Examples with AccountController org.jbei.ice.lib.account.AccountController used on opensource projects

Example 1 with AccountController

use of org.jbei.ice.lib.account.AccountController in project ice by JBEI.

the class RemoteEntries method transferEntries.

/**
     * Schedules a task to handle the transfer
     *
     * @param userId    identifier of user making request
     * @param remoteId  local unique identifier for partner to transfer to
     * @param selection context for generating entries to transfer or list of entries
     * @throws PermissionException if user making request is not an administrator
     */
public void transferEntries(String userId, long remoteId, EntrySelection selection) {
    AccountController accountController = new AccountController();
    if (!accountController.isAdministrator(userId))
        throw new PermissionException("Administrative privileges required to transfer entries");
    TransferTask task = new TransferTask(userId, remoteId, selection);
    IceExecutorService.getInstance().runTask(task);
}

Example 2 with AccountController

use of org.jbei.ice.lib.account.AccountController in project ice by JBEI.

the class ModelToInfoFactory method getCommon.

public static PartData getCommon(PartData info, Entry entry) {
    info.setId(entry.getId());
    info.setRecordId(entry.getRecordId());
    info.setPartId(entry.getPartNumber());
    info.setName(entry.getName());
    String owner = entry.getOwner();
    if (owner.trim().isEmpty())
        owner = entry.getOwnerEmail();
    info.setOwner(owner);
    info.setOwnerEmail(entry.getOwnerEmail());
    Account ownerAccount = DAOFactory.getAccountDAO().getByEmail(info.getOwnerEmail());
    if (ownerAccount != null)
        info.setOwnerId(ownerAccount.getId());
    info.setCreator(entry.getCreator());
    info.setCreatorEmail(entry.getCreatorEmail());
    Account creatorAccount = DAOFactory.getAccountDAO().getByEmail(info.getCreatorEmail());
    if (creatorAccount != null)
        info.setCreatorId(creatorAccount.getId());
    AccountController accountController = new AccountController();
    try {
        long ownerId = accountController.getAccountId(entry.getOwnerEmail());
        info.setOwnerId(ownerId);
        if (entry.getCreatorEmail() != null && !entry.getCreatorEmail().isEmpty()) {
            long creatorId = accountController.getAccountId(entry.getCreatorEmail());
            info.setCreatorId(creatorId);
        }
    } catch (Exception ce) {
        Logger.debug(ce.getMessage());
    }
    info.setAlias(entry.getAlias());
    info.setKeywords(entry.getKeywords());
    info.setStatus(entry.getStatus());
    info.setShortDescription(entry.getShortDescription());
    info.setCreationTime(entry.getCreationTime().getTime());
    info.setModificationTime(entry.getModificationTime().getTime());
    info.setBioSafetyLevel(entry.getBioSafetyLevel());
    info.setLongDescription(entry.getLongDescription());
    info.setIntellectualProperty(entry.getIntellectualProperty());
    info.setSelectionMarkers(EntryUtil.getSelectionMarkersAsList(entry.getSelectionMarkers()));
    // funding sources
    info.setFundingSource(entry.getFundingSource());
    info.setPrincipalInvestigator(entry.getPrincipalInvestigator());
    try {
        if (!StringUtils.isEmpty(entry.getPrincipalInvestigatorEmail())) {
            Account piAccount = accountController.getByEmail(entry.getPrincipalInvestigatorEmail());
            if (piAccount != null) {
                info.setPrincipalInvestigator(piAccount.getFullName());
                info.setPrincipalInvestigatorEmail(piAccount.getEmail());
                info.setPrincipalInvestigatorId(piAccount.getId());
            } else
                info.setPrincipalInvestigatorEmail(entry.getPrincipalInvestigatorEmail());
        }
    } catch (Exception e) {
        Logger.debug(e.getMessage());
    }
    ArrayList<String> links = new ArrayList<>();
    if (entry.getLinks() != null) {
        for (Link link : entry.getLinks()) {
            links.add(link.getLink());
        }
    }
    info.setLinks(links);
    ArrayList<CustomField> params = new ArrayList<>();
    if (entry.getParameters() != null) {
        for (Parameter parameter : entry.getParameters()) {
            CustomField paramInfo = new CustomField();
            paramInfo.setId(parameter.getId());
            paramInfo.setName(parameter.getKey());
            paramInfo.setValue(parameter.getValue());
            params.add(paramInfo);
        }
    }
    info.setCustomFields(params);
    // get visibility
    info.setVisibility(Visibility.valueToEnum(entry.getVisibility()));
    info.setLongDescription(entry.getLongDescription());
    info.setShortDescription(entry.getShortDescription());
    info.setReferences(entry.getReferences());
    // linked entries
    for (Entry linkedEntry : entry.getLinkedEntries()) {
        PartData linkedPartData = getInfo(linkedEntry);
        if (linkedPartData != null)
            info.getLinkedParts().add(linkedPartData);
    }
    return info;
}

Example 3 with AccountController

use of org.jbei.ice.lib.account.AccountController in project ice by JBEI.

the class Entries method updateVisibility.

public boolean updateVisibility(List<Long> entryIds, Visibility visibility) {
    Account account = accountDAO.getByEmail(userId);
    List<Group> accountGroups = new GroupController().getAllGroups(account);
    if (!new AccountController().isAdministrator(userId) && !permissionDAO.canWrite(account, accountGroups, entryIds))
        return false;
    for (long entryId : entryIds) {
        Entry entry = dao.get(entryId);
        if (entry.getVisibility() == visibility.getValue())
            continue;
        entry.setVisibility(visibility.getValue());
        dao.update(entry);
    }
    return true;
}

Example 4 with AccountController

use of org.jbei.ice.lib.account.AccountController 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 5 with AccountController

use of org.jbei.ice.lib.account.AccountController in project ice by JBEI.

the class ConfigurationController method retrieveSystemSettings.

public ArrayList<Setting> retrieveSystemSettings(String userId) {
    ArrayList<Setting> settings = new ArrayList<>();
    if (!new AccountController().isAdministrator(userId))
        return settings;
    for (ConfigurationKey key : ConfigurationKey.values()) {
        Configuration configuration = dao.get(key);
        Setting setting;
        if (configuration == null)
            setting = new Setting(key.name(), "");
        else
            setting = new Setting(configuration.getKey(), configuration.getValue());
        settings.add(setting);
    }
    return settings;
}