Examples with Group org.jbei.ice.storage.model.Group used on opensource projects

Example 41 with Group

use of org.jbei.ice.storage.model.Group in project ice by JBEI.

the class GroupDAO method getByIdList.

public List<Group> getByIdList(Set<Long> idsSet) {
    try {
        CriteriaQuery<Group> query = getBuilder().createQuery(Group.class);
        Root<Group> from = query.from(Group.class);
        query.where(from.get("id").in(idsSet));
        return currentSession().createQuery(query).list();
    } catch (HibernateException he) {
        Logger.error(he);
        throw new DAOException(he);
    }
}

Example 42 with Group

use of org.jbei.ice.storage.model.Group in project ice by JBEI.

the class MessageDAO method retrieveNewMessageCount.

public int retrieveNewMessageCount(Account account) {
    try {
        StringBuilder builder = new StringBuilder();
        builder.append("select count(id) from message m where m.is_read=false AND (m.id in ").append("(select message_id from message_destination_accounts where account_id = ").append(account.getId()).append(")");
        if (!account.getGroups().isEmpty()) {
            builder.append(" OR m.id in (select message_id from message_destination_groups where group_id in (");
            int i = 0;
            for (Group group : account.getGroups()) {
                if (i > 0)
                    builder.append(", ");
                builder.append(group.getId());
                i += 1;
            }
            builder.append("))");
        }
        builder.append(")");
        NativeQuery query = currentSession().createNativeQuery(builder.toString());
        Number number = (Number) query.uniqueResult();
        return number.intValue();
    } catch (HibernateException he) {
        Logger.error(he);
        throw new DAOException(he);
    }
}

Example 43 with Group

use of org.jbei.ice.storage.model.Group in project ice by JBEI.

the class AccountController method authenticate.

/**
     * Authenticate a user in the database.
     * <p>
     * Using the {@link org.jbei.ice.lib.account.authentication.IAuthentication} specified in the
     * settings file, authenticate the user, and return the sessionData
     *
     * @param login
     * @param password
     * @param ip       IP Address of the user.
     * @return the account identifier (email) on a successful login, otherwise {@code null}
     */
protected Account authenticate(final String login, final String password, final String ip) {
    final IAuthentication authentication = new LocalAuthentication();
    String email;
    try {
        email = authentication.authenticates(login.trim(), password);
        if (email == null) {
            loginFailureCooldown();
            return null;
        }
    } catch (final AuthenticationException e2) {
        loginFailureCooldown();
        return null;
    }
    Account account = dao.getByEmail(email);
    if (account == null)
        return null;
    AccountPreferences accountPreferences = accountPreferencesDAO.getAccountPreferences(account);
    if (accountPreferences == null) {
        accountPreferences = new AccountPreferences();
        accountPreferences.setAccount(account);
        accountPreferencesDAO.create(accountPreferences);
    }
    // add to public groups
    List<Group> groups = groupDAO.getGroupsBy(GroupType.PUBLIC, true);
    try {
        if (groups != null) {
            for (Group group : groups) {
                if (!account.getGroups().contains(group)) {
                    account.getGroups().add(group);
                }
            }
            dao.update(account);
        }
    } catch (Exception e) {
        Logger.error(e);
    }
    account.setIp(ip);
    account.setLastLoginTime(Calendar.getInstance().getTime());
    account = save(account);
    UserSessions.createNewSessionForUser(account.getEmail());
    return account;
}

Example 44 with Group

use of org.jbei.ice.storage.model.Group in project ice by JBEI.

the class EntriesAsCSV method writeList.

/**
     * Iterate through list of entries and extract values
     *
     * @param userId identifier of user making request
     * @throws IOException on Exception write values to file
     */
private void writeList(String userId, EntryField... fields) throws IOException {
    // filter entries based on what the user is allowed to see if the user is not an admin
    Account account = this.accountDAO.getByEmail(userId);
    if (account.getType() != AccountType.ADMIN) {
        List<Group> accountGroups = new GroupController().getAllGroups(account);
        entries = permissionDAO.getCanReadEntries(account, accountGroups, entries);
    }
    if (entries == null) {
        Logger.warn("No entries to convert to csv format");
        return;
    }
    // write headers
    Path tmpPath = Paths.get(Utils.getConfigValue(ConfigurationKey.TEMPORARY_DIRECTORY));
    File tmpFile = File.createTempFile("ice-", ".csv", tmpPath.toFile());
    csvPath = tmpFile.toPath();
    FileWriter fileWriter = new FileWriter(tmpFile);
    if (fields == null || fields.length == 0)
        fields = getEntryFields();
    String[] headers = getCSVHeaders(fields);
    Set<Long> sequenceSet = new HashSet<>();
    try (CSVWriter writer = new CSVWriter(fileWriter)) {
        writer.writeNext(headers);
        // write entry fields
        for (long entryId : entries) {
            Entry entry = dao.get(entryId);
            //  get contents and write data out
            String[] line = new String[fields.length + 3];
            line[0] = entry.getCreationTime().toString();
            line[1] = entry.getPartNumber();
            int i = 1;
            for (EntryField field : fields) {
                line[i + 1] = EntryUtil.entryFieldToValue(entry, field);
                i += 1;
            }
            if (this.includeSequences && sequenceDAO.hasSequence(entryId)) {
                line[i + 1] = getSequenceName(entry);
                sequenceSet.add(entryId);
            } else {
                line[i + 1] = "";
            }
            writer.writeNext(line);
        }
    }
    writeZip(userId, sequenceSet);
}

Example 45 with Group

use of org.jbei.ice.storage.model.Group in project ice by JBEI.

the class Entries method getCollectionEntries.

protected List<Long> getCollectionEntries(String collection, boolean all, EntryType type) {
    if (collection == null || collection.isEmpty())
        return null;
    Account account = accountDAO.getByEmail(userId);
    List<Long> entries;
    switch(collection.toLowerCase()) {
        case "personal":
            if (all)
                type = null;
            entries = dao.getOwnerEntryIds(userId, type);
            break;
        case "shared":
            entries = dao.sharedWithUserEntryIds(account, account.getGroups());
            break;
        case "available":
            Group publicGroup = new GroupController().createOrRetrievePublicGroup();
            entries = dao.getVisibleEntryIds(account.getType() == AccountType.ADMIN, publicGroup);
            break;
        default:
            return null;
    }
    return entries;
}