Examples with PageWithBucketAggregations org.snomed.snowstorm.core.data.services.pojo.PageWithBucketAggregations used on opensource projects

Example 1 with PageWithBucketAggregations

use of org.snomed.snowstorm.core.data.services.pojo.PageWithBucketAggregations in project snowstorm by IHTSDO.

the class DescriptionController method findBrowserDescriptions.

@ApiOperation(value = "Search for concept descriptions.", notes = "The Accept-Language header is used to specify the user's preferred language, 'en' is always added as a fallback if not already included in the list. " + "Each language is used as an optional clause for matching and will include the correct character folding behaviour for that language. " + "The Accept-Language header list is also used to chose the best translated FSN and PT values in the response.")
@RequestMapping(value = "browser/{branch}/descriptions", method = RequestMethod.GET)
@JsonView(value = View.Component.class)
public Page<BrowserDescriptionSearchResult> findBrowserDescriptions(@PathVariable String branch, @RequestParam(required = false) String term, @RequestParam(required = false) Boolean active, @RequestParam(required = false) Set<String> module, @ApiParam(value = "Set of two character language codes to match. " + "The English language code 'en' will not be added automatically, in contrast to the Accept-Language header which always includes it. " + "Accept-Language header still controls result FSN and PT language selection.") @RequestParam(required = false) Set<String> language, @ApiParam(value = "Set of description type ids to use include. Defaults to any. " + "Pick descendants of '900000000000446008 | Description type (core metadata concept) |'. " + "Examples: 900000000000003001 (FSN), 900000000000013009 (Synonym), 900000000000550004 (Definition)") @RequestParam(required = false) Set<Long> type, @Deprecated @RequestParam(required = false) String semanticTag, @ApiParam(value = "Set of semantic tags.") @RequestParam(required = false) Set<String> semanticTags, @ApiParam(value = "Set of description language reference sets. The description must be preferred in at least one of these to match.") @RequestParam(required = false) Set<Long> preferredIn, @ApiParam(value = "Set of description language reference sets. The description must be acceptable in at least one of these to match.") @RequestParam(required = false) Set<Long> acceptableIn, @ApiParam(value = "Set of description language reference sets. The description must be preferred OR acceptable in at least one of these to match.") @RequestParam(required = false) Set<Long> preferredOrAcceptableIn, @RequestParam(required = false) Boolean conceptActive, @RequestParam(required = false) String conceptRefset, @RequestParam(defaultValue = "false") boolean groupByConcept, @RequestParam(defaultValue = "STANDARD") DescriptionService.SearchMode searchMode, @RequestParam(defaultValue = "0") int offset, @RequestParam(defaultValue = "50") int limit, @RequestHeader(value = "Accept-Language", defaultValue = Config.DEFAULT_ACCEPT_LANG_HEADER) String acceptLanguageHeader) throws TooCostlyException {
    branch = BranchPathUriUtil.decodePath(branch);
    PageRequest pageRequest = ControllerHelper.getPageRequest(offset, limit);
    List<LanguageDialect> languageDialects = ControllerHelper.parseAcceptLanguageHeaderWithDefaultFallback(acceptLanguageHeader);
    PageWithBucketAggregations<Description> page = descriptionService.findDescriptionsWithAggregations(branch, new DescriptionCriteria().term(term).active(active).modules(module).searchLanguageCodes(language).type(type).semanticTag(semanticTag).semanticTags(semanticTags).preferredIn(preferredIn).acceptableIn(acceptableIn).preferredOrAcceptableIn(preferredOrAcceptableIn).conceptActive(conceptActive).conceptRefset(conceptRefset).groupByConcept(groupByConcept).searchMode(searchMode), // Page
    pageRequest);
    Set<String> conceptIds = page.getContent().stream().map(Description::getConceptId).collect(Collectors.toSet());
    Map<String, ConceptMini> conceptMinis = conceptService.findConceptMinis(branch, conceptIds, languageDialects).getResultsMap();
    List<BrowserDescriptionSearchResult> results = new ArrayList<>();
    page.getContent().forEach(d -> results.add(new BrowserDescriptionSearchResult(d.getTerm(), d.isActive(), d.getLanguageCode(), d.getModuleId(), conceptMinis.get(d.getConceptId()))));
    PageWithBucketAggregations<BrowserDescriptionSearchResult> pageWithBucketAggregations = new PageWithBucketAggregations<>(results, page.getPageable(), page.getTotalElements(), page.getBuckets());
    addBucketConcepts(branch, languageDialects, pageWithBucketAggregations);
    addLanguageNames(pageWithBucketAggregations);
    return pageWithBucketAggregations;
}

