Metacat

/**

 *  '$RCSfile$'

 *  Copyright: 2011 Regents of the University of California and the

 *              National Center for Ecological Analysis and Synthesis

 *

 *   '$Author: Serhan AKIN $'

 *     '$Date: 2009-06-13 15:28:13 +0300  $'

 *

 * 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., 59 Temple Place, Suite 330, Boston, MA  02111-1307  USA

 */

package edu.ucsb.nceas.metacat.restservice;

import java.io.File;

import java.io.FileInputStream;

import java.io.FileNotFoundException;

import java.io.IOException;

import java.io.InputStream;

import java.io.OutputStream;

import java.io.PrintWriter;

import java.util.Enumeration;

import java.util.Hashtable;

import java.util.Iterator;

import java.util.List;

import java.util.Map;

import java.util.Timer;

import javax.servlet.ServletContext;

import javax.servlet.http.HttpServletRequest;

import javax.servlet.http.HttpServletResponse;

import javax.xml.parsers.ParserConfigurationException;

import org.apache.commons.fileupload.FileUploadException;

import org.apache.commons.io.IOUtils;

import org.apache.log4j.Logger;

import org.dataone.client.auth.CertificateManager;

import org.dataone.mimemultipart.MultipartRequest;

import org.dataone.mimemultipart.MultipartRequestResolver;

import org.dataone.service.exceptions.BaseException;

import org.dataone.service.exceptions.InvalidRequest;

import org.dataone.service.exceptions.ServiceFailure;

import org.dataone.service.types.v1.AccessPolicy;

import org.dataone.service.types.v1.Replica;

import org.dataone.service.types.v1.ReplicationPolicy;

import org.dataone.service.types.v1.Session;

import org.dataone.service.types.v1.SystemMetadata;

import org.dataone.service.util.ExceptionHandler;

import org.dataone.service.util.TypeMarshaller;

import org.jibx.runtime.JiBXException;

import org.xml.sax.SAXException;

import edu.ucsb.nceas.metacat.MetacatHandler;

import edu.ucsb.nceas.metacat.properties.PropertyService;

import edu.ucsb.nceas.utilities.Log;

import edu.ucsb.nceas.utilities.PropertyNotFoundException;

/**

 * 

 * Base class for handling D1 REST calls in Metacat

 * 

 * @author leinfelder

 */

public class D1ResourceHandler {

    /**HTTP Verb GET*/

    public static final byte GET = 1;

    /**HTTP Verb POST*/

    public static final byte POST = 2;

    /**HTTP Verb PUT*/

    public static final byte PUT = 3;

    /**HTTP Verb DELETE*/

    public static final byte DELETE = 4;

    /**HTTP Verb HEAD*/

    public static final byte HEAD = 5;

    /*

     * API Resources

     */

    protected static final String RESOURCE_BASE_URL = "d1";

    protected static final String RESOURCE_OBJECTS = "object";

    protected static final String RESOURCE_META = "meta";

    protected static final String RESOURCE_LOG = "log";

    protected static final String RESOURCE_CHECKSUM = "checksum";

    protected static final String RESOURCE_IS_AUTHORIZED = "isAuthorized";

    protected static final String RESOURCE_ACCESS_RULES = "accessRules";

    /*

     * API Functions used as URL parameters

     */

    protected static final String FUNCTION_NAME_INSERT = "insert";

    protected static final String FUNCTION_NAME_UPDATE = "update";

    protected ServletContext servletContext;

    protected Logger logMetacat;

    protected MetacatHandler handler;

    protected HttpServletRequest request;

    protected HttpServletResponse response;

    protected Hashtable<String, String[]> params;

    protected Map<String, List<String>> multipartparams;

    // D1 certificate-based authentication

    protected Session session;

    /**Initializes new instance by setting servlet context,request and response*/

    public D1ResourceHandler(ServletContext servletContext,

            HttpServletRequest request, HttpServletResponse response) {

        this.servletContext = servletContext;

        this.request = request;

        this.response = response;

    }

    /**

     * This function is called from REST API servlet and handles each request 

     * 

     * @param httpVerb (GET, POST, PUT or DELETE)

