ConfigTools.java

package net.sourceforge.seqware.common.util.configtools;

import io.seqware.pipeline.SqwKeys;
import java.io.File;
import java.util.HashMap;
import java.util.Map;
import javax.naming.Context;
import javax.naming.InitialContext;
import javax.naming.NamingException;
import net.sourceforge.seqware.common.util.maptools.MapTools;

/**
 * <p>
 * ConfigTools class.
 * </p>
 *
 * @author boconnor
 * @version $Id: $Id
 */
public class ConfigTools {

    /** Constant <code>SEQWARE_SETTINGS_PROPERTY="SEQWARE_SETTINGS"</code> */
    public static final String SEQWARE_SETTINGS_PROPERTY = "SEQWARE_SETTINGS";

    /**
     * The output keys are always uppercase!
     *
     * @return a {@link java.util.Map} object.
     */
    public static Map<String, String> getSettings() {

        // first, try to figure out the location of the settings file
        String settings = getSettingsFilePath();

        // Log.info(settings);
        File settingsFile = new File(settings);

        if (!settingsFile.exists()) {
            throw new RuntimeException("The settings file " + settings + " does not exist, or user '" + System.getProperty("user.name")
                    + "' does not have permissions to read it!");
        } else if (!settingsFile.isFile()) {
            throw new RuntimeException("The settings file " + settings + " is not a file!");
        }

        HashMap<String, String> hm = new HashMap<>();

        // now read back the values from the settings file
        MapTools.ini2Map(settings, hm, true);

        return hm;
    }

    /**
     * Get the value of a key if defined or the default value if not defined.
     * 
     * @param key
     * @return
     */
    public static String getSettingsValue(SqwKeys key) {
        Map<String, String> settings = ConfigTools.getSettings();
        return settings.containsKey(key.getSettingKey()) ? settings.get(key.getSettingKey()) : key.getDefaultValue();
    }

    /**
     * <p>
     * getProperty.
     * </p>
     *
     * @param name
     *            a {@link java.lang.String} object.
     * @return a {@link java.lang.String} object.
     */
    public static String getProperty(String name) {

        String value = null;

        // try pulling from standard env variable for running as standalone web
        // server
        value = System.getProperty(name);

        if (value == null) {
            value = System.getenv(name);
        }

        // if that's null then try pulling from web.xml or context.xml
        if (value == null) {
            Context initCtx;
            try {
                initCtx = new InitialContext();
                Context envCtx = (Context) initCtx.lookup("java:comp/env");
                value = (String) envCtx.lookup(name);
            } catch (NamingException e) {
                // WARNING: This method of pulling env vars from a Context works
                // in a web server, this may fail in a stand-alone application.
                // If you see this warning you probably don't have a
                // needed/recommended environmental variable set
                // (e.g. SEQWARE_SETTINGS). SEQWARE_SETTINGS by default points
                // to ~/.seqware/settings.");
                // e.printStackTrace();
                value = null;
            }
        }

        return value;

    }

    public static String getSettingsFilePath() {
        String settings = ConfigTools.getProperty(SEQWARE_SETTINGS_PROPERTY);
        if (settings == null || "".equals(settings)) {
            settings = ConfigTools.getProperty("HOME") + File.separator + ".seqware/settings";
        }
        if (ConfigTools.getProperty("HOME") == null || "".equals(ConfigTools.getProperty("HOME"))) {
            settings = ConfigTools.getProperty("user.home") + File.separator + ".seqware/settings";
        }
        return settings;
    }

    public static boolean isValidDBConnectionParam(HashMap<String, String> settings) {
        // do a defensive check to see if we have a direct database connection available
        String server = settings.get(SqwKeys.SW_DB_SERVER.getSettingKey());
        String dbName = settings.get(SqwKeys.SW_DB.getSettingKey());
        String user = settings.get(SqwKeys.SW_DB_USER.getSettingKey());
        String pass = settings.get(SqwKeys.SW_DB_PASS.getSettingKey());
        if (server == null || dbName == null || user == null || pass == null) {
            return false;
        }
        return true;
    }
}