Examples with SSHApiException org.apache.airavata.gfac.core.SSHApiException used on opensource projects

Example 1 with SSHApiException

use of org.apache.airavata.gfac.core.SSHApiException in project airavata by apache.

the class BESJobSubmissionTask method copyInputFilesToLocal.

private void copyInputFilesToLocal(TaskContext taskContext) throws GFacException {
    ProcessContext pc = taskContext.getParentProcessContext();
    StorageResourceDescription storageResource = pc.getStorageResource();
    if (storageResource != null) {
        hostName = storageResource.getHostName();
    } else {
        throw new GFacException("Storage Resource is null");
    }
    inputPath = pc.getStorageFileSystemRootLocation();
    inputPath = (inputPath.endsWith(File.separator) ? inputPath : inputPath + File.separator);
    String remoteFilePath = null, fileName = null, localFilePath = null;
    URI remoteFileURI = null;
    try {
        authenticationInfo = Factory.getStorageSSHKeyAuthentication(pc);
        ServerInfo serverInfo = pc.getStorageResourceServerInfo();
        Session sshSession = Factory.getSSHSession(authenticationInfo, serverInfo);
        List<InputDataObjectType> processInputs = pc.getProcessModel().getProcessInputs();
        for (InputDataObjectType input : processInputs) {
            if (input.getType() == DataType.URI) {
                remoteFileURI = new URI(input.getValue());
                remoteFilePath = remoteFileURI.getPath();
                fileName = remoteFilePath.substring(remoteFilePath.lastIndexOf("/") + 1);
                localFilePath = pc.getInputDir() + File.separator + fileName;
                log.info("SCP remote file :{} -> to local :{}", remoteFilePath, localFilePath);
                SSHUtils.scpFrom(remoteFilePath, localFilePath, sshSession);
                input.setValue("file:/" + localFilePath);
            }
        }
    } catch (IOException | JSchException | SSHApiException | URISyntaxException e) {
        log.error("Error while coping remote file " + remoteFilePath + " to local " + localFilePath, e);
        throw new GFacException("Error while scp input files to local file location", e);
    } catch (CredentialStoreException e) {
        String msg = "Authentication issue, make sure you are passing valid credential token";
        log.error(msg, e);
        throw new GFacException(msg, e);
    }
}

Example 2 with SSHApiException

use of org.apache.airavata.gfac.core.SSHApiException in project airavata by apache.

the class SSHUtils method scpFrom.

/**
 * This method will copy a remote file to a local directory
 *
 * @param remoteFile remote file path, this has to be a full qualified path
 * @param localFile  This is the local file to copy, this can be a directory too
 * @return returns the final local file path of the new file came from the remote resource
 */
public static void scpFrom(String remoteFile, String localFile, Session session) throws IOException, JSchException, SSHApiException {
    FileOutputStream fos = null;
    try {
        String prefix = null;
        if (new File(localFile).isDirectory()) {
            prefix = localFile + File.separator;
        }
        // exec 'scp -f remotefile' remotely
        String command = "scp -f " + remoteFile;
        Channel channel = session.openChannel("exec");
        ((ChannelExec) channel).setCommand(command);
        StandardOutReader stdOutReader = new StandardOutReader();
        ((ChannelExec) channel).setErrStream(stdOutReader.getStandardError());
        // get I/O streams for remote scp
        OutputStream out = channel.getOutputStream();
        InputStream in = channel.getInputStream();
        if (!channel.isClosed()) {
            channel.connect();
        }
        byte[] buf = new byte[1024];
        // send '\0'
        buf[0] = 0;
        out.write(buf, 0, 1);
        out.flush();
        while (true) {
            int c = checkAck(in);
            if (c != 'C') {
                break;
            }
            // read '0644 '
            in.read(buf, 0, 5);
            long filesize = 0L;
            while (true) {
                if (in.read(buf, 0, 1) < 0) {
                    // error
                    break;
                }
                if (buf[0] == ' ')
                    break;
                filesize = filesize * 10L + (long) (buf[0] - '0');
            }
            String file = null;
            for (int i = 0; ; i++) {
                in.read(buf, i, 1);
                if (buf[i] == (byte) 0x0a) {
                    file = new String(buf, 0, i);
                    break;
                }
            }
            // System.out.println("filesize="+filesize+", file="+file);
            // send '\0'
            buf[0] = 0;
            out.write(buf, 0, 1);
            out.flush();
            // read a content of lfile
            fos = new FileOutputStream(prefix == null ? localFile : prefix + file);
            int foo;
            while (true) {
                if (buf.length < filesize)
                    foo = buf.length;
                else
                    foo = (int) filesize;
                foo = in.read(buf, 0, foo);
                if (foo < 0) {
                    // error
                    break;
                }
                fos.write(buf, 0, foo);
                filesize -= foo;
                if (filesize == 0L)
                    break;
            }
            fos.close();
            fos = null;
            if (checkAck(in) != 0) {
                String error = "Error transfering the file content";
                log.error(error);
                throw new SSHApiException(error);
            }
            // send '\0'
            buf[0] = 0;
            out.write(buf, 0, 1);
            out.flush();
        }
        stdOutReader.onOutput(channel);
        if (stdOutReader.getStdErrorString().contains("scp:")) {
            throw new SSHApiException(stdOutReader.getStdErrorString());
        }
    } catch (Exception e) {
        log.error(e.getMessage(), e);
    } finally {
        try {
            if (fos != null)
                fos.close();
        } catch (Exception ee) {
        }
    }
}

Example 3 with SSHApiException

use of org.apache.airavata.gfac.core.SSHApiException in project airavata by apache.

the class SSHUtils method scpTo.

