Commit 739325fd authored by Sara Bertocco's avatar Sara Bertocco
Browse files

Original author Is Marco Molinaro. The class has been changed by Sara Bertocco in getDataSource.

parent 5d140905

pom.xml

+24 −4
Original line number Diff line number Diff line
@@ -46,13 +46,33 @@ 
            <type>jar</type>

        </dependency>

        <dependency>

            <groupId>ca.nrc.cadc.</groupId>

            <artifactId>cadcUtil</artifactId>

            <groupId>com.mysql.jdbc</groupId>

            <artifactId>mysql-connector</artifactId>

            <version>0.0</version>

        </dependency>

        <dependency>

            <groupId>com.mysql.jdbc</groupId>

            <artifactId>mysql-connector</artifactId>

            <groupId>ca.nrc.cadc.vos</groupId>

            <artifactId>cadcVOS</artifactId>

            <version>0.0</version>

        </dependency>

        <dependency>

            <groupId>ca.nrc.cadc.vos</groupId>

            <artifactId>cadcVOS-Server</artifactId>

            <version>0.0</version>

        </dependency>

        <dependency>

            <groupId>ca.nrc.cadc.uws</groupId>

            <artifactId>cadcUWS-Server</artifactId>

            <version>0.0</version>

        </dependency>

        <dependency>

            <groupId>ca.nrc.cadc.uws</groupId>

            <artifactId>cadcUWS</artifactId>

            <version>0.0</version>

        </dependency>

        <dependency>

            <groupId>ca.nrc.cadc</groupId>

            <artifactId>cadcUtil</artifactId>

            <version>0.0</version>

        </dependency>

        <dependency>

src/main/java/DelegationTokenKey.pub

0 → 100644
+1 −0
Original line number Diff line number Diff line 
ssh-rsa AAAAB3NzaC1yc2EAAAADAQABAAABAQDE+lo2eU+lvaqNfyE1K2PiEcVw7D6VoaVeFTQuEow9uGM4NyTLSYz4yD82jXNhheFzo399BzAk+EqdEWmx7P24OOSsCY1rzbohdeLgMDCURh+6wh4aeeKn+XptA9aXRs/Vlji337gG6BGS4zPICwCSWiHg8eGT0R3EIECLdI0+MBAwBxmOkkvrFMdDxcO4lRTu5lCWpR0gUvUde22kVUXfNoK+ZG92Ujxaw9zZapFaUEdDeCzFQCR9Bn4V4yWmSaJrVY+SsACzqz4A4vQ+FQh1+ayrNsoa0kgpPFCnv+Hv0lpPQ23yPpWO8mvdHs/OtJ5jT+jwdr/C3p87CFCkhGtP root@marmolada.oats.inaf.it

src/main/java/it/inaf/oats/vospacebackend/VOSpaceBackendApplication.java

+2 −2
Original line number Diff line number Diff line
@@ -38,8 +38,8 @@ public class VOSpaceBackendApplication extends Application { 
        Router router = new Router(getContext());

        // Defines a route for the resource "list of items"

        router.attach("/myResource", VOSpaceBackendResource.class );

        router.attach("/myResource/{security_token}/{unique_file_id_string}/{fileToManage}", VOSpaceBackendResource.class );

        //router.attach("/vospaceBackendGet", VOSpaceBackendResourceGet.class );

        //router.attach("/myResource/{security_token}/{unique_file_id_string}/{fileToManage}", VOSpaceBackendResource.class );

        router.attach("/myResource/{parameters}",  VOSpaceBackendResource.class );      

        

        return router;

src/main/java/it/inaf/oats/vospacebackend/VOSpaceBackendResource.java

+166 −34
Original line number Diff line number Diff line
@@ -34,17 +34,22 @@ import java.io.File; 
import java.io.FileOutputStream;

import java.io.InputStream;

import java.io.IOException;

import java.io.BufferedReader;

import java.io.InputStreamReader;

import java.text.MessageFormat;

import java.util.HashMap;

import java.util.Map;

import java.util.List;

import java.util.Iterator;



import javax.servlet.ServletContext;



import org.apache.log4j.Logger;

import org.apache.commons.fileupload.FileItem;

import org.apache.commons.fileupload.disk.DiskFileItemFactory;

import org.apache.commons.codec.digest.DigestUtils;

import org.apache.commons.io.IOUtils; 

import org.apache.commons.codec.binary.Hex;



import org.restlet.resource.Get;

import org.restlet.resource.Post;
@@ -62,6 +67,18 @@ import org.restlet.ext.fileupload.RestletFileUpload; 
import org.restlet.data.MediaType;

import org.restlet.data.Status;



import java.security.InvalidKeyException;

import java.io.IOException;

import java.io.ByteArrayInputStream;

import java.io.UnsupportedEncodingException;  

import java.io.OutputStream;

import java.util.UUID;

import javax.xml.bind.DatatypeConverter;



import ca.nrc.cadc.util.RsaSignatureGenerator;

import ca.nrc.cadc.util.RsaSignatureVerifier;

import java.security.MessageDigest;