Example 2 with PageWithBucketAggregations

use of org.snomed.snowstorm.core.data.services.pojo.PageWithBucketAggregations in project snowstorm by IHTSDO.

the class MultiSearchController method findDescriptionsReferenceSets.

@ApiOperation("Search descriptions across multiple Code Systems returning reference set membership bucket.")
@RequestMapping(value = "multisearch/descriptions/referencesets", method = RequestMethod.GET)
@JsonView(value = View.Component.class)
public Page<BrowserDescriptionSearchResult> findDescriptionsReferenceSets(// Required!
@RequestParam String term, @RequestParam(required = false) Boolean active, @RequestParam(required = false) Collection<String> module, @ApiParam(value = "Set of two character language codes to match. " + "The English language code 'en' will not be added automatically, in contrast to the Accept-Language header which always includes it. " + "Accept-Language header still controls result FSN and PT language selection.") @RequestParam(required = false) Set<String> language, @ApiParam(value = "Set of description types to include. Pick descendants of '900000000000446008 | Description type (core metadata concept) |'.") @RequestParam(required = false) Set<Long> type, @RequestParam(required = false) Boolean conceptActive, @RequestParam(defaultValue = "ALL_PUBLISHED_CONTENT") ContentScope contentScope, @RequestParam(defaultValue = "0") int offset, @RequestParam(defaultValue = "50") int limit, @RequestHeader(value = "Accept-Language", defaultValue = Config.DEFAULT_ACCEPT_LANG_HEADER) String acceptLanguageHeader) throws TooCostlyException {
    TimerUtil timer = new TimerUtil("MultiSearch - Descriptions with Reference Set buckets");
    DescriptionCriteria descriptionCriteria = new DescriptionCriteria().term(term).active(active).modules(module).searchLanguageCodes(language).type(type).conceptActive(conceptActive);
    PageRequest pageRequest = ControllerHelper.getPageRequest(offset, limit);
    PageWithBucketAggregations<Description> page = multiSearchService.findDescriptionsReferenceSets(descriptionCriteria, pageRequest);
    timer.checkpoint("description search with reference sets");
    Map<String, List<Description>> branchDescriptions = new HashMap<>();
    Map<String, List<String>> branchConceptIds = new HashMap<>();
    for (Description description : page) {
        branchDescriptions.computeIfAbsent(description.getPath(), s -> new ArrayList<>()).add(description);
        branchConceptIds.computeIfAbsent(description.getPath(), s -> new ArrayList<>()).add(description.getConceptId());
    }
    List<LanguageDialect> languageDialects = ControllerHelper.parseAcceptLanguageHeaderWithDefaultFallback(acceptLanguageHeader);
    Map<String, ConceptMini> conceptMiniMap = new HashMap<>();
    for (String branchPath : branchConceptIds.keySet()) {
        conceptMiniMap.putAll(conceptService.findConceptMinis(branchPath, branchConceptIds.get(branchPath), languageDialects).getResultsMap());
        timer.checkpoint("Join concepts from " + branchPath);
    }
    timer.finish();
    List<BrowserDescriptionSearchResult> results = new ArrayList<>();
    page.getContent().forEach(d -> results.add(new BrowserDescriptionSearchResult(d.getTerm(), d.isActive(), d.getLanguageCode(), d.getModuleId(), conceptMiniMap.get(d.getConceptId()))));
    PageWithBucketAggregations<BrowserDescriptionSearchResult> pageWithBucketAggregations = new PageWithBucketAggregations<>(results, page.getPageable(), page.getTotalElements(), page.getBuckets());
    return pageWithBucketAggregations;
}

