// BamFtp_p.cpp (c) 2011 Derek Barnett
// Marth Lab, Department of Biology, Boston College
// ---------------------------------------------------------------------------
-// Last modified: 25 October 2011 (DB)
+// Last modified: 8 November 2011 (DB)
// ---------------------------------------------------------------------------
// Provides reading/writing of BAM files on FTP server
// ***************************************************************************
+#include "api/BamAux.h"
#include "api/internal/io/BamFtp_p.h"
+#include "api/internal/io/TcpSocket_p.h"
using namespace BamTools;
using namespace BamTools::Internal;
+#include <iostream> // debug
+
+#include <cctype>
+#include <cstdlib>
+#include <sstream>
+#include <vector>
using namespace std;
+namespace BamTools {
+namespace Internal {
+
+// -----------
+// constants
+// -----------
+
+static const uint16_t FTP_PORT = 21;
+static const string FTP_PREFIX = "ftp://";
+static const size_t FTP_PREFIX_LENGTH = 6;
+static const string FTP_NEWLINE = "\r\n";
+static const string DEFAULT_USER = "anonymous";
+static const string DEFAULT_PASS = "anonymous@";
+static const string ABOR_CMD = "ABOR";
+static const string USER_CMD = "USER";
+static const string PASS_CMD = "PASS";
+static const string PASV_CMD = "PASV";
+static const string REIN_CMD = "REIN";
+static const string REST_CMD = "REST";
+static const string RETR_CMD = "RETR";
+static const string TYPE_CMD = "TYPE";
+static const char COLON_CHAR = ':';
+static const char COMMA_CHAR = ',';
+static const char DOT_CHAR = '.';
+static const char MINUS_CHAR = '-';
+static const char SLASH_CHAR = '/';
+static const char SPACE_CHAR = ' ';
+static const char LEFT_PAREN_CHAR = '(';
+static const char RIGHT_PAREN_CHAR = ')';
+
+// -----------------
+// utility methods
+// -----------------
+
+static inline
+vector<string> split(const string& source, const char delim) {
+
+ stringstream ss(source);
+ string field;
+ vector<string> fields;
+
+ while ( getline(ss, field, delim) )
+ fields.push_back(field);
+ return fields;
+}
+
+static inline
+bool startsWith(const string& source, const string& pattern) {
+ return ( source.find(pattern) == 0 );
+}
+
+static inline
+string toLower(const string& s) {
+ string out;
+ const size_t sSize = s.size();
+ out.reserve(sSize);
+ for ( size_t i = 0; i < sSize; ++i )
+ out[i] = tolower(s[i]);
+ return out;
+}
+
+} // namespace Internal
+} // namespace BamTools
+
+// -----------------------
+// BamFtp implementation
+// -----------------------
+
BamFtp::BamFtp(const string& url)
: IBamIODevice()
+ , m_commandSocket(new TcpSocket)
+ , m_dataSocket(new TcpSocket)
+ , m_port(FTP_PORT)
+ , m_dataPort(0)
+ , m_username(DEFAULT_USER)
+ , m_password(DEFAULT_PASS)
+ , m_isUrlParsed(false)
+ , m_filePosition(-1)
{
- BT_ASSERT_X(false, "BamFtp not yet implemented");
+ ParseUrl(url);
}
-BamFtp::~BamFtp(void) { }
+BamFtp::~BamFtp(void) {
+
+ // close connection & clean up
+ Close();
+ if ( m_commandSocket )
+ delete m_commandSocket;
+ if ( m_dataSocket )
+ delete m_dataSocket;
+}
void BamFtp::Close(void) {
- return ;
+
+ // disconnect socket
+ m_commandSocket->DisconnectFromHost();
+ m_dataSocket->DisconnectFromHost();
+
+ // reset state - necessary??
