uk.ac.ebi.sail.server.service.UploadSvc.java Source code

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Here is the source code for uk.ac.ebi.sail.server.service.UploadSvc.java

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/**
 * SAIL - biological samples availability index
 * 
 * Copyright (C) 2008,2009 Microarray Informatics Team, EMBL-European Bioinformatics Institute
 *
 *   This program is free software: you can redistribute it and/or modify
 *  it under the terms of the GNU Affero General Public License as
 *  published by the Free Software Foundation, either version 3 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.
 *
 *
 *  @author Mikhail Gostev <gostev@ebi.ac.uk>
 *
 */

package uk.ac.ebi.sail.server.service;

import java.io.ByteArrayOutputStream;
import java.io.IOException;
import java.io.InputStream;
import java.io.OutputStreamWriter;
import java.io.Writer;

import javax.servlet.http.HttpServlet;
import javax.servlet.http.HttpServletRequest;
import javax.servlet.http.HttpServletResponse;

import org.apache.commons.fileupload.FileItemIterator;
import org.apache.commons.fileupload.FileItemStream;
import org.apache.commons.fileupload.servlet.ServletFileUpload;
import org.apache.commons.fileupload.util.Streams;
import org.json.JSONObject;

import uk.ac.ebi.sail.client.common.ParseException;
import uk.ac.ebi.sail.server.data.DataManager;

import com.pri.util.stream.StreamPump;

public class UploadSvc extends HttpServlet {

    /**
        * 
        */
    private static final long serialVersionUID = 1L;

    protected void doPost(HttpServletRequest req, HttpServletResponse resp) throws IOException {
        // Check that we have a file upload request
        boolean isMultipart = ServletFileUpload.isMultipartContent(req);

        // Create a new file upload handler
        ServletFileUpload upload = new ServletFileUpload();

        String res = null;
        int studyID = -1;
        int collectionID = -1;

        String fileContent = null;

        String upType = null;

        try {
            // Parse the request
            FileItemIterator iter = upload.getItemIterator(req);
            while (iter.hasNext()) {
                FileItemStream item = iter.next();
                String name = item.getFieldName();
                InputStream stream = item.openStream();
                if (item.isFormField()) {
                    if ("CollectionID".equals(name)) {
                        try {
                            collectionID = Integer.parseInt(Streams.asString(stream));
                        } catch (Exception e) {
                        }
                    }
                    if ("StudyID".equals(name)) {
                        try {
                            studyID = Integer.parseInt(Streams.asString(stream));
                        } catch (Exception e) {
                        }
                    } else if ("UploadType".equals(name)) {
                        upType = Streams.asString(stream);
                    }

                    //     System.out.println("Form field " + name + " with value " + Streams.asString(stream) + " detected.");
                } else {
                    //     System.out.println("File field " + name + " with file name " + item.getName() + " detected.");
                    InputStream uploadedStream = item.openStream();
                    ByteArrayOutputStream baos = new ByteArrayOutputStream();

                    StreamPump.doPump(uploadedStream, baos);

                    byte[] barr = baos.toByteArray();

                    if ((barr[0] == -1 && barr[1] == -2) || (barr[0] == -2 && barr[1] == -1))
                        fileContent = new String(barr, "UTF-16");
                    else
                        fileContent = new String(barr);
                }
            }
        } catch (Exception ex) {
            res = ex.getMessage();
            ex.printStackTrace();
        }

        if (fileContent != null) {
            if ("AvailabilityData".equals(upType)) {
                if (collectionID != -1) {
                    try {
                        DataManager.getInstance().importData(fileContent, collectionID);
                    } catch (Exception ex) {
                        res = ex.getMessage();
                        ex.printStackTrace();
                    }
                } else
                    res = "Invalid or absent collection ID";
            } else if ("RelationMap".equals(upType)) {
                try {
                    DataManager.getInstance().importRelations(new String(fileContent));
                } catch (Exception ex) {
                    res = ex.getMessage();
                    ex.printStackTrace();
                }
            } else if ("Study2SampleRelation".equals(upType)) {
                try {
                    DataManager.getInstance().importSample2StudyRelations(new String(fileContent), studyID,
                            collectionID);
                } catch (Exception ex) {
                    res = ex.getMessage();
                    ex.printStackTrace();
                }
            } else {
                try {
                    DataManager.getInstance().importParameters(fileContent);
                } catch (ParseException pex) {
                    res = "Line " + pex.getLineNumber() + ": " + pex.getMessage();
                } catch (Exception ex) {
                    res = ex.getMessage();
                    ex.printStackTrace();
                }

            }

        } else {
            res = "File content not found";
        }

        JSONObject response = null;
        try {
            response = new JSONObject();
            response.put("success", res == null);
            response.put("error", res == null ? "uploaded successfully" : res);
            response.put("code", "232");
        } catch (Exception e) {

        }

        Writer w = new OutputStreamWriter(resp.getOutputStream());
        w.write(response.toString());
        System.out.println(response.toString());
        w.close();
        resp.setStatus(HttpServletResponse.SC_OK);
    }

}