Examples with SortaServiceUtil.getEntityAsMap org.molgenis.ontology.utils.SortaServiceUtil.getEntityAsMap used on opensource projects

Example 1 with SortaServiceUtil.getEntityAsMap

use of org.molgenis.ontology.utils.SortaServiceUtil.getEntityAsMap 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);
}