+ m_isUrlParsed = false;
+ m_filePosition = -1;
+ m_username = DEFAULT_USER;
+ m_password = DEFAULT_PASS;
+ m_dataHostname.clear();
+ m_dataPort = 0;
+}
+
+bool BamFtp::ConnectCommandSocket(void) {
+
+ BT_ASSERT_X(m_commandSocket, "null command socket?");
+
+ // connect to FTP server
+ if ( !m_commandSocket->ConnectToHost(m_hostname, m_port, m_mode) ) {
+ SetErrorString("BamFtp::ConnectCommandSocket", "could not connect to host");
+ return false;
+ }
+
+ // receive initial reply from host
+ if ( !ReceiveReply() ) {
+ Close();
+ return false;
+ }
+
+ // send USER command
+ string userCommand = USER_CMD + SPACE_CHAR + m_username + FTP_NEWLINE;
+ if ( !SendCommand(userCommand, true) ) {
+ Close();
+ return false;
+ }
+
+ // send PASS command
+ string passwordCommand = PASS_CMD + SPACE_CHAR + m_password + FTP_NEWLINE;
+ if ( !SendCommand(passwordCommand, true) ) {
+ Close();
+ return false;
+ }
+
+ // send TYPE command
+ string typeCommand = TYPE_CMD + SPACE_CHAR + "I" + FTP_NEWLINE;
+ if ( !SendCommand(typeCommand, true) ) {
+ Close();
+ return false;
+ }
+
+ // return success
+ return true;
+}
+
+bool BamFtp::ConnectDataSocket(void) {
+
+ // failure if can't connect to command socket first
+ if ( !m_commandSocket->IsConnected() ) {
+ if ( !ConnectCommandSocket() )
+ return false;
+ }
+
+ // make sure we're starting with a fresh data channel
+ if ( m_dataSocket->IsConnected() )
+ m_dataSocket->DisconnectFromHost();
+
+ // send passive connection command
+ const string passiveCommand = PASV_CMD + FTP_NEWLINE;
+ if ( !SendCommand(passiveCommand, true) ) {
+ // TODO: set error string
+ return false;
+ }
+
+ // retrieve passive connection port
+ if ( !ParsePassiveResponse() ) {
+ // TODO: set error string
+ return false;
+ }
+
+ // set up restart command (tell server where to start fetching bytes from)
+ if ( m_filePosition >= 0 ) {
+
+ stringstream fpStream("");
+ fpStream << m_filePosition;
+ string restartCommand = REST_CMD + SPACE_CHAR + fpStream.str() + FTP_NEWLINE;
+ if ( !SendCommand(restartCommand, true) ) {
+ // TODO: set error string
+ return false;
+ }
+ }
+
+ // main file retrieval request
+ string retrieveCommand = RETR_CMD + SPACE_CHAR + m_filename + FTP_NEWLINE;
+ if ( !SendCommand(retrieveCommand, false) ) {
+ // TODO: set error string
+ return false;
+ }
+
+ // make data channel connection
+ if ( !m_dataSocket->ConnectToHost(m_dataHostname, m_dataPort) ) {
+ // TODO: set error string
+ return false;
+ }
+
+ // fetch intial reply from server
+ if ( !ReceiveReply() ) {
+ // TODO: set error string
+ m_dataSocket->DisconnectFromHost();
+ return false;
+ }
+
+ // make sure we have reply code 150 (all good)
+ if ( !startsWith(m_response, "150") ) {
+ // TODO: set error string
+ m_dataSocket->DisconnectFromHost();
+ return false;
+ }
+
+ // return success
+ return true;
+}
+
+bool BamFtp::IsOpen(void) const {
+ return IBamIODevice::IsOpen() && m_isUrlParsed;
}
bool BamFtp::IsRandomAccess(void) const {
bool BamFtp::Open(const IBamIODevice::OpenMode mode) {
+ // BamFtp only supports read-only access
if ( mode != IBamIODevice::ReadOnly ) {
SetErrorString("BamFtp::Open", "writing on this device is not supported");
return false;
}
+ // initialize basic valid state
+ m_mode = mode;
+ m_filePosition = 0;