Example 3 with PageWithBucketAggregations

use of org.snomed.snowstorm.core.data.services.pojo.PageWithBucketAggregations in project snowstorm by IHTSDO.

the class DescriptionService method findDescriptionsWithAggregations.

public PageWithBucketAggregations<Description> findDescriptionsWithAggregations(String path, DescriptionCriteria criteria, PageRequest pageRequest) throws TooCostlyException {
    TimerUtil timer = new TimerUtil("Search", Level.INFO, 5, new TimerUtil("Search DEBUG", Level.DEBUG));
    final BranchCriteria branchCriteria = versionControlHelper.getBranchCriteria(path);
    timer.checkpoint("Build branch criteria");
    // Fetch all matching description and concept ids
    // ids of concepts where all descriptions and concept criteria are met
    DescriptionMatches descriptionMatches = findDescriptionAndConceptIds(criteria, Collections.EMPTY_SET, branchCriteria, timer);
    BoolQueryBuilder descriptionQuery = descriptionMatches.getDescriptionQuery();
    // Apply concept and acceptability filtering for final search
    BoolQueryBuilder descriptionFilter = boolQuery();
    descriptionFilter.must(termsQuery(Description.Fields.DESCRIPTION_ID, descriptionMatches.getMatchedDescriptionIds()));
    // Start fetching aggregations..
    List<Aggregation> allAggregations = new ArrayList<>();
    Set<Long> conceptIds = descriptionMatches.getMatchedConceptIds();
    // Fetch FSN semantic tag aggregation
    BoolQueryBuilder fsnClauses = boolQuery();
    String semanticTag = criteria.getSemanticTag();
    Set<String> semanticTags = criteria.getSemanticTags();
    boolean semanticTagFiltering = !Strings.isNullOrEmpty(semanticTag) || !CollectionUtils.isEmpty(semanticTags);
    Set<String> allSemanticTags = new HashSet<>();
    if (semanticTagFiltering) {
        if (!Strings.isNullOrEmpty(semanticTag)) {
            allSemanticTags.add(semanticTag);
        }
        if (!CollectionUtils.isEmpty(semanticTags)) {
            allSemanticTags.addAll(semanticTags);
        }
        fsnClauses.must(termsQuery(Description.Fields.TAG, allSemanticTags));
    }
    NativeSearchQueryBuilder fsnQueryBuilder = new NativeSearchQueryBuilder().withQuery(fsnClauses.must(branchCriteria.getEntityBranchCriteria(Description.class)).must(termsQuery(Description.Fields.ACTIVE, true)).must(termsQuery(Description.Fields.TYPE_ID, Concepts.FSN)).must(termsQuery(Description.Fields.CONCEPT_ID, conceptIds))).addAggregation(AggregationBuilders.terms("semanticTags").field(Description.Fields.TAG).size(AGGREGATION_SEARCH_SIZE));
    if (!semanticTagFiltering) {
        fsnQueryBuilder.withPageable(PAGE_OF_ONE);
        SearchHits<Description> semanticTagResults = elasticsearchTemplate.search(fsnQueryBuilder.build(), Description.class);
        allAggregations.add(semanticTagResults.getAggregations().get("semanticTags"));
        timer.checkpoint("Semantic tag aggregation");
    } else {
        // Apply semantic tag filter
        fsnQueryBuilder.withPageable(LARGE_PAGE).withFields(Description.Fields.CONCEPT_ID);
        Set<Long> conceptSemanticTagMatches = new LongOpenHashSet();
        if (allSemanticTags.size() == 1) {
            try (SearchHitsIterator<Description> descriptionStream = elasticsearchTemplate.searchForStream(fsnQueryBuilder.build(), Description.class)) {
                descriptionStream.forEachRemaining(hit -> conceptSemanticTagMatches.add(parseLong(hit.getContent().getConceptId())));
            }
            allAggregations.add(new SimpleAggregation("semanticTags", allSemanticTags.iterator().next(), conceptSemanticTagMatches.size()));
        } else {
            SearchHits<Description> semanticTagResults = elasticsearchTemplate.search(fsnQueryBuilder.build(), Description.class);
            semanticTagResults.stream().forEach((hit -> conceptSemanticTagMatches.add(parseLong(hit.getContent().getConceptId()))));
            allAggregations.add(semanticTagResults.getAggregations().get("semanticTags"));
        }
        conceptIds = conceptSemanticTagMatches;
    }
    // Fetch concept refset membership aggregation
    SearchHits<ReferenceSetMember> membershipResults = elasticsearchTemplate.search(new NativeSearchQueryBuilder().withQuery(boolQuery().must(branchCriteria.getEntityBranchCriteria(ReferenceSetMember.class)).must(termsQuery(ReferenceSetMember.Fields.ACTIVE, true)).filter(termsQuery(ReferenceSetMember.Fields.REFERENCED_COMPONENT_ID, conceptIds))).withPageable(PAGE_OF_ONE).addAggregation(AggregationBuilders.terms("membership").field(ReferenceSetMember.Fields.REFSET_ID)).build(), ReferenceSetMember.class);
    allAggregations.add(membershipResults.getAggregations().get("membership"));
    timer.checkpoint("Concept refset membership aggregation");
    // Perform final paged description search with description property aggregations
    descriptionFilter.must(termsQuery(Description.Fields.CONCEPT_ID, conceptIds));
    final NativeSearchQueryBuilder queryBuilder = new NativeSearchQueryBuilder().withQuery(descriptionQuery.filter(descriptionFilter)).addAggregation(AggregationBuilders.terms("module").field(Description.Fields.MODULE_ID)).addAggregation(AggregationBuilders.terms("language").field(Description.Fields.LANGUAGE_CODE)).withPageable(pageRequest);
    NativeSearchQuery aggregateQuery = addTermSort(queryBuilder.build());
    aggregateQuery.setTrackTotalHits(true);
    SearchHits<Description> descriptions = elasticsearchTemplate.search(aggregateQuery, Description.class);
    allAggregations.addAll(descriptions.getAggregations().asList());
    timer.checkpoint("Fetch descriptions including module and language aggregations");
    timer.finish();
    // Merge aggregations
    return PageWithBucketAggregationsFactory.createPage(descriptions, new Aggregations(allAggregations), pageRequest);
}

