viewfile.java

package services;

import java.io.BufferedInputStream;
import java.io.File;
import java.io.IOException;
import java.io.InputStream;
import java.io.OutputStream;
import java.io.PrintWriter;
import java.net.URL;
import java.net.URLConnection;
import java.text.ParseException;
import java.util.List;

import org.apache.log4j.Logger;
import org.molgenis.core.MolgenisFile;
import org.molgenis.framework.db.Database;
import org.molgenis.framework.db.DatabaseException;
import org.molgenis.framework.db.QueryRule;
import org.molgenis.framework.db.QueryRule.Operator;
import org.molgenis.framework.server.MolgenisContext;
import org.molgenis.framework.server.MolgenisRequest;
import org.molgenis.framework.server.MolgenisResponse;
import org.molgenis.framework.server.MolgenisService;

import decorators.MolgenisFileHandler;

public class viewfile implements MolgenisService
{

	private static Logger logger = Logger.getLogger(viewfile.class);

	private MolgenisContext mc;

	public viewfile(MolgenisContext mc)
	{
		this.mc = mc;
	}

	@Override
	public void handleRequest(MolgenisRequest request, MolgenisResponse response) throws ParseException,
			DatabaseException, IOException
	{

		boolean databaseIsAvailable = false;
		boolean paramsPresent = false;
		boolean fileFound = false;
		Database db = null;
		File file = null;
		MolgenisFile mf = null;
		// String type = null;
		// String investigationname = null;
		String name = null;

		try
		{
			db = request.getDatabase();
			databaseIsAvailable = true;
		}
		catch (Exception e)
		{
			PrintWriter out = response.getResponse().getWriter();
			response.getResponse().setContentType("text/plain");
			out.print("Database unavailable.");
			out.print("\n\n");
			e.printStackTrace(out);
			out.close();
		}

		if (databaseIsAvailable)
		{
			try
			{

				// type = request.getString("type");
				// investigationname = request.getString("investigationname");
				name = request.getString("name");

				// if(type == null){
				// throw new NullPointerException("Not specified: 'type'");
				// }

				// regular syntax:
				// http://localhost:8080/xqtl/viewfile?name=hapmap1_bim
				if (name == null)
				{

					// allow alternative syntax:
					// http://localhost:8080/xqtl/viewfile/hapmap1_bim
					// required for linking to external services, e.g. UCSC
					// browser
					String reqUrl = request.getRequestPath().substring(request.getServicePath().length());
					if (reqUrl.startsWith("/") && reqUrl.length() > 1)
					{
						name = reqUrl.substring(1);
						System.out.println("special syntax, getting name: " + name);
					}
					else
					{
						throw new NullPointerException("Not specified: 'name'");
					}
				}

				// if(investigationname == null){
				// throw new
				// NullPointerException("Not specified: 'investigationname'");
				// }

				paramsPresent = true;

			}
			catch (Exception e)
			{
				PrintWriter out = response.getResponse().getWriter();
				response.getResponse().setContentType("text/plain");
				displayUsage(out, db);
				out.print("\n\n");
				e.printStackTrace(out);
				out.close();
			}
		}

		if (paramsPresent)
		{
			try
			{

				// file = new File("");

				MolgenisFileHandler mfh = new MolgenisFileHandler(db);
				// File storageDir =
				// mfh.getValidatedFileDeployStorageLocationToFile();
				List<MolgenisFile> mfList = db.find(MolgenisFile.class, new QueryRule("name", Operator.EQUALS, name));

				if (mfList.size() == 0)
				{
					throw new Exception("No file with name '" + name + "' found");
				}
				else if (mfList.size() > 1)
				{
					throw new Exception("Severe error: multiple files found for name '" + name + "'");
				}

				mf = mfList.get(0);
				// file = FindBackend.getFileFor(db, mf);
				file = mfh.getFile(mf, db);

				if ((int) file.length() > Integer.MAX_VALUE)
				{
					throw new IOException("File too large! > Integer.MAX_VALUE");
				}

				fileFound = true;

			}
			catch (Exception e)
			{
				PrintWriter out = response.getResponse().getWriter();
				response.getResponse().setContentType("text/plain");
				displayUsage(out, db);
				out.print("\n\n");
				e.printStackTrace(out);
				out.close();
			}
		}

		if (fileFound)
		{
			OutputStream outFile = response.getResponse().getOutputStream();
			try
			{
				URL localURL = file.toURI().toURL();
				URLConnection conn = localURL.openConnection();
				InputStream in = new BufferedInputStream(conn.getInputStream());
				response.getResponse().setContentType(mc.getServletContext().getMimeType(mf.getExtension()));
				response.getResponse().setContentLength((int) file.length());
				// response.setHeader("Content-disposition","attachment; filename=\""+mf.getName()+"."+mf.getExtension()+"\"");
				// response.setStatus(arg0)
				byte[] buffer = new byte[(int) file.length()];
				while (in.available() != 0)
				{
					in.read(buffer);
					outFile.write(buffer);
					// in.skip(5); -> skip in case file length > MAX_INT
				}
				outFile.flush();
			}
			catch (Exception e)
			{
				logger.error(e);
			}
			finally
			{
				outFile.close();
			}
		}
	}

	public void displayUsage(PrintWriter out, Database db)
	{
		String usage = "To view file content, please specify 'name' (ie. /viewfile?name=myresultfile or /viewfile/myresultfile) \n\n";
		out.print(usage);
	}

}