/**

 *

 * @author bertocco
@@ -77,31 +94,28 @@ public class VOSpaceBackendResource extends ServerResource { 
        

        log.info("Entering in PUT operation");

 

        String security_token = "";

        String unique_file_id_str = ""; 

        String fileToManage = "";       

        String vosuri = null;

        String encodedParameters;

        InputStream is;

        if (entity != null) {

            log.info("Received good entity");

            try {

                log.debug("Trying to read attributes");

                Request request = getRequest();

                log.debug("AAA");

                security_token = (String)getRequest().getAttributes().get("security_token");

                unique_file_id_str = (String)getRequest().getAttributes().get("unique_file_id_string");

                fileToManage = (String)getRequest().getAttributes().get("fileToManage");

                log.debug("\nsecurity token = " + security_token +

                          "\nunique_file_id_str = " + unique_file_id_str +

                          "\nfileToManage = " + fileToManage);

                encodedParameters = (String)getRequest().getAttributes().get("parameters");

                log.debug("Received encoded parameters : " + encodedParameters);

                vosuri = manageParametersDecoding(encodedParameters);

                log.debug("Received parameters decoded = " + vosuri);

            } catch (Exception e) {

                log.debug("Exception reading string parameters");

                log.debug(e);

            }   

                       

            try {

 

                is = entity.getStream();

                log.debug("Input stream get");

                result = readAndSaveFile(fileToManage, unique_file_id_str, is);

                result = readAndSaveFile(vosuri, is);

                

            } catch (Exception e) {

                result = this.printMessage("File NOT Uploaded! Something went wrong.");
@@ -112,7 +126,7 @@ public class VOSpaceBackendResource extends ServerResource { 
        return result;

    }

    

        

/*        

    @Post

    public Representation doPost(Representation entity) throws Exception {
@@ -143,15 +157,16 @@ public class VOSpaceBackendResource extends ServerResource { 
            setStatus(Status.CLIENT_ERROR_BAD_REQUEST);

            result = this.printMessage("POST request with no entity.");

        }

        

        return result;

    

    }

*/

    

    @Get

    public Representation doGet(){

        

        Representation result = null;

        

        log.info("Entering in GET operation");

        String fileName = (String)getRequestAttributes().get("fileToManage");

        log.debug("File to download is: " + fileName);
@@ -162,6 +177,7 @@ public class VOSpaceBackendResource extends ServerResource { 
            result = this.printMessage("GET request: failed to download file.");  

        }  

        

        

        return result;

    }
@@ -172,6 +188,7 @@ public class VOSpaceBackendResource extends ServerResource { 
        Representation result;

        

        log.info("Entering in DELETE operation");

        

        String fileName = (String)getRequestAttributes().get("fileToManage");

        log.debug("File to delete is: " + fileName);

        try {
@@ -179,10 +196,10 @@ public class VOSpaceBackendResource extends ServerResource { 
        } catch (Exception e) {         

            result = this.printMessage("DELETE request: failed to delete file " + fileName);  

        }   

         

        return result;                

    }

        

    }

/*    

    private Representation uploadFile(Representation entity) throws Exception {

                

        Representation result = null;
@@ -269,13 +286,14 @@ public class VOSpaceBackendResource extends ServerResource { 
        log.debug("fileName = " + origFileName);

        

        

        result = readAndSaveFile(origFileName, unique_file_id_str, fileItemToStore);

        result = readAndSaveFile(vosuri, fileItemToStore);

        

        return result;

        

    }

    */

    

    private Representation readAndSaveFile(String origFileName, String unique_file_id_str, FileItem fi)

    private Representation readAndSaveFile(String vosuri, FileItem fi)

                           throws IOException, VOSpaceBackendException {

                

        Representation result;
@@ -284,22 +302,21 @@ public class VOSpaceBackendResource extends ServerResource { 
        InputStream is = fi.getInputStream();

        log.debug("Input stream get");

        

        return readAndSaveFile(origFileName, unique_file_id_str, is);

        return readAndSaveFile(vosuri, is);

        

    }

    

    

    private Representation readAndSaveFile(String origFileName, String unique_file_id_str, InputStream is)

    private Representation readAndSaveFile(String vosuri, InputStream is)

                           throws IOException, VOSpaceBackendException {

        

        Representation 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);

        

        byte[] data = IOUtils.toByteArray(is);

        log.debug("toByteArray OK");

        // Calculate the file MD5 checksum (so will not need to re-read 

        // the file a new time later

        String md5sum = new String(DigestUtils.md5Hex(data));

        log.debug("MD5Sum del file: " + md5sum);