     */

    public void handle(byte httpVerb) {

        logMetacat = Logger.getLogger(D1ResourceHandler.class);

        try {

            // load session from certificate in request

            session = CertificateManager.getInstance().getSession(request);

            // initialize the parameters

            params = new Hashtable<String, String[]>();

            initParams();

            // create the handler for interacting with Metacat

            Timer timer = new Timer();

            handler = new MetacatHandler(timer);

        } catch (Exception e) {

        	// TODO: more D1 structure when failing here

        	response.setStatus(400);

            printError("Incorrect resource!", response);

            logMetacat.error(e.getClass() + ": " + e.getMessage(), e);

        }

    }

    protected String parseTrailing(String resource, String token) {

    	// get the rest

        String extra = null;

        if (resource.indexOf(token) != -1) {

        	// what comes after the token?

            extra = resource.substring(resource.indexOf(token) + token.length());

            // remove the slash

            if (extra.startsWith("/")) {

            	extra = extra.substring(1);

            }

            // is there anything left?

            if (extra.length() == 0) {

            	extra = null;

            }

        }

        return extra;

    }

    /**

     * Parse the BaseException information for replication status failures if any

     * 

     * @return failure  the BaseException failure, one of it's subclasses, or null

     * @throws ServiceFailure

     * @throws InvalidRequest

     * @throws JiBXException 

     * @throws IllegalAccessException 

     * @throws InstantiationException 

     * @throws IOException 

     */

    protected BaseException collectReplicationStatus() 

        throws ServiceFailure, InvalidRequest, IOException, 

        InstantiationException, IllegalAccessException, JiBXException {

        BaseException failure = null;

        File tmpDir = getTempDirectory();

        MultipartRequest mr = null;

        Map<String, File> mmFileParts = null;

        File exceptionFile = null;

        InputStream exceptionFileStream = null;

        // Read the incoming data from its Mime Multipart encoding

        logMetacat.debug("Parsing BaseException from the mime multipart entity");

        // handle MMP inputs

        MultipartRequestResolver mrr = 

            new MultipartRequestResolver(tmpDir.getAbsolutePath(),1000000000, 0);

        try {

            mr = mrr.resolveMultipart(request);

            logMetacat.debug("Resolved the replication status BaseException multipart request.");

        } catch (IOException e) {

            throw new ServiceFailure("4700", "Couldn't resolve the multipart request: " +

                e.getMessage());

        } catch (FileUploadException e) {

            throw new ServiceFailure("4700", "Couldn't resolve the multipart request: " +

                e.getMessage());

        } catch (Exception e) {

            throw new ServiceFailure("4700", "Couldn't resolve the multipart request: " +

                e.getMessage());

        }

        // get the map of file parts

        mmFileParts = mr.getMultipartFiles();

        if ( mmFileParts == null || mmFileParts.keySet() == null) {

            logMetacat.debug("BaseException for setReplicationStatus is null");            

        }

        multipartparams = mr.getMultipartParameters();

        exceptionFile = mmFileParts.get("failure");

        if ( exceptionFile != null ) {

            // deserialize the BaseException subclass

            exceptionFileStream = new FileInputStream(exceptionFile);

            try {

                failure = ExceptionHandler.deserializeXml(exceptionFileStream, 

                    "Replication failed for an unknown reason.");

            } catch (ParserConfigurationException e) {

                throw new ServiceFailure("4700", "Couldn't parse the replication failure exception: " +

                        e.getMessage());

            } catch (SAXException e) {

                throw new ServiceFailure("4700", "Couldn't traverse the replication failure exception: " +

                        e.getMessage());

            }

        }

        return failure;

    }

    /**

     * Parse the replication policy document out of the mime-multipart form data

     * 

     * @return policy  the encoded policy

     * @throws ServiceFailure

     * @throws InvalidRequest

     * @throws IOException

     * @throws InstantiationException

     * @throws IllegalAccessException

     * @throws JiBXException

     */

    protected ReplicationPolicy collectReplicationPolicy() 

        throws ServiceFailure, InvalidRequest, IOException, InstantiationException, 

        IllegalAccessException, JiBXException {

        ReplicationPolicy policy = null;

        File tmpDir = getTempDirectory();

        MultipartRequest mr = null;