/**
 * This will copy a local file to a remote location
 *
 * @param remoteFile remote location you want to transfer the file, this cannot be a directory, if user pass
 *                   a dirctory we do copy it to that directory but we simply return the directory name
 *                   todo handle the directory name as input and return the proper final output file name
 * @param localFile  Local file to transfer, this can be a directory
 * @return returns the final remote file path, so that users can use the new file location
 */
public static String scpTo(String localFile, String remoteFile, Session session) throws IOException, JSchException, SSHApiException {
    FileInputStream fis = null;
    String prefix = null;
    if (new File(localFile).isDirectory()) {
        prefix = localFile + File.separator;
    }
    boolean ptimestamp = true;
    // exec 'scp -t rfile' remotely
    String command = "scp " + (ptimestamp ? "-p" : "") + " -t " + remoteFile;
    Channel channel = session.openChannel("exec");
    StandardOutReader stdOutReader = new StandardOutReader();
    ((ChannelExec) channel).setErrStream(stdOutReader.getStandardError());
    ((ChannelExec) channel).setCommand(command);
    // get I/O streams for remote scp
    OutputStream out = channel.getOutputStream();
    InputStream in = channel.getInputStream();
    channel.connect();
    if (checkAck(in) != 0) {
        String error = "Error Reading input Stream";
        log.error(error);
        throw new SSHApiException(error);
    }
    File _lfile = new File(localFile);
    if (ptimestamp) {
        command = "T" + (_lfile.lastModified() / 1000) + " 0";
        // The access time should be sent here,
        // but it is not accessible with JavaAPI ;-<
        command += (" " + (_lfile.lastModified() / 1000) + " 0\n");
        out.write(command.getBytes());
        out.flush();
        if (checkAck(in) != 0) {
            String error = "Error Reading input Stream";
            log.error(error);
            throw new SSHApiException(error);
        }
    }
    // send "C0644 filesize filename", where filename should not include '/'
    long filesize = _lfile.length();
    command = "C0644 " + filesize + " ";
    if (localFile.lastIndexOf('/') > 0) {
        command += localFile.substring(localFile.lastIndexOf('/') + 1);
    } else {
        command += localFile;
    }
    command += "\n";
    out.write(command.getBytes());
    out.flush();
    if (checkAck(in) != 0) {
        String error = "Error Reading input Stream";
        log.error(error);
        throw new SSHApiException(error);
    }
    // send a content of localFile
    fis = new FileInputStream(localFile);
    byte[] buf = new byte[1024];
    while (true) {
        int len = fis.read(buf, 0, buf.length);
        if (len <= 0)
            break;
        // out.flush();
        out.write(buf, 0, len);
    }
    fis.close();
    fis = null;
    // send '\0'
    buf[0] = 0;
    out.write(buf, 0, 1);
    out.flush();
    if (checkAck(in) != 0) {
        String error = "Error Reading input Stream";
        log.error(error);
        throw new SSHApiException(error);
    }
    out.close();
    stdOutReader.onOutput(channel);
    channel.disconnect();
    if (stdOutReader.getStdErrorString().contains("scp:")) {
        throw new SSHApiException(stdOutReader.getStdErrorString());
    }
    // since remote file is always a file  we just return the file
    return remoteFile;
}

Example 4 with SSHApiException

use of org.apache.airavata.gfac.core.SSHApiException in project airavata by apache.

the class BESJobSubmissionTask method copyOutputFilesToStorage.

private void copyOutputFilesToStorage(TaskContext taskContext, List<OutputDataObjectType> copyOutput) throws GFacException {
    ProcessContext pc = taskContext.getParentProcessContext();
    String remoteFilePath = null, fileName = null, localFilePath = null;
    try {
        authenticationInfo = Factory.getStorageSSHKeyAuthentication(pc);
        ServerInfo serverInfo = pc.getComputeResourceServerInfo();
        Session sshSession = Factory.getSSHSession(authenticationInfo, serverInfo);
        for (OutputDataObjectType output : copyOutput) {
            switch(output.getType()) {
                case STDERR:
                case STDOUT:
                case STRING:
                case URI:
                    localFilePath = output.getValue();
                    if (localFilePath.contains("://")) {
                        localFilePath = localFilePath.substring(localFilePath.indexOf("://") + 2, localFilePath.length());
                    }
                    fileName = localFilePath.substring(localFilePath.lastIndexOf("/") + 1);
                    URI destinationURI = TaskUtils.getDestinationURI(taskContext, hostName, inputPath, fileName);
                    remoteFilePath = destinationURI.getPath();
                    log.info("SCP local file :{} -> from remote :{}", localFilePath, remoteFilePath);
                    SSHUtils.scpTo(localFilePath, remoteFilePath, sshSession);
                    output.setValue(destinationURI.toString());
                    break;
                default:
                    break;
            }
        }
    } catch (IOException | JSchException | SSHApiException | URISyntaxException | CredentialStoreException e) {
        log.error("Error while coping local file " + localFilePath + " to remote " + remoteFilePath, e);
        throw new GFacException("Error while scp output files to remote storage file location", e);
    }
}