Examples with StudyPatchRequest uk.ac.ebi.spot.goci.curation.dto.StudyPatchRequest used on opensource projects

Example 1 with StudyPatchRequest

use of uk.ac.ebi.spot.goci.curation.dto.StudyPatchRequest in project goci by EBISPOT.

the class FileHandler method getStudyPatchRequests.

public static List<StudyPatchRequest> getStudyPatchRequests(FileUploadRequest fileUploadRequest) {
    CsvMapper mapper = new CsvMapper();
    CsvSchema schema = getSchemaFromMultiPartFile(fileUploadRequest.getMultipartFile());
    List<StudyPatchRequest> studyPatchRequests;
    try {
        InputStream inputStream = fileUploadRequest.getMultipartFile().getInputStream();
        MappingIterator<StudyPatchRequest> iterator = mapper.readerFor(StudyPatchRequest.class).with(schema).readValues(inputStream);
        studyPatchRequests = iterator.readAll();
    } catch (IOException e) {
        throw new FileUploadException("Could not read the file");
    }
    return studyPatchRequests;
}

Example 2 with StudyPatchRequest

use of uk.ac.ebi.spot.goci.curation.dto.StudyPatchRequest in project goci by EBISPOT.

the class StudyRestController method multiUploadFileModel.

@PostMapping(Endpoint.STUDIES)
public Object multiUploadFileModel(@Valid FileUploadRequest fileUploadRequest, BindingResult result) {
    if (result.hasErrors()) {
        throw new FileValidationException(result);
    }
    List<StudyPatchRequest> studyPatchRequests = FileHandler.getStudyPatchRequests(fileUploadRequest);
    List<Study> updatedStudies = new ArrayList<>();
    for (StudyPatchRequest request : studyPatchRequests) {
        log.info("Dataset with GCST {} and Curated Trait {} was loaded from file", request.getGcst(), request.getCuratedReportedTrait());
        String gcst = request.getGcst().trim();
        String curatedReportedTrait = request.getCuratedReportedTrait().trim();
        updatedStudies.add(studyDataService.updateStudyDiseaseTraitByAccessionId(curatedReportedTrait, gcst));
    }
    return new ResponseEntity<>(updatedStudies, HttpStatus.OK);
}