Examples with PermissionException org.jbei.ice.lib.access.PermissionException used on opensource projects

Example 41 with PermissionException

use of org.jbei.ice.lib.access.PermissionException in project ice by JBEI.

the class FolderContents method addEntrySelection.

/**
 * Adds entries in the selection context, to specified folders
 *
 * @param userId        unique identifier for user making request
 * @param entryLocation entry selection context which also contains the folders to
 *                      add the entries obtained from the context to
 * @return list of folders that the entries where added to. They should correspond to the specified
 * folders in the selection context
 */
public List<FolderDetails> addEntrySelection(String userId, EntrySelection entryLocation) {
    Entries retriever = new Entries(userId);
    if (entryLocation.getRemoteEntries() != null && !entryLocation.getRemoteEntries().isEmpty())
        return addRemoteEntries(userId, entryLocation.getRemoteEntries(), entryLocation.getDestination());
    List<Long> entries = retriever.getEntriesFromSelectionContext(entryLocation);
    if (StringUtils.isEmpty(userId)) {
        List<FolderDetails> destination = entryLocation.getDestination();
        // check that folder is transferred before rejecting
        if (destination == null || destination.isEmpty())
            throw new IllegalArgumentException("Cannot add without valid user id or destination");
        Folder folder = folderDAO.get(destination.get(0).getId());
        if (folder == null)
            throw new IllegalArgumentException("Cannot find folder");
        if (folder.getType() != FolderType.TRANSFERRED)
            throw new PermissionException("Can only add to transferred folder without id");
        FolderDetails details = addEntriesToTransferredFolder(entries, folder);
        List<FolderDetails> result = new ArrayList<>();
        result.add(details);
        return result;
    }
    return addEntriesToFolders(userId, entries, entryLocation.getDestination());
}

Example 42 with PermissionException

use of org.jbei.ice.lib.access.PermissionException in project ice by JBEI.

the class CollectionEntries method getPersonalEntries.

/**
 * Retrieves entries owned by user
 *
 * @param field  sort field
 * @param asc    sort order
 * @param offset paging start
 * @param limit  maximum number of entries to retrieve
 * @param filter optional text to filter entries by
 * @return wrapper around list of parts that conform to the parameters and the maximum number
 * of such entries that are available
 * @throws PermissionException on null user id which is required for owner entries
 */
private Results<PartData> getPersonalEntries(ColumnField field, boolean asc, int offset, int limit, String filter, List<String> fields) {
    if (userId == null || userId.isEmpty())
        throw new PermissionException("User id is required to retrieve owner entries");
    OwnerEntries ownerEntries = new OwnerEntries(userId, userId);
    final List<PartData> entries = ownerEntries.retrieveOwnerEntries(field, asc, offset, limit, filter, fields);
    final long count = ownerEntries.getNumberOfOwnerEntries();
    Results<PartData> results = new Results<>();
    results.setResultCount(count);
    results.setData(entries);
    return results;
}

Example 43 with PermissionException

use of org.jbei.ice.lib.access.PermissionException in project ice by JBEI.

the class Annotations method curate.

/**
 * Curates a specified set of annotations. The curation properties are contained in each annotation (feature)
 * object
 *
 * @param features set of features to be curated
 */
public void curate(List<DNAFeature> features) {
    if (!isAdministrator())
        throw new PermissionException("Administrative privileges required to curate features");
    for (DNAFeature dnaFeature : features) {
        if (dnaFeature.getCuration() == null)
            continue;
        Feature feature = featureDAO.get(dnaFeature.getId());
        if (feature == null)
            continue;
        FeatureCurationModel curationModel = feature.getCuration();
        if (feature.getCuration() == null) {
            if (dnaFeature.getCuration().isExclude()) {
                curationModel = new FeatureCurationModel();
                curationModel.setFeature(feature);
                curationModel.setExclude(true);
                curationModel = curationModelDAO.create(curationModel);
            }
        } else {
            curationModel.setExclude(dnaFeature.getCuration().isExclude());
            curationModel = curationModelDAO.update(curationModel);
        }
        if (curationModel != null) {
            feature.setCuration(curationModel);
            featureDAO.update(feature);
        }
    }
}

Example 44 with PermissionException

use of org.jbei.ice.lib.access.PermissionException in project ice by JBEI.

the class Annotations method get.

/**
 * Retrieves list of annotations that are available
 *
 * @param offset paging start
 * @param limit  maximum number of annotations to return
 * @param sort   paging sort
 * @return available annotations that conform to parameters along with the total number that are available
 * @throws PermissionException if the requesting user's account does not have administrative privileges
 */
public Results<DNAFeatures> get(int offset, int limit, String sort) {
    if (!isAdministrator())
        throw new PermissionException("Administrative privileges required to retrieve features");
    long count = this.featureDAO.getFeaturesGroupByCount();
    Results<DNAFeatures> results = new Results<>();
    results.setResultCount(count);
    Map<String, List<Feature>> map = this.featureDAO.getFeaturesGroupBy(offset, limit);
    for (String key : map.keySet()) {
        DNAFeatures features = new DNAFeatures(key);
        for (Feature feature : map.get(key)) {
            DNAFeature dnaFeature = feature.toDataTransferObject();
            dnaFeature.setSequence(feature.getSequence());
            List<Long> entries = this.sequenceFeatureDAO.getEntryIdsByFeature(feature);
            if (entries != null)
                dnaFeature.getEntries().addAll(entries);
            features.getFeatures().add(dnaFeature);
        }
        results.getData().add(features);
    }
    return results;
}

Example 45 with PermissionException

use of org.jbei.ice.lib.access.PermissionException in project ice by JBEI.

the class AccountController method updateAccount.

/**
 * @param requester
 * @param userId
 * @param transfer
 * @return updated account object
 */
public AccountTransfer updateAccount(final String requester, final long userId, final AccountTransfer transfer) {
    final Account account = dao.get(userId);
    boolean requesterIsAdmin = isAdministrator(requester);
    if (!account.getEmail().equalsIgnoreCase(requester) && !requesterIsAdmin) {
        return null;
    }
    // if transfer has password then it is a password change
    if (!StringUtils.isEmpty(transfer.getFirstName())) {
        account.setFirstName(transfer.getFirstName());
    }
    if (!StringUtils.isEmpty(transfer.getLastName())) {
        account.setLastName(transfer.getLastName());
    }
    if (!StringUtils.isEmpty(transfer.getDescription())) {
        account.setDescription(transfer.getDescription());
    }
    if (!StringUtils.isEmpty(transfer.getInstitution())) {
        account.setInstitution(transfer.getInstitution());
    }
    if (transfer.getAccountType() != null) {
        if (transfer.getAccountType() != account.getType() && !requesterIsAdmin)
            throw new PermissionException("Only admins can change account type");
        account.setType(transfer.getAccountType());
    }
    AccountTransfer result = dao.update(account).toDataTransferObject();
    result.setAdmin(isAdministrator(account.getEmail()));
    return result;
}