Examples with Study uk.ac.ebi.spot.goci.model.Study used on opensource projects

Example 46 with Study

use of uk.ac.ebi.spot.goci.model.Study in project goci by EBISPOT.

the class StudyAncestryService method addAncestry.

public void addAncestry(Long studyId, Ancestry ancestry, SecureUser user) {
    Study study = studyRepository.findOne(studyId);
    // Set the study for our ancestry and save
    ancestry.setStudy(study);
    trackingOperationService.create(ancestry, user);
    ancestryRepository.save(ancestry);
    getLog().info("Ancestry ".concat(ancestry.getId().toString()).concat(" created"));
}

Example 47 with Study

use of uk.ac.ebi.spot.goci.model.Study in project goci by EBISPOT.

the class StudyAncestryService method deleteAll.

public void deleteAll(Long studyId, SecureUser user) {
    // Get all study ancestry's
    Study study = studyRepository.findOne(studyId);
    Collection<Ancestry> studyAncestry = ancestryRepository.findByStudyId(studyId);
    // Delete ancestry
    studyAncestry.forEach(ancestry -> deleteAncestry(ancestry, user));
}

Example 48 with Study

use of uk.ac.ebi.spot.goci.model.Study in project goci by EBISPOT.

the class StudyDataService method updateStudyDiseaseTraitByAccessionId.

public Study updateStudyDiseaseTraitByAccessionId(String trait, String accessionId) {
    Study study = this.getStudyByAccessionId(accessionId).orElseThrow(() -> new ResourceNotFoundException("Study", accessionId));
    DiseaseTrait diseaseTrait = Optional.ofNullable(diseaseTraitRepository.findByTraitIgnoreCase(trait)).orElseThrow(() -> new ResourceNotFoundException("Disease Trait", trait));
    study.setDiseaseTrait(diseaseTrait);
    studyRepository.save(study);
    log.info("Study with accession Id: {} found and updated", accessionId);
    return study;
}

Example 49 with Study

use of uk.ac.ebi.spot.goci.model.Study in project goci by EBISPOT.

the class StudyFileService method createFileUploadEvent.

/**
 * Record file upload event
 *
 * @param studyId Study ID which is used to find study specific dir
 * @param user    User carrying out request
 */
public void createFileUploadEvent(Long studyId, SecureUser user) {
    Study study = studyRepository.findOne(studyId);
    trackingOperationService.update(study, user, "STUDY_FILE_UPLOAD");
    studyRepository.save(study);
    getLog().info("Study ".concat(String.valueOf(study.getId())).concat(" updated"));
}

Example 50 with Study

use of uk.ac.ebi.spot.goci.model.Study in project goci by EBISPOT.

the class BulkOperationsService method flipOpenTargets.

public void flipOpenTargets(Publication publication, SecureUser user) {
    Pair<Boolean, Boolean> existingStatus = getFlagStatus(publication);
    boolean existingOpenTargets = existingStatus.getLeft();
    boolean newOpenTargets = !existingOpenTargets;
    getLog().info("[{}] Changing 'Open Targets' flag for {} studies", publication.getPubmedId(), publication.getStudies().size());
    List<Long> ids = new ArrayList<>();
    for (Study study : publication.getStudies()) {
        ids.add(study.getId());
    }
    for (Long studyId : ids) {
        Study existingStudy = studyRepository.findOne(studyId);
        existingStudy.setOpenTargets(newOpenTargets);
        String updateDescription = "Changed 'Open Targets' flag to: " + Boolean.toString(newOpenTargets);
        trackingOperationService.update(existingStudy, user, "STUDY_UPDATE", updateDescription);
        studyRepository.save(existingStudy);
        getLog().info("Study ".concat(String.valueOf(studyId)).concat(" updated"));
    }
}