Examples with AssociationType org.broadinstitute.consent.http.enumeration.AssociationType used on opensource projects

Example 1 with AssociationType

use of org.broadinstitute.consent.http.enumeration.AssociationType in project consent by DataBiosphere.

the class DatasetService method createConsentForDataset.

/**
 * Create a minimal consent from the data provided in a Dataset.
 *
 * @param dataset The DataSetDTO
 * @return The created Consent
 */
public Consent createConsentForDataset(DatasetDTO dataset) {
    String consentId = UUID.randomUUID().toString();
    Optional<DataSetPropertyDTO> nameProp = dataset.getProperties().stream().filter(p -> p.getPropertyName().equalsIgnoreCase(DATASET_NAME_KEY)).findFirst();
    // Typically, this is a construct from ORSP consisting of dataset name and some form of investigator code.
    // In our world, we'll use that dataset name if provided, or the alias.
    String groupName = nameProp.isPresent() ? nameProp.get().getPropertyValue() : dataset.getAlias();
    String name = CONSENT_NAME_PREFIX + dataset.getDataSetId();
    Date createDate = new Date();
    if (Objects.nonNull(dataset.getDataUse())) {
        boolean manualReview = isConsentDataUseManualReview(dataset.getDataUse());
        /*
             * Consents created for a dataset do not need the following properties:
             * data user letter
             * data user letter name
             */
        UseRestriction useRestriction = converter.parseUseRestriction(dataset.getDataUse());
        String translatedUseRestriction = converter.translateDataUse(dataset.getDataUse(), DataUseTranslationType.DATASET);
        consentDAO.useTransaction(h -> {
            try {
                h.insertConsent(consentId, manualReview, useRestriction.toString(), dataset.getDataUse().toString(), null, name, null, createDate, createDate, translatedUseRestriction, groupName, dataset.getDacId());
                if (Objects.nonNull(dataset.getDacId())) {
                    h.updateConsentDac(consentId, dataset.getDacId());
                }
                String associationType = AssociationType.SAMPLE_SET.getValue();
                h.insertConsentAssociation(consentId, associationType, dataset.getDataSetId());
            } catch (Exception e) {
                h.rollback();
                logger.error("Exception creating consent: " + e.getMessage());
                throw e;
            }
        });
        return consentDAO.findConsentById(consentId);
    } else {
        throw new IllegalArgumentException("Dataset is missing Data Use information. Consent could not be created.");
    }
}