+ // attempt connection to command & data sockets
+ return ( ConnectCommandSocket() && ConnectDataSocket() );
+}
+
+bool BamFtp::ParsePassiveResponse(void) {
+
+ // fail if empty
+ if ( m_response.empty() )
+ return false;
+
+ // find parentheses
+ const size_t leftParenFound = m_response.find(LEFT_PAREN_CHAR);
+ const size_t rightParenFound = m_response.find(RIGHT_PAREN_CHAR);
+ if ( leftParenFound == string::npos || rightParenFound == string::npos )
+ return false;
+
+ // grab everything between ( should be "h1,h2,h3,h4,p1,p2" )
+ string::const_iterator responseBegin = m_response.begin();
+ const string hostAndPort(responseBegin+leftParenFound+1, responseBegin+rightParenFound);
+
+ // parse into string fields
+ vector<string> fields = split(hostAndPort, COMMA_CHAR);
+ if ( fields.size() != 6 )
+ return false;
+
+ // fetch passive connection IP
+ m_dataHostname = fields[0] + DOT_CHAR +
+ fields[1] + DOT_CHAR +
+ fields[2] + DOT_CHAR +
+ fields[3];
+
+ // fetch passive connection port
+ const uint8_t portUpper = static_cast<uint8_t>(atoi(fields[4].c_str()));
+ const uint8_t portLower = static_cast<uint8_t>(atoi(fields[5].c_str()));
+ m_dataPort = ( portUpper<<8 ) + portLower;
+
+ // return success
return true;
}
+void BamFtp::ParseUrl(const string& url) {
+
+ // clear flag to start
+ m_isUrlParsed = false;
+
+ // make sure url starts with "ftp://", case-insensitive
+ string tempUrl(url);
+ toLower(tempUrl);
+ const size_t prefixFound = tempUrl.find(FTP_PREFIX);
+ if ( prefixFound == string::npos )
+ return;
+
+ // find end of host name portion (first '/' hit after the prefix)
+ const size_t firstSlashFound = tempUrl.find(SLASH_CHAR, FTP_PREFIX_LENGTH);
+ if ( firstSlashFound == string::npos ) {
+ ; // no slash found... no filename given along with host?
+ }
+
+ // fetch hostname
+ string hostname = tempUrl.substr(FTP_PREFIX_LENGTH, (firstSlashFound - FTP_PREFIX_LENGTH));
+ m_hostname = hostname;
+ m_port = FTP_PORT;
+
+ // store remainder of URL as filename (must be non-empty)
+ string filename = tempUrl.substr(firstSlashFound);
+ if ( filename.empty() )
+ return;
+ m_filename = filename;
+
+ // set parsed OK flag
+ m_isUrlParsed = true;
+}
+
int64_t BamFtp::Read(char* data, const unsigned int numBytes) {
- (void)data;
- (void)numBytes;
- return 0;
+
+ // if BamHttp not in a valid state
+ if ( !IsOpen() )
+ return -1;
+
+ // read until hit desired @numBytes
+ int64_t bytesReadSoFar = 0;
+ while ( bytesReadSoFar < numBytes ) {
+
+ // calculate number of bytes we're going to try to read this iteration
+ const size_t remainingBytes = ( numBytes - bytesReadSoFar );
+
+ // if either disconnected somehow, or (more likely) we have seeked since last read
+ if ( !m_dataSocket->IsConnected() ) {
+ if ( !ConnectDataSocket() ) {
+ // TODO: set error string
+ return -1;
+ }
+ }
+
+ // read bytes from data socket
+ const int64_t socketBytesRead = ReadDataSocket(data+bytesReadSoFar, remainingBytes);
+ if ( socketBytesRead < 0 )
+ return -1;
+ bytesReadSoFar += socketBytesRead;
+ m_filePosition += socketBytesRead;
+ }
+
+ // return actual number bytes successfully read
+ return bytesReadSoFar;
+}
+
+int64_t BamFtp::ReadCommandSocket(char* data, const unsigned int maxNumBytes) {
+
+ // try to read 'remainingBytes' from socket