        // Get temporary document root from configuration file

        String tmpStorageRoot = new String();

        try {
@@ -320,10 +337,14 @@ public class VOSpaceBackendResource extends ServerResource { 
        // 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);

        outStream.write(data);

        outStream.close();

        try {

            if (this.storeUploadedFile(unique_file_id_str, origFileName, md5sum)) {  

            md5sum = readWriteAndGetChecksum(is, outStream);

        } catch (Exception e) {

            result = this.printMessage("File NOT Uploaded! Something went wrong." + e.getMessage());    

        }

        

        try {

            if (this.storeUploadedFile(vosuri, unique_file_id_str, md5sum)) {  

                setStatus(Status.SUCCESS_OK); 

                result = this.printMessage("File successfully uploaded");

            } else {
@@ -337,7 +358,7 @@ public class VOSpaceBackendResource extends ServerResource { 
    }

    

    

    private boolean storeUploadedFile(String tmp_file_name, String orig_f_name, 

    private boolean storeUploadedFile(String vosuri, String tmp_file_name, 

                                      String md5_sum) throws Exception {

        boolean stored = false;

        log.debug("Entering in storeUploadedFile");
@@ -345,7 +366,7 @@ public class VOSpaceBackendResource extends ServerResource { 
        log.debug("myVOSpaceFactory created");

        VOSpaceBackend myVOSpace = myVOSpaceFactory.getVOSpaceBackImpl();

        log.debug("myVOSpace get");

        stored = myVOSpace.createFile(orig_f_name, tmp_file_name, md5_sum);

        stored = myVOSpace.createFile(vosuri, tmp_file_name, md5_sum);

        log.debug("File stored: " + stored);

        return stored;
@@ -406,6 +427,118 @@ public class VOSpaceBackendResource extends ServerResource { 
    }

    

    

    



    private String manageParametersDecoding(String toBeVerified) {

        

        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");

            log.debug(ioe.getMessage());

        } catch (InvalidKeyException ike) {

            log.debug("InvalidKeyException");           

            log.debug(ike.getMessage());       

        }

                

        return vosuri;

        

    }

    

    public String readWriteAndGetChecksum(InputStream istream, FileOutputStream ostream) throws Exception {

        

        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 Exception("Cannot write a zero-length file.");

            } else

                log.debug("First bytes read OK");

        } 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 TransferAbortedException(errorMsg);

            throw new Exception(errorMsg);

        }



        // Loop reading and writing data.

        msgDigest.update(buffer, 0, bytesRead);

        log.debug("First msgDigest.update OK");

        try {



            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();

                    //throw new TransferAbortedException(errorMsg);                    

                    log.debug(errorMsg);                   

                    log.debug("A Exception in reading/writing file" + ex.getMessage());

                    throw new Exception(errorMsg);

                } 

            } 

            ostream.flush();

            ostream.close();

                

        } catch (IOException ex) {

            log.debug("B Exception in reading/writing file" + ex.getMessage());

        }

        

        //Get the hash's bytes

        byte[] bytes = null;

        try {

            bytes = msgDigest.digest();

        } catch (Exception ex) {

           log.debug("Exception doing msgDigest.digest()");

        }

        String md5_checksum = new String(Hex.encodeHex(bytes));

        log.debug("************************ MD5 checksum calculated: " + md5_checksum);

        

        return md5_checksum;

        

    }

    

    

    private Representation printMessage(String error) {

        

            StringBuilder sb = new StringBuilder("");
@@ -413,5 +546,4 @@ public class VOSpaceBackendResource extends ServerResource { 
            sb.append("\n");

            return new StringRepresentation(sb.toString(), MediaType.TEXT_PLAIN);

    }



}

src/main/java/it/inaf/oats/vospacebackend/implementation/DatabaseJobPersistenceImpl.java

0 → 100644
+41 −0
Original line number Diff line number Diff line 
/*

 * To change this license header, choose License Headers in Project Properties.

 * To change this template file, choose Tools | Templates

 * and open the template in the editor.

 */

package it.inaf.oats.vospacebackend.implementation;



import ca.nrc.cadc.uws.server.DatabaseJobPersistence;

import ca.nrc.cadc.uws.server.JobDAO;

import com.mysql.jdbc.jdbc2.optional.MysqlDataSource;



import javax.sql.DataSource;

/**

 *

 * @author bertocco

 */

public class DatabaseJobPersistenceImpl extends DatabaseJobPersistence {

 

    



    protected JobDAO.JobSchema getJobSchema() {

        

        return new JobDAO.JobSchema("Job", "JobDetail", false);

        

    }

    

    /**

     * Providing a data source.

     */

    protected DataSource getDataSource() {

    

        MysqlDataSource dataSource = new MysqlDataSource();

        dataSource.setDatabaseName("cadctest");

        dataSource.setUser("oatsops");

        dataSource.setPassword("Peper0ne");

        dataSource.setServerName("localhost");

        

        return dataSource;

    }

    

}