New working version after Victoria trip - new file coming from... (56ca2730) · Commits · Sara Bertocco / vospacebackend

src/main/java/it/inaf/oats/vospacebackend/utils/ResourceManager.java

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		/**
		* _____________________________________________________________________________
		*
		* OATS - INAF
		* Osservatorio Astronomico di Tireste - Istituto Nazionale di Astrofisica
		* Astronomical Observatory of Trieste - National Institute for Astrophysics
		* ____________________________________________________________________________
		*
		* Copyright (C) 20016 Istituto Nazionale di Astrofisica
		*
		* This program is free software; you can redistribute it and/or
		* modify it under the terms of the GNU General Public License
		* as published by the Free Software Foundation; either version 2
		* of the License, or (at your option) any later version.
		*
		* This program is distributed in the hope that it will be useful,
		* but WITHOUT ANY WARRANTY; without even the implied warranty of
		* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
		* GNU General Public License for more details.
		*
		* You should have received a copy of the GNU General Public License
		* along with this program; if not, write to the Free Software Foundation, Inc.,
		* 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA.
		* _____________________________________________________________________________
		*
		*/
		package it.inaf.oats.vospacebackend.utils;

		import ca.nrc.cadc.net.TransientException;
		import org.apache.log4j.Logger;

		import ca.nrc.cadc.util.RsaSignatureVerifier;
		import ca.nrc.cadc.uws.ErrorSummary;
		import ca.nrc.cadc.uws.ExecutionPhase;
		import ca.nrc.cadc.uws.Job;
		import ca.nrc.cadc.uws.Result;
		import ca.nrc.cadc.uws.server.DatabaseJobPersistence;
		import ca.nrc.cadc.uws.server.JobNotFoundException;
		import ca.nrc.cadc.uws.server.JobPersistenceException;
		import ca.nrc.cadc.uws.server.JobUpdater;
		import it.inaf.oats.vospacebackend.VOSpaceBackendResource;
		import it.inaf.oats.vospacebackend.exceptions.ExceptionMessage;
		import it.inaf.oats.vospacebackend.exceptions.VOSpaceBackendException;
		import it.inaf.oats.vospacebackend.implementation.DatabaseJobPersistenceImpl;
		import it.inaf.oats.vospacebackend.implementation.VOSpaceBackendImplFactory;
		import it.inaf.oats.vospacebackend.implementation.VOSpaceBackend;
		import it.inaf.oats.vospacebackend.utils.ConfigReader;
		import java.io.ByteArrayInputStream;
		import java.io.File;
		import java.io.FileOutputStream;
		import java.io.IOException;
		import java.io.InputStream;
		import java.security.InvalidKeyException;
		import java.security.MessageDigest;
		import java.security.NoSuchAlgorithmException;
		import java.text.MessageFormat;
		import java.util.Date;
		import java.util.List;
		import java.util.UUID;
		import java.util.logging.Level;
		import javax.xml.bind.DatatypeConverter;
		import org.apache.commons.codec.binary.Hex;
		import org.apache.commons.fileupload.FileItem;
		import org.apache.http.HttpStatus;

		import org.restlet.data.MediaType;
		import org.restlet.representation.FileRepresentation;
		import org.restlet.representation.Representation;

		/**
		*
		* @author bertocco
		*/
		public class ResourceManager implements org.apache.http.HttpStatus {

		private static Logger log = Logger.getLogger(VOSpaceBackendResource.class);

		private static int readAndSaveFile(String vosuri, FileItem fi)
		throws IOException, VOSpaceBackendException {

		Representation result;
		log.debug("Entering in readAndSaveFile");

		InputStream is = fi.getInputStream();
		log.debug("Input stream get");

		return readAndSaveFile(vosuri, is);

		}

		public static int readAndSaveFile(String vosuri, InputStream is)
		throws IOException, VOSpaceBackendException {

		int result;
		String md5sum = null;

		// Generate the unique file identifier (storageFileID)
		String unique_file_id_str = UUID.randomUUID().toString();
		log.debug("Unique file identifyer " + unique_file_id_str);