+ const int64_t numBytesRead = m_commandSocket->Read(data, maxNumBytes);
+ if ( numBytesRead < 0 )
+ return -1;
+ return numBytesRead;
+}
+
+int64_t BamFtp::ReadDataSocket(char* data, const unsigned int maxNumBytes) {
+
+ // try to read 'remainingBytes' from socket
+ const int64_t numBytesRead = m_dataSocket->Read(data, maxNumBytes);
+ if ( numBytesRead < 0 )
+ return -1;
+ return numBytesRead;
+}
+
+bool BamFtp::ReceiveReply(void) {
+
+ // failure if not connected
+ if ( !m_commandSocket->IsConnected() ) {
+ SetErrorString("BamFtp::ReceiveReply()", "command socket not connected");
+ return false;
+ }
+
+ m_response.clear();
+
+ // read header data (& discard for now)
+ bool headerEnd = false;
+ while ( !headerEnd ) {
+
+ const string headerLine = m_commandSocket->ReadLine();
+ m_response += headerLine;
+
+ // if line is of form 'xyz ', quit reading lines
+ if ( (headerLine.length() >= 4 ) &&
+ isdigit(headerLine[0]) &&
+ isdigit(headerLine[1]) &&
+ isdigit(headerLine[2]) &&
+ ( headerLine[3] != MINUS_CHAR )
+ )
+ {
+ headerEnd = true;
+ }
+ }
+
+ // return success, depending on response
+ if ( m_response.empty() ) {
+ SetErrorString("BamFtp::ReceiveReply", "error reading server reply");
+ return false;
+ }
+ return true;
}
bool BamFtp::Seek(const int64_t& position) {
- (void)position;
+
+ // if FTP device not in a valid state
+ if ( !IsOpen() ) {
+ // TODO: set error string
+ return false;
+ }
+
+ // ----------------------
+ // UGLY !! but works??
+ // ----------------------
+ // disconnect from server
+ m_dataSocket->DisconnectFromHost();
+ m_commandSocket->DisconnectFromHost();
+
+ // update file position & return success
+ m_filePosition = position;
+ return true;
+}
+
+bool BamFtp::SendCommand(const string& command, bool waitForReply) {
+
+ // failure if not connected
+ if ( !m_commandSocket->IsConnected() ) {
+ SetErrorString("BamFtp::SendCommand", "command socket not connected");
+ return false;
+ }
+
+ // write command to 'command socket'
+ if ( WriteCommandSocket(command.c_str(), command.length()) == -1 ) {
+ SetErrorString("BamFtp::SendCommand", "error writing to socket");
+ // get actual error from command socket??
+ return false;
+ }
+
+ // if we sent a command that receives a response
+ if ( waitForReply )
+ return ReceiveReply();
+
+ // return success
return true;
}
int64_t BamFtp::Tell(void) const {
- return -1;
+ return ( IsOpen() ? m_filePosition : -1 );
}
int64_t BamFtp::Write(const char* data, const unsigned int numBytes) {
(void)data;
(void)numBytes;
BT_ASSERT_X(false, "BamFtp::Write : write-mode not supported on this device");
- return 0;
+ SetErrorString("BamFtp::Write", "write-mode not supported on this device");
+ return -1;
+}
+
+int64_t BamFtp::WriteCommandSocket(const char* data, const unsigned int numBytes) {
+ if ( !m_commandSocket->IsConnected() )
+ return -1;
+ m_commandSocket->ClearBuffer();
+ return m_commandSocket->Write(data, numBytes);
+}
+
+int64_t BamFtp::WriteDataSocket(const char* data, const unsigned int numBytes) {
+ (void)data;
+ (void)numBytes;
+ BT_ASSERT_X(false, "BamFtp::WriteDataSocket: write-mode not supported on this device");
+ SetErrorString("BamFtp::Write", "write-mode not supported on this device");
+ return -1;
}
projects / bamtools.git / blobdiff