ListStudies.java

/*
	
	Copyright 2012 VU Medical Center Amsterdam
	
	Licensed under the Apache License, Version 2.0 (the "License");
	you may not use this file except in compliance with the License.
	You may obtain a copy of the License at
	
	    http://www.apache.org/licenses/LICENSE-2.0
	
	Unless required by applicable law or agreed to in writing, software
	distributed under the License is distributed on an "AS IS" BASIS,
	WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
	See the License for the specific language governing permissions and
	limitations under the License.
	
*/

package nl.vumc.trait.oc.main;

import java.io.UnsupportedEncodingException;
import java.net.MalformedURLException;
import java.security.NoSuchAlgorithmException;

import javax.xml.datatype.DatatypeConfigurationException;
import javax.xml.parsers.ParserConfigurationException;

import nl.vumc.trait.oc.connect.OCConnectorException;
import nl.vumc.trait.oc.connect.OCWebServices;

import org.apache.commons.cli.OptionBuilder;
import org.apache.commons.cli.ParseException;
import org.openclinica.ws.beans.StudyType;
import org.openclinica.ws.study.v1.ListAllResponse;

/**
 * List all studies.
 * @author Arjan van der Velde (a.vandervelde (at) xs4all.nl)
 */
public class ListStudies extends Main {

	/**
	 * Constructor from Main. Setup processing command line arguments.
	 * @param command command string (see command attribute)
	 * @param args command line (i.e. as passed to main())
	 * @throws Exception 
	 * @throws ParserConfigurationException
	 */
	public ListStudies(String command, String[] args) throws Exception {
		super(command, args);
	}

	/**
	 * Constructor based on Main.
	 * @throws ParserConfigurationException 
	 */
	public ListStudies() throws ParserConfigurationException {
		super();
	}

	@SuppressWarnings("static-access")
	@Override
	protected void setupOptions() {
		// create the Options
		options.addOption(OptionBuilder.withLongOpt("base-url")
				.withDescription("OpenClinica base URL (i.e. https://www.example.org/OpenClinica-ws/)").hasArg()
				.withArgName("URL").isRequired(true).create("b"));
		options.addOption(OptionBuilder.withLongOpt("user").withDescription("OpenClinica username").hasArg()
				.withArgName("username").isRequired(true).create("u"));
		options.addOption(OptionBuilder.withLongOpt("password").withDescription("OpenClinica password").hasArg()
				.withArgName("password").isRequired(true).create("p"));
		options.addOption("h", "help", false, "this help screen");
		options.addOption("v", "verbose", false, "be (very) verbose");
	}

	@Override
	protected void processArgs(String[] args) throws ParseException, OCConnectorException {
		// parse the command line arguments
		line = parser.parse(options, args);
		if (line.hasOption("help")) {
			help();
		} else {
			if (line.hasOption("verbose")) {
				setDebug(true);
			}
			setConnectInfo(line.getOptionValue('b'), line.getOptionValue('u'), line.getOptionValue('p'));
		}
	}

	/**
	 * Perform all required OpenClinica web service calls to retrieve study information
	 * and print.
	 * @throws OCConnectorException
	 * @throws MalformedURLException
	 * @throws NoSuchAlgorithmException
	 * @throws UnsupportedEncodingException
	 * @throws ParserConfigurationException
	 * @throws DatatypeConfigurationException
	 */
	public void getStudies() throws OCConnectorException, MalformedURLException, NoSuchAlgorithmException,
			UnsupportedEncodingException, ParserConfigurationException, DatatypeConfigurationException {
		OCWebServices connector = OCWebServices.getInstance(connectInfo, debug, false);
		System.out.println("OID\tIdentifier\tName");
		ListAllResponse response = connector.listAllStudies();
		if (response != null) {
			if (response.getStudies() != null) {
				if (response.getStudies().getStudy() != null) {
					for (StudyType study : response.getStudies().getStudy()) {
						System.out.println(study.getOid() + "\t" + study.getIdentifier() + "\t" + study.getName());
					}
				}
			}
		}
	}

	@Override
	public void runCmd() throws Exception {
		getStudies();
	}

	/**
	 * main()
	 * @param args command line arguments
	 * @throws Exception 
	 */
	public static void main(String[] args) throws Exception {
		new ListStudies("studies", args);
	}

}