mast-server.c

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/*
 * $Id: mast-server.c 1339 2006-09-21 19:46:28Z tbailey $
 * 
 * $Log$
 * Revision 1.6  2005/10/28 22:44:19  nadya
 * fix typo in "rm"
 *
 * Revision 1.5  2005/09/15 21:27:12  nadya
 * fix db path for uploaded files
 *
 * Revision 1.4  2005/09/13 21:11:36  nadya
 * rm exit line from mast/meme submit scripts
 *
 * Revision 1.3  2005/08/30 22:46:21  nadya
 * update calls to mailer
 *
 * Revision 1.2  2005/08/24 04:37:07  nadya
 * change script layout. Don't assume a given directory,
 * just use full path where needed for files and binaries.
 *
 * Revision 1.1.1.1  2005/07/29 17:16:51  nadya
 * Importing from meme-3.0.14, and adding configure/make
 *
 */

/*
	mast-server

	Usage: mast-server <socket> <command>
		<socket>  socket number to listen on
		<command> command to execute; quote if spaces

        If the file sent to the socket contains just the word "ping",
        the program exits with success.
 
	6/02/96; created; tbailey

Format for input file read from the socket:
----------------------
ADDRESS <return address> 
PROGRAM mast
DESCRIPTION <1 line of text>
MOTIFS <original name of motif file>
DB_TYPE local | uploaded
DATABASE <name of database file to search (../mast_databases/ will be prepended)>
ALPHABET <alphabet used in database>
SWITCHES <other switches>
LOGINFO <information to log>
BEGIN_MOTIFS
<logodds matrices>
[
%
BEGIN_DB
<uploaded FASTA sequences>
%
]

Error messages:
---------------
  10 : Error opening file
  11 : Error reading from socket
  12 : Error writing to file
  13 : Error sending ack to client
  14 : Error binding socket
  15 : Error listening to socket
  16 : Error creating socket
  20 : Header field not found
  21 : Invalid field name
  22 : Illegal number of motifs
*/

/***********************************************************************
 * Include files
 ***********************************************************************/
#include "meme-cs.h"
#include <signal.h>
#include <sys/wait.h>
#include <sys/errno.h>

/***********************************************************************
 * Constants
 ***********************************************************************/
#define MAXHEADERLINE 256
#define NPROCS 1

/*
Error messages:
---------------
  10 : Error opening file
  11 : Error reading from socket
  12 : Error writing to file
  13 : Error sending ack to client
  14 : Error binding socket
  15 : Error listening to socket
  16 : Error creating socket
  20 : Header field not found
  21 : Invalid field name
  22 : Illegal number of motifs
*/

/***********************************************************************
 * Include files
 ***********************************************************************/
#include "meme-cs.h"
#include <signal.h>
#include <sys/wait.h>
#include <sys/errno.h>

/***********************************************************************
 * Constants
 ***********************************************************************/
#define MAXHEADERLINE 256
#define NPROCS 1
/* returned by system() */
#ifdef sunsparc
  int SYSTEM_OK = -1;
#else
  int SYSTEM_OK = 0;
#endif

/***********************************************************************
 * Type definitions
 ***********************************************************************/
typedef struct HEADER {
  char address[MAXHEADERLINE];
  char program[MAXHEADERLINE];
  char description[MAXHEADERLINE];
  char motif_file[MAXHEADERLINE];
  char db_type[MAXHEADERLINE];
  char database[MAXHEADERLINE];
  char alphabet[MAXHEADERLINE];
  char switches[MAXHEADERLINE];
  char loginfo[MAXHEADERLINE];
} HEADER;


/***********************************************************************
 * Globals 
 ***********************************************************************/

int SOCKET_NUMBER;		/* socket to listen on */
char *MAST;			/* name of mast executable */


/***********************************************************************
 *
 * void strlower
 *
 * Downcase a given string.
 *
 ***********************************************************************/
void strlower(char *a_string)
{
  int index;

  for (index = 0; a_string[index] != '\0'; index++)
    a_string[index] = tolower((int) a_string[index]);
}

/***********************************************************************
 *
 * void read_header_item
 *
 * Read one header line from a socket into a HEADER data structure.
 *
 ***********************************************************************/
void read_header_item(HEADER *a_header, int sock, char *fieldname)
{
  int i;
  char buffer[MAXHEADERLINE];
  char *info;
  
  /* Read the line into a local buffer. */
  if (readline(sock, buffer, MAXHEADERLINE) == 0) {
    fprintf(stderr, "Error reading from socket.\n");
    fflush(stderr);
    exit(11);
  }

  /* Check to see if this is a ping */
  if (strcmp(buffer, "ping") == 0) {
    exit(0);                            /* ping; exit with OK status */
  }
 
