Examples with SortaJobExecution org.molgenis.ontology.sorta.job.SortaJobExecution used on opensource projects

Example 6 with SortaJobExecution

use of org.molgenis.ontology.sorta.job.SortaJobExecution in project molgenis by molgenis.

the class SortaController method download.

@GetMapping("/match/download/{sortaJobExecutionId}")
public void download(@PathVariable String sortaJobExecutionId, HttpServletResponse response) throws IOException {
    try (CsvWriter csvWriter = new CsvWriter(response.getOutputStream(), SortaServiceImpl.DEFAULT_SEPARATOR)) {
        SortaJobExecution sortaJobExecution = findSortaJobExecution(sortaJobExecutionId);
        response.setContentType("text/csv");
        response.addHeader("Content-Disposition", "attachment; filename=" + generateCsvFileName());
        List<String> columnHeaders = new ArrayList<>();
        EntityType targetMetadata = entityTypeFactory.create("SortaDownload" + sortaJobExecutionId);
        EntityType sourceMetaData = dataService.getEntityType(sortaJobExecution.getSourceEntityName());
        for (Attribute attribute : sourceMetaData.getAttributes()) {
            if (!attribute.getName().equalsIgnoreCase(SortaCsvRepository.ALLOWED_IDENTIFIER)) {
                columnHeaders.add(attribute.getName());
                targetMetadata.addAttribute(attrMetaFactory.create().setName(attribute.getName()));
            }
        }
        columnHeaders.addAll(Arrays.asList(OntologyTermMetaData.ONTOLOGY_TERM_NAME, OntologyTermMetaData.ONTOLOGY_TERM_IRI, MatchingTaskContentMetaData.SCORE, MatchingTaskContentMetaData.VALIDATED));
        targetMetadata.addAttribute(ontologyTermMetaData.getAttribute(OntologyTermMetaData.ONTOLOGY_TERM_NAME));
        targetMetadata.addAttribute(ontologyTermMetaData.getAttribute(OntologyTermMetaData.ONTOLOGY_TERM_IRI));
        targetMetadata.addAttribute(Attribute.newInstance(matchingTaskContentMetaData.getAttribute(MatchingTaskContentMetaData.SCORE), EntityType.AttributeCopyMode.SHALLOW_COPY_ATTRS, attrMetaFactory).setDataType(AttributeType.STRING));
        targetMetadata.addAttribute(matchingTaskContentMetaData.getAttribute(MatchingTaskContentMetaData.VALIDATED));
        csvWriter.writeAttributeNames(columnHeaders);
        dataService.findAll(sortaJobExecution.getResultEntityName(), new QueryImpl<>()).forEach(resultEntity -> csvWriter.add(toDownloadRow(sortaJobExecution, resultEntity, targetMetadata)));
    }
}

Example 7 with SortaJobExecution

use of org.molgenis.ontology.sorta.job.SortaJobExecution 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);
}

Example 8 with SortaJobExecution

use of org.molgenis.ontology.sorta.job.SortaJobExecution in project molgenis by molgenis.

the class SortaController method getJobsForCurrentUser.

private List<SortaJobExecution> getJobsForCurrentUser() {
    final List<SortaJobExecution> jobs = new ArrayList<>();
    User currentUser = userAccountService.getCurrentUser();
    Query<SortaJobExecution> query = dataService.query(SORTA_JOB_EXECUTION, SortaJobExecution.class).eq(JobExecutionMetaData.USER, currentUser.getUsername());
    query.sort().on(JobExecutionMetaData.START_DATE, DESC);
    RunAsSystemAspect.runAsSystem(() -> query.findAll().forEach(job -> {
        // TODO: fetch the user as well
        job.set(JobExecutionMetaData.USER, currentUser.getUsername());
        jobs.add(job);
    }));
    return jobs;
}

Example 9 with SortaJobExecution

use of org.molgenis.ontology.sorta.job.SortaJobExecution in project molgenis by molgenis.

the class SortaController method findMatchingOntologyTerms.

@PostMapping("/match/entity")
@ResponseBody
public SortaServiceResponse findMatchingOntologyTerms(@RequestBody Map<String, Object> request) {
    // TODO: less obfuscated request object, let Spring do the matching
    if (request.containsKey("sortaJobExecutionId") && !isEmpty(request.get("sortaJobExecutionId").toString()) && request.containsKey(IDENTIFIER) && !isEmpty(request.get(IDENTIFIER).toString())) {
        String sortaJobExecutionId = request.get("sortaJobExecutionId").toString();
        SortaJobExecution sortaJobExecution = findSortaJobExecution(sortaJobExecutionId);
        if (sortaJobExecution == null)
            return new SortaServiceResponse("sortaJobExecutionId is invalid!");
        String inputTermIdentifier = request.get(IDENTIFIER).toString();
        Entity inputEntity = dataService.findOneById(sortaJobExecution.getSourceEntityName(), inputTermIdentifier);
        if (inputEntity == null)
            return new SortaServiceResponse("inputTerm identifier is invalid!");
        return new SortaServiceResponse(inputEntity, sortaService.findOntologyTermEntities(sortaJobExecution.getOntologyIri(), inputEntity));
    }
    return new SortaServiceResponse("Please check that sortaJobExecutionId and identifier keys exist in input and have nonempty value!");
}