        Map<String, File> mmFileParts = null;

        File replPolicyFile = null;

        InputStream replPolicyStream = null;

        // Read the incoming data from its Mime Multipart encoding

        logMetacat.debug("Parsing ReplicationPolicy from the mime multipart entity");

        // handle MMP inputs

        MultipartRequestResolver mrr = 

            new MultipartRequestResolver(tmpDir.getAbsolutePath(),1000000000, 0);

        try {

            mr = mrr.resolveMultipart(request);

            logMetacat.debug("Resolved the ReplicationPolicy multipart request.");

        } catch (IOException e) {

            throw new ServiceFailure("4882", "Couldn't resolve the multipart request: " +

                e.getMessage());

        } catch (FileUploadException e) {

            throw new ServiceFailure("4882", "Couldn't resolve the multipart request: " +

                e.getMessage());

        } catch (Exception e) {

            throw new ServiceFailure("4882", "Couldn't resolve the multipart request: " +

                e.getMessage());

        }

        // get the map of file parts

        mmFileParts = mr.getMultipartFiles();

        if ( mmFileParts == null || mmFileParts.keySet() == null) {

            throw new InvalidRequest("4883", "The multipart request must include " +

                "a file with the name 'policy'.");

        }

        multipartparams = mr.getMultipartParameters();

        replPolicyFile = mmFileParts.get("policy");

        if ( replPolicyFile == null ) {

            throw new InvalidRequest("4883", "The multipart request must include " +

            "a file with the name 'policy'.");

        }

        // deserialize the ReplicationPolicy

        replPolicyStream = new FileInputStream(replPolicyFile);

        policy = TypeMarshaller.unmarshalTypeFromStream(ReplicationPolicy.class, replPolicyStream);

        return policy;

    }

    /**

     * Parse the replica metadata document out of the mime-multipart form data

     * 

     * @return replica  the encoded replica

     * @throws ServiceFailure

     * @throws InvalidRequest

     * @throws IOException

     * @throws InstantiationException

     * @throws IllegalAccessException

     * @throws JiBXException

     */

    protected Replica collectReplicaMetadata() 

        throws ServiceFailure, InvalidRequest {

        Replica replica = null;

        File tmpDir = getTempDirectory();

        MultipartRequest mr = null;

        Map<String, File> mmFileParts = null;

        File replicaFile = null;

        InputStream replicaStream = null;

        // Read the incoming data from its Mime Multipart encoding

        logMetacat.debug("Parsing Replica from the mime multipart entity");

        // handle MMP inputs

        MultipartRequestResolver mrr = 

            new MultipartRequestResolver(tmpDir.getAbsolutePath(),1000000000, 0);

        try {

            mr = mrr.resolveMultipart(request);

            logMetacat.debug("Resolved the Replica multipart request.");

        } catch (IOException e) {

            throw new ServiceFailure("4852", "Couldn't resolve the multipart request: " +

                e.getMessage());

        } catch (FileUploadException e) {

            throw new ServiceFailure("4852", "Couldn't resolve the multipart request: " +

                    e.getMessage());

        } catch (Exception e) {

            throw new ServiceFailure("4852", "Couldn't resolve the multipart request: " +

                    e.getMessage());

        }

        // get the map of file parts

        mmFileParts = mr.getMultipartFiles();

        if ( mmFileParts == null || mmFileParts.keySet() == null) {

            throw new InvalidRequest("4853", "The multipart request must include " +

                "a file with the name 'replicaMetadata'.");

        }

        multipartparams = mr.getMultipartParameters();

        replicaFile = mmFileParts.get("replicaMetadata");

        if ( replicaFile == null ) {

            throw new InvalidRequest("4853", "The multipart request must include " +

            "a file with the name 'replicaMetadata'.");

        }

        // deserialize the ReplicationPolicy

        try {

            replicaStream = new FileInputStream(replicaFile);

        } catch (FileNotFoundException e) {

            throw new ServiceFailure("4852", "Couldn't find the multipart file: " +

                    e.getMessage());

        }

        try {

            replica = TypeMarshaller.unmarshalTypeFromStream(Replica.class, replicaStream);