Example 4 with PageWithBucketAggregations

use of org.snomed.snowstorm.core.data.services.pojo.PageWithBucketAggregations in project snowstorm by IHTSDO.

the class MultiSearchService method findDescriptionsReferenceSets.

public PageWithBucketAggregations<Description> findDescriptionsReferenceSets(DescriptionCriteria criteria, PageRequest pageRequest) {
    // all search results are required to determine total refset bucket membership
    SearchHits<Description> allSearchHits = findDescriptionsHelper(criteria, null);
    // paged results are required for the list of descriptions returned
    SearchHits<Description> searchHits = findDescriptionsHelper(criteria, pageRequest);
    List<Aggregation> allAggregations = new ArrayList<>();
    Set<Long> conceptIds = new HashSet<>();
    for (SearchHit<Description> desc : allSearchHits) {
        conceptIds.add(Long.parseLong(desc.getContent().getConceptId()));
    }
    // Fetch concept refset membership aggregation
    SearchHits<ReferenceSetMember> membershipResults = elasticsearchTemplate.search(new NativeSearchQueryBuilder().withQuery(boolQuery().must(termsQuery(ReferenceSetMember.Fields.ACTIVE, true)).filter(termsQuery(ReferenceSetMember.Fields.REFERENCED_COMPONENT_ID, conceptIds))).withPageable(PageRequest.of(0, 1)).addAggregation(AggregationBuilders.terms("membership").field(ReferenceSetMember.Fields.REFSET_ID).size(AGGREGATION_SEARCH_SIZE)).build(), ReferenceSetMember.class);
    allAggregations.add(membershipResults.getAggregations().get("membership"));
    PageWithBucketAggregations<Description> page = PageWithBucketAggregationsFactory.createPage(searchHits, new Aggregations(allAggregations), pageRequest);
    return page;
}