		// Get temporary document root from configuration file
		String tmpStorageRoot = new String();
		try {
		ConfigReader myConf = new ConfigReader("VOSpace.properties");
		tmpStorageRoot = myConf.getProperty("fs.posix.tmp.storage.root");
		} catch (Exception e) {
		ExceptionMessage exMsg = new ExceptionMessage();
		log.debug(MessageFormat.format(
		exMsg.getMessage("UNABLE_TO_READ_PROPERTIES"), "VOSpace.properties"));
		throw new VOSpaceBackendException(MessageFormat.format(
		exMsg.getMessage("PROPERTY_NOT_FOUND"), "fs.posix.tmp.storage.root", "VOSpace.properties"));
		}
		// Create the temporary directory, if needed
		File path = new File(tmpStorageRoot);
		if (!path.exists()) {
		boolean status = path.mkdirs();
		}
		// Seve the temporary file in temporary location with the new unique name
		File savedUploadedFile = new File(path + File.separator + unique_file_id_str);
		FileOutputStream outStream = new FileOutputStream(savedUploadedFile);
		try {
		md5sum = readWriteAndGetChecksum(is, outStream);
		} catch (VOSpaceBackendReadInputException e) {
		log.debug("File to upload received is a zero-length file");
		log.debug("File NOT Uploaded! Something went wrong in readWriteAndGetChecksum." + e.getMessage());
		result = HttpStatus.SC_INTERNAL_SERVER_ERROR;
		} catch (IOException e) {
		log.debug("Error reading file to upload");
		log.debug("File NOT Uploaded! Something went wrong in readWriteAndGetChecksum." + e.getMessage());
		result = HttpStatus.SC_INTERNAL_SERVER_ERROR;
		} catch (NoSuchAlgorithmException e) {
		log.debug("Exception in MD5 checksum generation");
		log.debug("File NOT Uploaded! Something went wrong in readWriteAndGetChecksum." + e.getMessage());
		result = HttpStatus.SC_INTERNAL_SERVER_ERROR;
		} catch (VOSpaceBackendTransferAbortedException e) {
		log.debug("Exception in reading file to upload");
		log.debug("File NOT Uploaded! Something went wrong in readWriteAndGetChecksum." + e.getMessage());
		result = HttpStatus.SC_INTERNAL_SERVER_ERROR;
		}

		try {
		if (storeUploadedFile(vosuri, unique_file_id_str, md5sum)) {
		log.debug("File successfully uploaded");
		result = HttpStatus.SC_OK;
		} else {
		log.debug("File NOT Uploaded! Something went wrong in storeUploadedFile.");
		result = HttpStatus.SC_INTERNAL_SERVER_ERROR;
		}
		} catch (Exception e) {

		log.debug("File NOT Uploaded! Something went wrong in readWriteAndGetChecksum." + e.getMessage());
		result = HttpStatus.SC_INTERNAL_SERVER_ERROR;
		}

		return result;
		}

		public static boolean storeUploadedFile(String vosuri, String tmp_file_name,
		String md5_sum) {
		boolean stored = false;
		log.debug("Entering in storeUploadedFile");
		try {
		VOSpaceBackendImplFactory myVOSpaceFactory = new VOSpaceBackendImplFactory();
		log.debug("myVOSpaceFactory created");
		VOSpaceBackend myVOSpace = myVOSpaceFactory.getVOSpaceBackImpl();
		log.debug("myVOSpace get");
		stored = myVOSpace.createFile(vosuri, tmp_file_name, md5_sum);
		log.debug("File stored: " + stored);
		} catch (Exception e) {
		log.debug("Unrecoverable exception storing file.");
		}
		return stored;

		}

		/* Return the file representation if ok, null elsewhere */
		public static Representation downloadFile(String fileName) throws Exception {

		Representation result;

		log.debug("Entering in downloadFile");
		VOSpaceBackendImplFactory myVOSpaceFactory = new VOSpaceBackendImplFactory();
		log.debug("myVOSpaceFactory created");
		VOSpaceBackend myVOSpace = myVOSpaceFactory.getVOSpaceBackImpl();
		log.debug("myVOSpace get");
		File fileToDownload = myVOSpace.returnFile(fileName);
		if (fileToDownload != null) {
		log.debug("File found, fileToDownload is not null");
		FileRepresentation fr = new FileRepresentation(fileToDownload.getAbsolutePath(),
		MediaType.APPLICATION_OCTET_STREAM);
		result = fr;

