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

Example 1 with Configuration

use of org.jbei.ice.storage.model.Configuration 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 2 with Configuration

use of org.jbei.ice.storage.model.Configuration 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;
}

Example 3 with Configuration

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

the class ConfigurationController method setPropertyValue.

public Configuration setPropertyValue(ConfigurationKey key, String value) {
    Configuration configuration = dao.get(key);
    if (configuration == null) {
        configuration = new Configuration();
        configuration.setKey(key.name());
        configuration.setValue(value);
        return dao.create(configuration);
    }
    configuration.setValue(value);
    return dao.update(configuration);
}

Example 4 with Configuration

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

the class ConfigurationDAOTest method testSave.

@Test
public void testSave() throws Exception {
    Configuration config = new Configuration();
    config.setKey("foo");
    config.setValue("bar");
    config = dao.create(config);
    Assert.assertNotNull(config);
    Assert.assertTrue(config.getId() > 0);
}

Example 5 with Configuration

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

the class ConfigurationDAOTest method testGet.

@Test
public void testGet() throws Exception {
    Configuration config = new Configuration();
    config.setKey(ConfigurationKey.NEW_REGISTRATION_ALLOWED.name());
    config.setValue("true");
    config = dao.create(config);
    Assert.assertNotNull(config);
    Assert.assertTrue(config.getId() > 0);
    config = dao.get(ConfigurationKey.NEW_REGISTRATION_ALLOWED);
    Assert.assertNotNull(config);
    Assert.assertEquals("true", config.getValue());
    config = dao.get(ConfigurationKey.NEW_REGISTRATION_ALLOWED.name());
    Assert.assertNotNull(config);
    Assert.assertEquals("true", config.getValue());
}