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

Example 1 with PermissionException

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

the class RequestRetriever method updateStatus.

public SampleRequest updateStatus(String userId, long requestId, SampleRequestStatus newStatus) {
    Request request = dao.get(requestId);
    if (request == null)
        return null;
    Account account = DAOFactory.getAccountDAO().getByEmail(userId);
    if (!request.getAccount().getEmail().equalsIgnoreCase(userId) && account.getType() != AccountType.ADMIN) {
        throw new PermissionException("No permissions for request");
    }
    if (request.getStatus() == newStatus)
        return request.toDataTransferObject();
    request.setStatus(newStatus);
    request.setUpdated(new Date());
    return dao.update(request).toDataTransferObject();
}

Example 2 with PermissionException

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

the class ConfigurationController method autoUpdateSetting.

// update the setting automatically. Currently works only for blast installations
public Setting autoUpdateSetting(String userId, Setting setting) {
    AccountController accountController = new AccountController();
    if (!accountController.isAdministrator(userId))
        throw new PermissionException("Cannot auto update system setting without admin privileges");
    Configuration configuration = dao.get(setting.getKey());
    if (configuration == null) {
        Logger.error("Could not retrieve setting " + setting.getKey());
        return null;
    }
    String osName = System.getProperty("os.name").replaceAll("\\s+", "").toLowerCase();
    String blast = "ncbi-blast-2.6.0+-x64-" + osName + ".tar.gz";
    Path path = Paths.get(dao.get(ConfigurationKey.TEMPORARY_DIRECTORY).getValue(), blast);
    Path dest = Paths.get(dao.get(ConfigurationKey.DATA_DIRECTORY).getValue());
    if (!Files.exists(dest)) {
        Logger.error("Cannot access access dir : " + dest.toString());
        return null;
    }
    try (InputStream is = (new URL(BLAST_FTP_DIR + blast)).openStream()) {
        Files.copy(is, path.toAbsolutePath(), StandardCopyOption.REPLACE_EXISTING);
        Archiver archiver = ArchiverFactory.createArchiver("tar", "gz");
        archiver.extract(path.toFile(), dest.toFile());
        Path valuePath = Paths.get(dest.toString(), "ncbi-blast-2.6.0+", "bin");
        configuration.setValue(valuePath.toString());
        Files.list(valuePath).forEach(dirPath -> {
            try {
                Files.setPosixFilePermissions(dirPath, PosixFilePermissions.fromString("rwxrwxrwx"));
            } catch (IOException e) {
                Logger.error(e);
            }
        });
        return dao.update(configuration).toDataTransferObject();
    } catch (Exception e) {
        Logger.error(e);
        return null;
    }
}

Example 3 with PermissionException

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

the class BulkUploads method deleteDraftById.

/**
 * Deletes a bulk import draft referenced by a unique identifier. only owners of the bulk import
 * or administrators are permitted to delete bulk imports
 *
 * @param userId  account of user making the request
 * @param draftId unique identifier for bulk import
 * @return deleted bulk import
 * @throws PermissionException if lacking permissions
 */
public BulkUploadInfo deleteDraftById(String userId, long draftId) throws PermissionException {
    BulkUpload draft = dao.get(draftId);
    if (draft == null)
        return null;
    Account draftAccount = draft.getAccount();
    if (!userId.equals(draftAccount.getEmail()) && !accountController.isAdministrator(userId))
        throw new PermissionException("No permissions to delete draft " + draftId);
    BulkUploadDeleteTask task = new BulkUploadDeleteTask(userId, draftId);
    IceExecutorService.getInstance().runTask(task);
    BulkUploadInfo draftInfo = draft.toDataTransferObject();
    AccountTransfer accountTransfer = draft.getAccount().toDataTransferObject();
    draftInfo.setAccount(accountTransfer);
    return draftInfo;
}

Example 4 with PermissionException

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

the class EntryController method getRequestedEntry.

public PartData getRequestedEntry(String remoteUserId, String token, String entryId, long folderId, RegistryPartner requestingPartner) {
    Entry entry = getEntry(entryId);
    if (entry == null)
        return null;
    // see folderContents.getRemoteSharedContents
    // folder that the entry is contained in
    Folder folder = DAOFactory.getFolderDAO().get(folderId);
    if (folder == null) {
        // must be a public entry (todo : move to separate method
        if (!permissionsController.isPubliclyVisible(entry))
            throw new PermissionException("Not a public entry");
        return retrieveEntryDetails(null, entry);
    }
    RemotePartner remotePartner = DAOFactory.getRemotePartnerDAO().getByUrl(requestingPartner.getUrl());
    // check that the remote user has the right token
    Permission shareModel = DAOFactory.getPermissionDAO().get(remoteUserId, remotePartner, folder);
    if (shareModel == null) {
        Logger.error("Could not retrieve share model");
        return null;
    }
    // validate access token
    TokenHash tokenHash = new TokenHash();
    String secret = tokenHash.encrypt(folderId + remotePartner.getUrl() + remoteUserId, token);
    if (!secret.equals(shareModel.getSecret())) {
        throw new PermissionException("Secret does not match");
    }
    // check that entry id is contained in folder
    return retrieveEntryDetails(null, entry);
}

Example 5 with PermissionException

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

the class Sequences method bulkUpdate.

/**
 * Bulk update sequences based on uploaded zip file
 * containing sequences, where the sequence name is the (unique) part number of the entry.
 * If there is an existing sequence associated with the entry, it is deleted.
 *
 * @param userId          userId of user making request
 * @param fileInputStream input stream of zip file
 */
public List<String> bulkUpdate(String userId, InputStream fileInputStream) throws IOException {
    if (!new AccountController().isAdministrator(userId))
        throw new PermissionException("Must have admin privileges to use this feature");
    List<String> errors = new ArrayList<>();
    Logger.info("Starting bulk update of sequences");
    try (ZipInputStream stream = new ZipInputStream(fileInputStream)) {
        ZipEntry zipEntry;
        while ((zipEntry = stream.getNextEntry()) != null) {
            if (zipEntry.isDirectory())
                continue;
            String name = zipEntry.getName();
            if (name.contains("/"))
                name = name.substring(name.lastIndexOf("/") + 1);
            if (name.startsWith(".") || name.startsWith("_"))
                continue;
            ByteArrayOutputStream out = new ByteArrayOutputStream();
            int len;
            byte[] data = new byte[1024];
            while ((len = stream.read(data)) > 0) {
                out.write(data, 0, len);
            }
            stream.closeEntry();
            String entryName = name.substring(0, name.indexOf('.'));
            Entry entry = DAOFactory.getEntryDAO().getByPartNumber(entryName);
            if (entry == null) {
                errors.add(name);
                continue;
            }
            String sequenceString = new String(out.toByteArray());
            FeaturedDNASequence dnaSequence = GeneralParser.parse(sequenceString);
            if (dnaSequence == null) {
                Logger.error("Could not parse sequence for " + name);
                errors.add(name);
                continue;
            }
            Logger.info("Updating sequence for entry " + entry.getPartNumber() + " as part of bulk update");
            PartSequence partSequence = new PartSequence(userId, entry.getPartNumber());
            partSequence.delete();
            partSequence.save(dnaSequence);
        }
    }
    Logger.info("Completed bulk upload of sequences with " + errors.size() + " errors");
    return errors;
}