        } catch (IOException e) {

            throw new ServiceFailure("4852", "Couldn't deserialize the replica document: " +

                    e.getMessage());

        } catch (InstantiationException e) {

            throw new ServiceFailure("4852", "Couldn't deserialize the replica document: " +

                    e.getMessage());

        } catch (IllegalAccessException e) {

            throw new ServiceFailure("4852", "Couldn't deserialize the replica document: " +

                    e.getMessage());

        } catch (JiBXException e) {

            throw new ServiceFailure("4852", "Couldn't deserialize the replica document: " +

                    e.getMessage());

        }

        return replica;

    }

    protected AccessPolicy collectAccessPolicy() 

        throws IOException, ServiceFailure, InvalidRequest, JiBXException, 

        InstantiationException, IllegalAccessException, ParserConfigurationException, 

        SAXException  {

		// Read the incoming data from its Mime Multipart encoding

		logMetacat.debug("Disassembling MIME multipart form");

		InputStream ap = null;

		// handle MMP inputs

		File tmpDir = getTempDirectory();

		logMetacat.debug("temp dir: " + tmpDir.getAbsolutePath());

		MultipartRequestResolver mrr = 

			new MultipartRequestResolver(tmpDir.getAbsolutePath(), 1000000000, 0);

		MultipartRequest mr = null;

		try {

			mr = mrr.resolveMultipart(request);

		} catch (Exception e) {

			throw new ServiceFailure("2161", 

					"Could not resolve multipart: " + e.getMessage());

		}

		logMetacat.debug("resolved multipart request");

		Map<String, File> files = mr.getMultipartFiles();

		if (files == null || files.keySet() == null) {

			throw new InvalidRequest("2163",

					"must have multipart file with name 'accessPolicy'");

		}

		logMetacat.debug("got multipart files");

		multipartparams = mr.getMultipartParameters();

		File apFile = files.get("accessPolicy");

		if (apFile == null) {

			throw new InvalidRequest("2163",

					"Missing the required file-part 'accessPolicy' from the multipart request.");

		}

		logMetacat.debug("apFile: " + apFile.getAbsolutePath());

		ap = new FileInputStream(apFile);

		AccessPolicy accessPolicy = TypeMarshaller.unmarshalTypeFromStream(AccessPolicy.class, ap);

		return accessPolicy;

	}

    protected SystemMetadata collectSystemMetadata() 

        throws IOException, FileUploadException, ServiceFailure, InvalidRequest, 

        JiBXException, InstantiationException, IllegalAccessException  {

		// Read the incoming data from its Mime Multipart encoding

		logMetacat.debug("Disassembling MIME multipart form");

		InputStream sysmeta = null;

		// handle MMP inputs

		File tmpDir = getTempDirectory();

		logMetacat.debug("temp dir: " + tmpDir.getAbsolutePath());

		MultipartRequestResolver mrr = 

			new MultipartRequestResolver(tmpDir.getAbsolutePath(), 1000000000, 0);

		MultipartRequest mr = null;

		try {

			mr = mrr.resolveMultipart(request);

		} catch (Exception e) {

			throw new ServiceFailure("1202", 

					"Could not resolve multipart: " + e.getMessage());

		}

		logMetacat.debug("resolved multipart request");

		Map<String, File> files = mr.getMultipartFiles();

		if (files == null) {

			throw new ServiceFailure("1202",

					"register meta must have multipart file with name 'sysmeta'");

		}

		logMetacat.debug("got multipart files");

		if (files.keySet() == null) {

			logMetacat.error("No file keys in MMP request.");

			throw new ServiceFailure(

					"1202",

					"No file keys found in MMP.  "

							+ "register meta must have multipart file with name 'sysmeta'");

		}

		// for logging purposes, dump out the key-value pairs that

		// constitute the request

		// 3 types exist: request params, multipart params, and

		// multipart files

		Iterator it = files.keySet().iterator();

		logMetacat.debug("iterating through request parts: " + it);

		while (it.hasNext()) {

			String key = (String) it.next();

			logMetacat.debug("files key: " + key);

			logMetacat.debug("files value: " + files.get(key));

