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

Example 31 with PermissionException

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

the class ConfigurationSettings 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.warn("Could not retrieve setting " + setting.getKey() + ". Creating...");
        if (setting.getValue() == null)
            setting.setValue("");
        configuration = dao.create(new Configuration(setting.getKey(), setting.getValue()));
    }
    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 32 with PermissionException

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

the class ConfigurationSettings method updateSetting.

public Setting updateSetting(String userId, Setting setting, String url) {
    AccountController accountController = new AccountController();
    if (!accountController.isAdministrator(userId))
        throw new PermissionException("Cannot update system setting without admin privileges");
    ConfigurationKey key = ConfigurationKey.valueOf(setting.getKey());
    Configuration configuration = setPropertyValue(key, setting.getValue());
    // check if the setting being updated is related to the web of registries
    if (key == ConfigurationKey.JOIN_WEB_OF_REGISTRIES) {
        WoRController woRController = new WoRController();
        boolean enable = "yes".equalsIgnoreCase(setting.getValue()) || "true".equalsIgnoreCase(setting.getValue());
        woRController.setEnable(userId, enable, url);
    }
    return configuration.toDataTransferObject();
}

Example 33 with PermissionException

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

the class WebPartners method addNewPartner.

/**
 * Adds the registry instance specified by the url to the list of existing partners (if not already in there)
 * and sends a request to the remote instance that includes a security token that the remote instance
 * can use to communicate with this instance.
 * <p>
 * Information about the remote instance is still saved even when it cannot be communicated with. This
 * allows a future communication attempt.
 *
 * @param userId  id of user performing action (must have admin privileges)
 * @param partner registry partner object that contains unique uniform resource identifier & name for the registry
 * @return add partner ofr
 */
public RegistryPartner addNewPartner(String userId, RegistryPartner partner, String thisUrl) {
    if (!isInWebOfRegistries())
        return null;
    // check for admin privileges before granting request
    if (!accountController.isAdministrator(userId))
        throw new PermissionException("Non admin attempting to add remote partner " + partner.getUrl());
    if (StringUtils.isEmpty(partner.getUrl()))
        throw new IllegalArgumentException("Cannot add partner without valid url");
    // check if there is a partner with that url
    RemotePartner remotePartner = dao.getByUrl(partner.getUrl());
    if (remotePartner != null) {
        // if so just update the api key
        return updateAPIKey(userId, remotePartner.getId());
    }
    Logger.info(userId + ": adding WoR partner [" + partner.getUrl() + "]");
    // create information about this instance to send to potential partner
    // including a random token for use when contacting this instance
    RegistryPartner thisPartner = getThisInstanceWithNewApiKey();
    // validate this url
    if (!isValidUrl(thisPartner.getUrl())) {
        if (isValidUrl(thisUrl))
            thisPartner.setUrl(thisUrl);
        else {
            Logger.error("Could not obtain a valid url for this instance.");
            thisPartner = null;
        }
    }
    if (thisPartner == null) {
        // will not contact
        Logger.error("Cannot exchange api token with remote host due to invalid local url");
        partner.setStatus(RemotePartnerStatus.NOT_CONTACTED);
    } else {
        RegistryPartner newPartner = remoteContact.contactPotentialPartner(thisPartner, partner.getUrl());
        if (newPartner == null) {
            // contact failed
            Logger.error("Remote contact of partner " + partner.getUrl() + " failed");
            partner.setStatus(RemotePartnerStatus.CONTACT_FAILED);
        } else {
            // contact succeeded with return of api key
            partner.setStatus(RemotePartnerStatus.APPROVED);
            partner.setApiKey(newPartner.getApiKey());
        }
    }
    // if status is not approved, then the token is irrelevant since it is not stored and was not
    // successfully transmitted
    String apiKey = thisPartner != null ? thisPartner.getApiKey() : null;
    return createRemotePartnerObject(partner, apiKey);
}

Example 34 with PermissionException

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

the class WebPartners method update.

// only updates the status
public RegistryPartner update(String userId, long id, RegistryPartner partner) {
    if (!isInWebOfRegistries())
        return null;
    if (!accountController.isAdministrator(userId))
        throw new PermissionException(userId + " is not an admin");
    RemotePartner existing = dao.get(id);
    if (existing == null)
        throw new IllegalArgumentException("Cannot retrieve partner with id " + id);
    Logger.info(userId + ": updating partner (" + existing.getUrl() + ") to " + partner.toString());
    existing.setPartnerStatus(partner.getStatus());
    return dao.update(existing).toDataTransferObject();
}

Example 35 with PermissionException

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

the class WebPartners method remove.

public boolean remove(String userId, long id) {
    if (!accountController.isAdministrator(userId))
        throw new PermissionException(userId + " is not an admin");
    RemotePartner partner = dao.get(id);
    if (partner == null)
        return false;
    dao.delete(partner);
    // todo : contact deleted partner since they cannot contact anymore?
    return true;
}