D2RMapFetch.java

/*******************************************************************************
 * Copyright (c) 2010-2011 VIVO Harvester Team. For full list of contributors, please see the AUTHORS file provided.
 * All rights reserved.
 * This program and the accompanying materials are made available under the terms of the new BSD license which accompanies this distribution, and is available at http://www.opensource.org/licenses/bsd-license.html
 ******************************************************************************/
package org.vivoweb.harvester.fetch;

import java.io.IOException;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import org.vivoweb.harvester.util.InitLog;
import org.vivoweb.harvester.util.args.ArgDef;
import org.vivoweb.harvester.util.args.ArgList;
import org.vivoweb.harvester.util.args.ArgParser;
import org.vivoweb.harvester.util.args.UsageException;
import org.vivoweb.harvester.util.repo.RecordHandler;
import de.fuberlin.wiwiss.d2r.D2rProcessor;

/**
 * Fetches database or csv data using D2RMap
 * @author Eliza Chan (elc2013@med.cornell.edu)
 */
public class D2RMapFetch {
	/**
	 * SLF4J Logger
	 */
	private static Logger log = LoggerFactory.getLogger(D2RMapFetch.class);
	/**
	 * Record Handler to write records to
	 */
	private RecordHandler outStore;
	/**
	 * D2RMap config file path
	 */
	private String d2rConfigPath;
	/**
	 * D2RMap working directory
	 */
	private String d2rWDir;

	/**
	 * Get the ArgParser for this task
	 * @return the ArgParser
	 */
	private static ArgParser getParser() {
		ArgParser parser = new ArgParser("D2RMapFetch");

		parser.addArgument(new ArgDef().setShortOption('o').setLongOpt("output").withParameter(true, "CONFIG_FILE").setDescription("RecordHandler config file path").setRequired(false));
		parser.addArgument(new ArgDef().setShortOption('O').setLongOpt("outputOverride").withParameterValueMap("RH_PARAM", "VALUE").setDescription("override the RH_PARAM of output recordhandler using VALUE").setRequired(false));
		
		// d2RMap specific arguments
		parser.addArgument(new ArgDef().setShortOption('u').setLongOpt("d2rMapConfigFile").withParameter(true, "D2RMAP_CONFIG_FILE").setDescription("D2RMap config file path").setRequired(true));
		
		// This option is for CSV data ingest only
		parser.addArgument(new ArgDef().setShortOption('a').setLongOpt("d2rMapWorkingDirectory").withParameter(true, "D2RMAP_WORKING_DIRECTORY").setDescription("D2RMap working directory").setRequired(false));

		return parser;
	}
	
	/**
	 * Command line Constructor
	 * @param args commandline arguments
	 * @throws IOException error creating task
	 * @throws UsageException user requested usage message
	 */
	private D2RMapFetch(String[] args) throws IOException, UsageException {
		this(getParser().parse(args));
	}
	
	/**
	 * Arglist Constructor
	 * @param opts option set of parsed args
	 * @throws IOException error creating task
	 */
	private D2RMapFetch(ArgList opts) throws IOException {
		this(
			opts.get("u"), 
			RecordHandler.parseConfig(opts.get("o"), opts.getValueMap("O")), 
			opts.get("a")
		);
	}
	
	/**
	 * Library style Constructor
	 * @param configPath D2RMap config file path
	 * @param rh Record Handler to write records to
	 * @param workingDir D2RMap working directory
	 */
	public D2RMapFetch(String configPath, RecordHandler rh, String workingDir) {
		this.d2rConfigPath = configPath;
		this.outStore = rh;
		this.d2rWDir = workingDir;
		if(this.outStore == null) {
			throw new IllegalArgumentException("Must provide an output RecordHandler");
		}
	}

	/**
	 * Executes the task
	 */
	public void execute() {
		log.info("Fetch: Start");
		D2rProcessor proc = new D2rProcessor();
		proc.harvesterInit();
		try {
			if(this.d2rConfigPath != null) {
				String output;
				if(this.d2rWDir != null) { // process CSV file
					output = proc.processCsvMap("RDF/XML", this.d2rWDir, this.d2rConfigPath);
				} else { // process data from database
					output = proc.processMap("RDF/XML", this.d2rConfigPath);
				}
				this.outStore.addRecord("id", output, this.getClass());
			}
			
		} catch(Exception e) {
			System.err.println("D2RMapFetch errors: " + e);
		}
		log.info("Fetch: End");
	}
	
	/**
	 * Main method
	 * @param args commandline arguments
	 */
	public static void main(String... args) {
		Exception error = null;
		try {
			InitLog.initLogger(args, getParser());
			log.info(getParser().getAppName() + ": Start");
			new D2RMapFetch(args).execute();
		} catch(IllegalArgumentException e) {
			log.error(e.getMessage());
			log.debug("Stacktrace:",e);
			System.out.println(getParser().getUsage());
			error = e;
		} catch(UsageException e) {
			log.info("Printing Usage:");
			System.out.println(getParser().getUsage());
			error = e;
		} catch(Exception e) {
			log.error(e.getMessage());
			log.debug("Stacktrace:",e);
			error = e;
		} finally {
			log.info(getParser().getAppName() + ": End");
			if(error != null) {
				System.exit(1);
			}
		}
	}
}