		}

		multipartparams = mr.getMultipartParameters();

		it = multipartparams.keySet().iterator();

		while (it.hasNext()) {

			String key = (String) it.next();

			logMetacat.debug("multipartparams key: " + key);

			logMetacat.debug("multipartparams value: " + multipartparams.get(key));

		}

		it = params.keySet().iterator();

		while (it.hasNext()) {

			String key = (String) it.next();

			logMetacat.debug("param key: " + key);

			logMetacat.debug("param value: " + params.get(key));

		}

		logMetacat.debug("done iterating the request...");

		File smFile = files.get("sysmeta");

		if (smFile == null) {

			throw new InvalidRequest("1102",

					"Missing the required file-part 'sysmeta' from the multipart request.");

		}

		logMetacat.debug("smFile: " + smFile.getAbsolutePath());

		sysmeta = new FileInputStream(smFile);

		logMetacat.debug("Commence creation...");

		SystemMetadata systemMetadata = TypeMarshaller.unmarshalTypeFromStream(SystemMetadata.class, sysmeta);

		return systemMetadata;

	}

    protected Map<String, File> collectMultipartFiles() 

        throws ServiceFailure, InvalidRequest {

        // Read the incoming data from its Mime Multipart encoding

        logMetacat.debug("Disassembling MIME multipart form");

        InputStream object = null;

        InputStream sysmeta = null;

        // handle MMP inputs

        File tmpDir = getTempDirectory();

        logMetacat.debug("temp dir: " + tmpDir.getAbsolutePath());

        MultipartRequestResolver mrr = 

        	new MultipartRequestResolver(tmpDir.getAbsolutePath(), 1000000000, 0);

        MultipartRequest mr = null;

		try {

			mr = mrr.resolveMultipart(request);

		} catch (Exception e) {

            throw new ServiceFailure("1202", 

            		"Could not resolve multipart files: " + e.getMessage());

		}

        logMetacat.debug("resolved multipart request");

        Map<String, File> files = mr.getMultipartFiles();

        if (files == null) {

            throw new ServiceFailure("1202", "create/update must have multipart files with names 'object' and 'sysmeta'");

        }

        logMetacat.debug("got multipart files");

        if (files.keySet() == null) {

            logMetacat.error("No file keys in MMP request.");

            throw new ServiceFailure("1202", "No file keys found in MMP.  " +

                    "create/update must have multipart files with names 'object' and 'sysmeta'");

        }

		// for logging purposes, dump out the key-value pairs that constitute the request

		// 3 types exist: request params, multipart params, and multipart files

        Iterator it = files.keySet().iterator();

        logMetacat.debug("iterating through files");

        while (it.hasNext()) {

            String key = (String)it.next();

            logMetacat.debug("files key: " + key);

            logMetacat.debug("files value: " + files.get(key));

        }

        multipartparams = mr.getMultipartParameters();

        it = multipartparams.keySet().iterator();

        logMetacat.debug("iterating through multipartparams");

        while (it.hasNext()) {

            String key = (String)it.next();

            logMetacat.debug("multipartparams key: " + key);

            logMetacat.debug("multipartparams value: " + multipartparams.get(key));

        }

        it = params.keySet().iterator();

        logMetacat.debug("iterating through params");

        while (it.hasNext()) {

            String key = (String)it.next();

            logMetacat.debug("param key: " + key);

            logMetacat.debug("param value: " + params.get(key));

        }

        logMetacat.debug("done iterating the request...");

        File smFile = files.get("sysmeta");

		if (smFile == null) {

		    throw new InvalidRequest("1102", "Missing the required file-part 'sysmeta' from the multipart request.");

		}

        logMetacat.debug("smFile: " + smFile.getAbsolutePath());

        File objFile = files.get("object");

		if (objFile == null) {

		    throw new InvalidRequest("1102", "Missing the required file-part 'object' from the multipart request.");

		}

        logMetacat.debug("objectfile: " + objFile.getAbsolutePath());

        return files;

    }

		/**

     *  copies request parameters to a hashtable which is given as argument to 

     *  native metacathandler functions  

     */

    protected void initParams() {

        String name = null;

        String[] value = null;

        Enumeration paramlist = request.getParameterNames();

        while (paramlist.hasMoreElements()) {

            name = (String) paramlist.nextElement();

            value = request.getParameterValues(name);

            params.put(name, value);