		} else {
		log.debug("File NOT found, fileToDownload is null");
		result = null;
		}

		return result;
		}

		public static String manageParametersDecoding(String toBeVerified) throws VOSpaceBackendException {

		String vosuri;
		int count = 0;

		log.debug("manageParametersEncoding BEGIN");
		String urlStr = new String(DatatypeConverter.parseBase64Binary(toBeVerified));
		log.debug("urlStr = " + urlStr);
		vosuri = urlStr.substring(0, urlStr.indexOf("\|"));
		log.debug("vosuri = " + vosuri);
		String remaining = urlStr.substring(urlStr.indexOf("\|") + 1, urlStr.length());
		log.debug("Remaining after get vosuri = " + remaining);
		String signature = remaining.substring(remaining.indexOf("\|") + 1, remaining.length());
		log.debug("signature = \n" + signature);

		// Validation
		log.debug("I am going to create RsaSignatureVerifier");
		RsaSignatureVerifier su = new RsaSignatureVerifier();
		log.debug("Created");

		boolean valid = false;
		try {
		valid = su.verify(new ByteArrayInputStream(vosuri.getBytes()),
		DatatypeConverter.parseBase64Binary(signature));
		} catch (IOException ioe) {
		log.debug("IOException in valid = su.verify(new ByteArrayInputStream(vosuri.getBytes()),\n"
		+ "DatatypeConverter.parseBase64Binary(signature))");
		throw new VOSpaceBackendException(ioe.getMessage());
		} catch (InvalidKeyException ike) {
		log.debug("InvalidKeyException in valid = su.verify(new ByteArrayInputStream(vosuri.getBytes()),\n"
		+ "DatatypeConverter.parseBase64Binary(signature))");
		log.debug("InvalidKeyException");
		throw new VOSpaceBackendException(ike.getMessage());
		}

		return vosuri;

		}

		/* Read a file from the InputStream parameter,
		write the file in the FileOutputStream parameter.
		Returns the MD5 checksum of the stored file.
		*/
		public static String readWriteAndGetChecksum(InputStream istream, FileOutputStream ostream)
		throws VOSpaceBackendReadInputException, IOException, NoSuchAlgorithmException,
		VOSpaceBackendTransferAbortedException {

		log.debug("Entering in readWriteAndGetChecksum(InputStream, FileOutputStream)");

		int DEFAULT_BUFFER_SIZE = 1024 * 4;
		String checksum = null;
		byte[] buffer = new byte[DEFAULT_BUFFER_SIZE];
		int bytesRead;

		MessageDigest msgDigest = MessageDigest.getInstance("MD5");

		// do an initial read to ensure there are bytes in the stream
		try {
		bytesRead = istream.read(buffer, 0, DEFAULT_BUFFER_SIZE);
		if (bytesRead <= 0) {
		// do not allow the creation of zero-length files
		log.debug("Cannot write a zero-length file.");
		throw new VOSpaceBackendReadInputException("Cannot write a zero-length file.");
		} else {
		log.debug("First bytes read OK. Input stream available and readable");
		}
		} catch (IOException ex) {
		String errorMsg = "Upstream exception while reading from "
		+ istream.getClass().getName() + ": "
		+ ex.getMessage();
		log.debug("IOException in the first byte reading of the incoming file");
		log.debug(errorMsg);
		throw new VOSpaceBackendTransferAbortedException(errorMsg);
		}

		// Loop reading and writing data.
		msgDigest.update(buffer, 0, bytesRead);
		log.debug("First msgDigest.update OK");

		while (bytesRead >= 0) {
		ostream.write(buffer, 0, bytesRead);
		try {
		bytesRead = istream.read(buffer, 0, DEFAULT_BUFFER_SIZE);
		if (bytesRead > 0) {
		msgDigest.update(buffer, 0, bytesRead);
		}
		} catch (IOException ex) {
		String errorMsg = "Upstream exception while reading from "
		+ istream.getClass().getName() + ": "
		+ ex.getMessage();
		log.debug(errorMsg);
		log.debug("A Exception in reading/writing file" + ex.getMessage());
		throw new VOSpaceBackendTransferAbortedException(errorMsg);
		}
		}
		ostream.flush();
		ostream.close();

