getValue().getConceptId())).sorted().collect(Collectors.toList());
            result.setAcceptabilities(acceptabilities);
        } else {
            result.setAcceptabilities(Collections.emptyList());
        }
    }
    // additional expansions supported inside the acceptabilities() expand
    final Options expandOptions = expand().get("acceptabilities", Options.class).getOptions("expand");
    if (expandOptions.containsKey("acceptability")) {
        final Options acceptabilityExpand = expandOptions.get("acceptability", Options.class);
        final Iterable<String> acceptabilityIds = results.stream().flatMap(d -> d.getAcceptabilities().stream().map(AcceptabilityMembership::getAcceptabilityId))::iterator;
        context().service(SnomedConceptRequestCache.class).request(acceptabilityIds, acceptabilityExpand.getOptions("expand"), locales(), acceptabilitiesById -> {
            for (SnomedDescription result : results) {
                result.getAcceptabilities().forEach(acceptabilityMembership -> {
                    acceptabilityMembership.setAcceptability(acceptabilitiesById.get(acceptabilityMembership.getAcceptabilityId()));
                });
            }
        });
    }
    if (expandOptions.containsKey("languageRefSet")) {
        final Options languageRefSetExpand = expandOptions.get("languageRefSet", Options.class);
        final Iterable<String> languageRefSetIds = results.stream().flatMap(d -> d.getAcceptabilities().stream().map(AcceptabilityMembership::getLanguageRefSetId))::iterator;
        context().service(SnomedConceptRequestCache.class).request(languageRefSetIds, languageRefSetExpand.getOptions("expand"), locales(), languageRefSetsById -> {
            for (SnomedDescription result : results) {
                result.getAcceptabilities().forEach(acceptabilityMembership -> {
                    acceptabilityMembership.setLanguageRefSet(languageRefSetsById.get(acceptabilityMembership.getLanguageRefSetId()));
                });
            }
        });
    }
}