        }

    }

    /**

     * Collect the multipart params from the request

     * @throws Exception 

     */

	protected void initMultipartParams() throws Exception {

		// Read the incoming data from its Mime Multipart encoding

		logMetacat.debug("Disassembling MIME multipart form");

		// handle MMP inputs

		File tmpDir = getTempDirectory();

		logMetacat.debug("temp dir: " + tmpDir.getAbsolutePath());

		MultipartRequestResolver mrr = 

			new MultipartRequestResolver(tmpDir.getAbsolutePath(), 1000000000, 0);

		MultipartRequest mr = mrr.resolveMultipart(request);

		multipartparams = mr.getMultipartParameters();

	}

    /**

     * locate the boundary marker for an MMP

     * @param is

     * @return

     * @throws IOException

     */

    protected static String[] findBoundaryString(InputStream is)

        throws IOException {

        String[] endResult = new String[2];

        String boundary = "";

        String searchString = "boundary=";

        byte[] b = new byte[1024];

        int numbytes = is.read(b, 0, 1024);

        while(numbytes != -1)

        {

            String s = new String(b, 0, numbytes);

            int searchStringIndex = s.indexOf(searchString);

            if(s.indexOf("\"", searchStringIndex + searchString.length() + 1) == -1)

            { //the end of the boundary is in the next byte array

                boundary = s.substring(searchStringIndex + searchString.length() + 1, s.length());

            }

            else if(!boundary.startsWith("--"))

            { //we can read the whole boundary from this byte array

                boundary = s.substring(searchStringIndex + searchString.length() + 1, 

                    s.indexOf("\"", searchStringIndex + searchString.length() + 1));

                boundary = "--" + boundary;

                endResult[0] = boundary;

                endResult[1] = s.substring(s.indexOf("\"", searchStringIndex + searchString.length() + 1) + 1,

                        s.length());

                break;

            }

            else

            { //we're now reading the 2nd byte array to get the rest of the boundary

                searchString = "\"";

                searchStringIndex = s.indexOf(searchString);

                boundary += s.substring(0, searchStringIndex);

                boundary = "--" + boundary;

                endResult[0] = boundary;

                endResult[1] = s.substring(s.indexOf("\"", searchStringIndex + searchString.length() + 1) + 1,

                        s.length());

                break;

            }

        }

        return endResult;

    }

    /**

     * return the directory where temp files are stored

     * @return

     */

    protected static File getTempDirectory()

    {

        File tmpDir = null;

        Logger logMetacat = Logger.getLogger(D1ResourceHandler.class);

        try {

            tmpDir = new File(PropertyService.getProperty("application.tempDir"));

        }

        catch(PropertyNotFoundException pnfe) {

            logMetacat.error("D1ResourceHandler.writeMMPPartstoFiles: " +

                    "application.tmpDir not found.  Using /tmp instead.");

            tmpDir = new File("/tmp");

        }

        return tmpDir;

    }

    /**

     * Prints xml response

     * @param message Message to be displayed

     * @param response Servlet response that xml message will be printed 

     * */

    protected void printError(String message, HttpServletResponse response) {

        try {

            logMetacat.error("D1ResourceHandler: Printing error to servlet response: " + message);

            PrintWriter out = response.getWriter();

            response.setContentType("text/xml");

            out.println("<?xml version=\"1.0\"?>");

            out.println("<error>");

            out.println(message);

            out.println("</error>");

            out.close();

        } catch (IOException e) {

            e.printStackTrace();

        }

    }

    /**

     * serialize a D1 exception using jibx

     * @param e

     * @param out

     */

    protected void serializeException(BaseException e, OutputStream out) {

        // TODO: Use content negotiation to determine which return format to use

        response.setContentType("text/xml");

        response.setStatus(e.getCode());

        logMetacat.error("D1ResourceHandler: Serializing exception with code " + e.getCode() + ": " + e.getMessage());

        e.printStackTrace();

        try {

            IOUtils.write(e.serialize(BaseException.FMT_XML), out);

        } catch (IOException e1) {

            logMetacat.error("Error writing exception to stream. " 

                    + e1.getMessage());

        }

    }

}