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A utility for managing documents stored in a PostgreSQL database. The documents are imported into a PostgreSQL DB as full texts with the goal to be able to retrieve the documents by their PubMedID efficiently. For more sophisticated tasks, a user configuration file can be delivered which can take control of the table schema to use, the PostgreSQL schema to use and the actual database server to connect to as well as the concrete database.

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package de.julielab.xmlData.config;

import java.io.IOException;

import org.slf4j.Logger;
import org.slf4j.LoggerFactory;

import com.ximpleware.AutoPilot;
import com.ximpleware.VTDException;
import com.ximpleware.VTDGen;
import com.ximpleware.VTDNav;
import com.ximpleware.XPathParseException;

import de.julielab.xmlData.dataBase.DataBaseConnector;



public abstract class ConfigBase {
	protected static final Logger LOG = LoggerFactory.getLogger(DataBaseConnector.class);
	/**
	 * Inserts the user schemes into the default configuration. This makes all
	 * data available in one place, which is useful for referencing default
	 * values from within a user configuration.
	 * 
	 * @param defaultConfData
	 *            - prepared default configuration file
	 * @param userConfData
	 *            - prepared user specific configuration file
	 * @param xpath
	 *            - path to the part to merge
	 * @return - the merged configuration
	 * @throws VTDException
	 * @throws IOException
	 */
//	protected byte[] mergeConfigData(byte[] defaultConfData,
//			byte[] userConfData, String xpath) throws VTDException, IOException {
//		VTDGen vg = new VTDGen();
//		vg.setDoc(defaultConfData);
//		vg.parse(true);
//		VTDNav vn = vg.getNav();
//		AutoPilot ap = new AutoPilot(vn);
//		ap.selectXPath(xpath);
//		if (ap.evalXPath() != -1) {
//			XMLModifier xm = new XMLModifier(vn);
//			xm.insertAfterElement(userConfData);
//			ByteArrayOutputStream os = new ByteArrayOutputStream();
//			xm.output(os);
//			return os.toByteArray();
//		}
//		return null;
//	}

	/**
	 * Retrieves XML elements (determined by the used path) 
	 * from the configuration.
	 * 
	 * @param confData
	 *            - prepared XML
	 * @param xpath
	 *            - path to the retrieved configuration element
	 * @return - the retrieved element
	 * @throws IOException
	 * @throws VTDException
	 */
	protected byte[] extractConfigData(byte[] confData, String xpath)
			throws IOException, VTDException {
		byte[] configData;
		VTDGen vg = new VTDGen();
		vg.setDoc(confData);
		vg.parse(true);
		VTDNav vn = vg.getNav();
		AutoPilot ap = new AutoPilot(vn);
		ap.selectXPath(xpath);
		StringBuilder sb = new StringBuilder();

		while (ap.evalXPath() != -1) {
			long fragment = vn.getElementFragment();
			int offset = (int) fragment;
			int length = (int) (fragment >> 32);
			sb.append(vn.toRawString(offset, length));
		}

		configData = sb.toString().getBytes();
		return configData;
	}

	/**
	 * Used to determine which of the elements in the configuration file
	 * is set as active.
	 * 
	 * @param data - the configuration file
	 * @param activePath - xpath to the element which defines the active configuration
	 * @return - the name of the active configuration
	 * @throws IOException
	 * @throws VTDException
	 */
	public static String getActiveConfig(byte[] data, String activePath)
			throws IOException, VTDException {
		VTDGen vg = new VTDGen();
		vg.setDoc(data);
		vg.parse(true);
		VTDNav vn = vg.getNav();
		AutoPilot ap = new AutoPilot(vn);
		ap.selectXPath(activePath);
		if (ap.evalXPath() != -1) {
			int textNodeIndex = vn.getText();
			if (textNodeIndex != -1)
				return vn.toRawString(textNodeIndex);
		}
		return null;
	}
	
	/**
	 * Used to get an element by its relative xpath.
	 * 
	 * @param ap - a vtd autopilot
	 * @param xpath - xpath to the element which shall be returned
	 * @return - String representation of the element
	 * @throws XPathParseException
	 */
	protected String stringFromXpath(AutoPilot ap, String xpath)
			throws XPathParseException {
		ap.selectXPath(xpath);
		String string = ap.evalXPathToString();
		ap.resetXPath();
		return string;
	}

}