Examples with EntityPager org.molgenis.data.rest.EntityPager used on opensource projects

Example 1 with EntityPager

use of org.molgenis.data.rest.EntityPager in project molgenis by molgenis.

the class RestControllerV2 method createEntityCollectionResponse.

private EntityCollectionResponseV2 createEntityCollectionResponse(String entityTypeId, EntityCollectionRequestV2 request, HttpServletRequest httpRequest, boolean includeCategories) {
    EntityType meta = dataService.getEntityType(entityTypeId);
    Query<Entity> q = request.getQ() != null ? request.getQ().createQuery(meta) : new QueryImpl<>();
    q.pageSize(request.getNum()).offset(request.getStart()).sort(request.getSort());
    Fetch fetch = AttributeFilterToFetchConverter.convert(request.getAttrs(), meta, LocaleContextHolder.getLocale().getLanguage());
    if (fetch != null) {
        q.fetch(fetch);
    }
    if (request.getAggs() != null) {
        // return aggregates for aggregate query
        AggregateQuery aggsQ = request.getAggs().createAggregateQuery(meta, q);
        Attribute xAttr = aggsQ.getAttributeX();
        Attribute yAttr = aggsQ.getAttributeY();
        if (xAttr == null && yAttr == null) {
            throw new MolgenisQueryException("Aggregate query is missing 'x' or 'y' attribute");
        }
        AggregateResult aggs = dataService.aggregate(entityTypeId, aggsQ);
        AttributeResponseV2 xAttrResponse = xAttr != null ? new AttributeResponseV2(entityTypeId, meta, xAttr, fetch, permissionService, dataService) : null;
        AttributeResponseV2 yAttrResponse = yAttr != null ? new AttributeResponseV2(entityTypeId, meta, yAttr, fetch, permissionService, dataService) : null;
        return new EntityAggregatesResponse(aggs, xAttrResponse, yAttrResponse, BASE_URI + '/' + entityTypeId);
    } else {
        Long count = dataService.count(entityTypeId, new QueryImpl<>(q).setOffset(0).setPageSize(0));
        Iterable<Entity> it;
        if (count > 0 && q.getPageSize() > 0) {
            it = () -> dataService.findAll(entityTypeId, q).iterator();
        } else {
            it = Collections.emptyList();
        }
        EntityPager pager = new EntityPager(request.getStart(), request.getNum(), count, it);
        List<Map<String, Object>> entities = new ArrayList<>();
        for (Entity entity : it) {
            Map<String, Object> responseData = new LinkedHashMap<>();
            createEntityValuesResponse(entity, fetch, responseData);
            entities.add(responseData);
        }
        UriComponentsBuilder builder = UriComponentsBuilder.fromUriString(getFullURL(httpRequest));
        String prevHref = null;
        if (pager.getPrevStart() != null) {
            builder.replaceQueryParam("start", pager.getPrevStart());
            prevHref = builder.build(false).toUriString();
        }
        String nextHref = null;
        if (pager.getNextStart() != null) {
            builder.replaceQueryParam("start", pager.getNextStart());
            nextHref = builder.build(false).toUriString();
        }
        return new EntityCollectionResponseV2(pager, entities, fetch, BASE_URI + '/' + entityTypeId, meta, permissionService, dataService, prevHref, nextHref, includeCategories);
    }
}

Example 2 with EntityPager

use of org.molgenis.data.rest.EntityPager in project molgenis by molgenis.

the class SortaController method retrieveSortaJobResults.

@PostMapping("/match/retrieve")
@ResponseBody
public EntityCollectionResponse retrieveSortaJobResults(@RequestBody SortaServiceRequest sortaServiceRequest) {
    List<Map<String, Object>> entityMaps = new ArrayList<>();
    String sortaJobExecutionId = sortaServiceRequest.getSortaJobExecutionId();
    String filterQuery = sortaServiceRequest.getFilterQuery();
    String ontologyIri = sortaServiceRequest.getOntologyIri();
    EntityPager entityPager = sortaServiceRequest.getEntityPager();
    SortaJobExecution sortaJobExecution = findSortaJobExecution(sortaJobExecutionId);
    String resultEntityName = sortaJobExecution.getResultEntityName();
    double threshold = sortaJobExecution.getThreshold();
    boolean isMatched = sortaServiceRequest.isMatched();
    QueryRule queryRuleInputEntities = new QueryRule(Arrays.asList(new QueryRule(VALIDATED, EQUALS, isMatched), new QueryRule(isMatched ? OR : AND), new QueryRule(SCORE, isMatched ? GREATER_EQUAL : LESS, threshold)));
    List<QueryRule> queryRuleInputEntitiesInOneMatchingTask = singletonList(queryRuleInputEntities);
    // Add filter to the query if query string is not empty
    if (isNotEmpty(filterQuery)) {
        Iterable<String> filteredInputTermIds = dataService.findAll(sortaJobExecution.getSourceEntityName(), new QueryImpl<>().search(filterQuery)).map(inputEntity -> inputEntity.getString(SortaServiceImpl.DEFAULT_MATCHING_IDENTIFIER)).collect(Collectors.toList());
        QueryRule previousQueryRule = new QueryRule(queryRuleInputEntitiesInOneMatchingTask);
        QueryRule queryRuleFilterInput = new QueryRule(MatchingTaskContentMetaData.INPUT_TERM, Operator.IN, filteredInputTermIds);
        queryRuleInputEntitiesInOneMatchingTask = Arrays.asList(previousQueryRule, new QueryRule(Operator.AND), queryRuleFilterInput);
    }
    Query<Entity> query = new QueryImpl<>(queryRuleInputEntitiesInOneMatchingTask);
    long count = dataService.count(resultEntityName, query);
    int start = entityPager.getStart();
    int num = entityPager.getNum();
    Stream<Entity> findAll = dataService.findAll(sortaJobExecution.getResultEntityName(), query.offset(start).pageSize(num).sort(new Sort().on(VALIDATED, DESC).on(SCORE, DESC)));
    findAll.forEach(mappingEntity -> {
        Map<String, Object> outputEntity = new HashMap<>();
        outputEntity.put("inputTerm", getEntityAsMap(mappingEntity.getEntity(INPUT_TERM)));
        outputEntity.put("matchedTerm", getEntityAsMap(mappingEntity));
        Object matchedTerm = mappingEntity.get(MATCHED_TERM);
        if (matchedTerm != null) {
            outputEntity.put("ontologyTerm", SortaServiceUtil.getEntityAsMap(sortaService.getOntologyTermEntity(matchedTerm.toString(), ontologyIri)));
        }
        entityMaps.add(outputEntity);
    });
    EntityPager pager = new EntityPager(start, num, count, null);
    return new EntityCollectionResponse(pager, entityMaps, "/match/retrieve", ontologyTermMetaData, permissionService, dataService);
}