		//Get the hash's bytes
		byte[] bytes = msgDigest.digest();

		String md5_checksum = new String(Hex.encodeHex(bytes));
		log.debug("MD5 checksum calculated: " + md5_checksum);

		return md5_checksum;

		}

		public static ExecutionPhase getJobPhase(String jobID) {

		ExecutionPhase execPhase = null;
		try {
		MyJobUpdater ju = new MyJobUpdater();
		execPhase = ju.getPhase(jobID);

		log.debug("Execution phase get!");
		} catch (JobNotFoundException jnfe) {
		log.debug("JobNotFoundException in getting job persistence");
		} catch (JobPersistenceException ex) {
		log.debug("JobPersistenceException setting job phase");
		}
		if(execPhase != null)
		return execPhase;
		else
		return null;

		}

		public static void setJobPhase(String jobID, ExecutionPhase start, ExecutionPhase end) {

		try {
		MyJobUpdater ju = new MyJobUpdater();
		ju.setPhase(jobID, start, end);
		log.debug("Execution phase set!");
		} catch (JobNotFoundException jnfe) {
		log.debug("JobNotFoundException in getting job persistence");
		} catch (JobPersistenceException ex) {
		log.debug("JobPersistenceException setting job phase");
		}

		}

		public static class MyJobUpdater implements JobUpdater {

		public ExecutionPhase getPhase(String jobID) throws JobNotFoundException, JobPersistenceException {

		DatabaseJobPersistence dbJobPers = new DatabaseJobPersistenceImpl();
		Job myJob;
		try {
		log.debug("Going to get Job from jobID = " + jobID);
		myJob = dbJobPers.get(jobID);
		log.debug("Job get! I am going to set the execution phase to completed");
		} catch (JobNotFoundException jnfe) {
		log.debug("JobNotFoundException in getting job persistence or setting");
		throw new JobNotFoundException(jobID);
		} catch (JobPersistenceException jpe) {
		log.debug("JobPersistenceException in getting job persistence or setting");
		throw new JobNotFoundException(jobID);
		} catch (TransientException te) {
		log.debug("TransientException in getting job persistence or setting");
		throw new JobNotFoundException(jobID);
		}
		if (myJob == null) {
		throw new JobNotFoundException(jobID);
		}
		return myJob.getExecutionPhase();
		}

		public ExecutionPhase setPhase(String jobID, ExecutionPhase start, ExecutionPhase end) throws JobNotFoundException, JobPersistenceException {

		DatabaseJobPersistence dbJobPers = new DatabaseJobPersistenceImpl();
		Job myJob;
		try {
		log.debug("Going to get Job from jobID = " + jobID);
		myJob = dbJobPers.get(jobID);
		log.debug("Job get! I am going to set the execution phase to completed");
		} catch (JobNotFoundException jnfe) {
		log.debug("JobNotFoundException in getting job persistence or setting");
		throw new JobNotFoundException(jobID);
		} catch (JobPersistenceException jpe) {
		log.debug("JobPersistenceException in getting job persistence or setting");
		throw new JobNotFoundException(jobID);
		} catch (TransientException te) {
		log.debug("TransientException in getting job persistence or setting");
		throw new JobNotFoundException(jobID);
		}
		if (myJob == null) {
		throw new JobNotFoundException(jobID);
		}
		ExecutionPhase phase = myJob.getExecutionPhase();
		if (phase.equals(start)) {
		myJob.setExecutionPhase(end);
		}
		return myJob.getExecutionPhase();
		}

		public ExecutionPhase setPhase(String jobID, ExecutionPhase start, ExecutionPhase end, Date date) throws JobNotFoundException, JobPersistenceException {
		return setPhase(jobID, start, end);
		}

		public ExecutionPhase setPhase(String jobID, ExecutionPhase start, ExecutionPhase end, List<Result> results, Date date) throws JobNotFoundException, JobPersistenceException {
		return setPhase(jobID, start, end);
		}

		public ExecutionPhase setPhase(String jobID, ExecutionPhase start, ExecutionPhase end, ErrorSummary error, Date date) throws JobNotFoundException, JobPersistenceException {
		return setPhase(jobID, start, end);
		}
		}

		}