  /* Search for the field name in the line. */
  if ((info = (char *)strstr(buffer, fieldname)) == NULL) {
    fprintf(stderr, "Field %s not found in %s.\n", fieldname, buffer);
    fflush(stderr);
    exit(20);
  }

  /* Move past the end of the field name. */
  info += strlen(fieldname);
  if (*info != '\0') info++;

  /* Get the first character of the field name. */
  switch (fieldname[0]) {
    case 'A' : 
      switch (fieldname[1]) {
	case 'D' :  /* ADDRESS */
	  strcpy(a_header->address, info);
	  break;
	case 'L' :  /* ALPHABET */
	  strcpy(a_header->alphabet, info);
	  break;
      }
      break;
    case 'M' :  /* MOTIFS */
      strcpy(a_header->motif_file, info);
      break;
    case 'P' :  /* PROGRAM */
      strcpy(a_header->program, info);
      break;
    case 'D' : 
      switch (fieldname[1]) {
	case 'E' :  /* DESCRIPTION */
	  strcpy(a_header->description, info);
	  break;
	case 'A' :  /* DATABASE */
	  strcpy(a_header->database, info);
	  break;
	case 'B' :  /* DB_TYPE */
	  strcpy(a_header->db_type, info);
	  break;
      }
      break;
    case 'S' :  /* SWITCHES */
      /* copy removing any nasty semi-colons to prevent security breach */
      for (i=0; info[i]; i++) { 
        if (info[i] != ';') {
          a_header->switches[i] = info[i];
        } else { 
          a_header->switches[i] = ' ';
        }
      }
      a_header->switches[i] = '\0';
      break;
    case 'L' :  /* LOGINFO */
      strcpy(a_header->loginfo, info);
      break;
    case 'B' :  /* BEGIN_LO or BEGIN_MOTIFS */
      /* Don't do anything except skip header line */
      break;
    default: 
      fprintf(stderr, "Invalid fieldname: %s\n", fieldname);
      fflush(stderr);
      exit(21);
  }
} /* read_header_item */


/***********************************************************************
 *
 * write_data_file
 *
 * Read in some lines from a socket and write them to a file.
 *
 ***********************************************************************/
void write_data_file(int sock, char *filename, char terminator)
{
  int filedescriptor, nread;
  char achar;

  /* Create the data file and open it in write-only mode. */
  if ((filedescriptor = open(filename, 
			     O_WRONLY | O_CREAT | O_TRUNC, 400)) == -1) {
    fprintf(stderr, "Error creating file %s\n", filename);
    fflush(stderr);
    exit(10);
  }
      
  /* Read from the socket until line containing only terminator reached. */
  for (nread = readn(sock, &achar, 1); nread == 1 && achar != terminator;
       nread = readn(sock, &achar, 1)) {
    
    /*printf("%c", achar);*/

    /* Echo incoming data to the file. */
    if (write(filedescriptor, &achar, 1) != 1) {
      fprintf(stderr, "Error writing to file %s.\n", filename);
      fflush(stderr);
      exit(12);
    }
  }

  /* Throw away newline after terminator. */
  if (achar == terminator) {
    nread = readn(sock, &achar, 1);
  }
     
  /* Close the file. */
  close(filedescriptor);
}

/***********************************************************************
 *
 * receive_file
 *
 * Read in a file from the socket.
 *
 ***********************************************************************/
void receive_file(
  int sock, 
  char *motif_filename, 
  char *db_filename,
  HEADER *a_header
)
{
  /* Read in the header. */
  read_header_item(a_header, sock, "ADDRESS");
  read_header_item(a_header, sock, "PROGRAM");
  read_header_item(a_header, sock, "DESCRIPTION");
  read_header_item(a_header, sock, "MOTIFS");
  read_header_item(a_header, sock, "DB_TYPE");
  read_header_item(a_header, sock, "DATABASE");
  read_header_item(a_header, sock, "ALPHABET");
  read_header_item(a_header, sock, "SWITCHES");
  read_header_item(a_header, sock, "LOGINFO");
  read_header_item(a_header, sock, "BEGIN_MOTIFS");
  /* Echo the motifs to a file. */
  write_data_file(sock, motif_filename, '%');
  if (strcmp(a_header->db_type, "uploaded") == 0) {
    /* Echo the uploaded sequence data to a file. */
    read_header_item(a_header, sock, "BEGIN_DB");
    write_data_file(sock, db_filename, '%');
  }
}

/***********************************************************************
 *
 * send_ack
 *
 * Send a single-byte ack to the client.
 *
 ***********************************************************************/
void send_ack(int sock)
{
  char achar = '1';

  if (writen(sock, &achar, 1) != 1) {