msdsearch_soap_service.cc

// httpd -f /ebi/msd/work/siamak/apache/conf/httpd.conf
// ps -x (returns PID)
// kill PID
// httpd -f /ebi/msd/work/siamak/apache/conf/phoenix_httpd.conf 
//  ./soapcpp2 -2 -i -pmsdsearch_soap msdsearch_soap.h 

//msdsearch_soap_service.cgi:
//~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
// #!/bin/csh -f
// # disable filename globbing
// source /ebi/msd/work/siamak/apache/cgi-bin/apisercnf.csh
// exec /ebi/msd/work/siamak/apache/cgi-bin/msdsearch_soap_service
//~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
// For final web services:
//  more /ebi/msd/software/common/tns_admin/tnsnames.ora

// **** This process should be executed on web6-node2 machine: ***** //

// make fsoap [VER=-2]-----> for making SOAP 1.2 (default is  SOAP 1.1)
// make fsoapcopy
// make fwservice
// make fwclient
// http://parrot.ebi.ac.uk:8099/cgi-bin/msdsearch_soap_client
// or http://www.ebi.ac.uk/msd-srv/ssm/cgi-bin/ws/msd_soap_client

// to config expat:  
//          ./configure --prefix=/home/me/mystuff
// cd /ebi/msd/work/siamak/expat-1.95.5
//./configure --prefix=/ebi/msd/work/siamak/msd_api
//make
//make install

// make shared
// make cleanj
// make msdj
// java MSDJapi






#include <iostream>
#include <fstream>
#include <string.h>

//#include <stdio.h>
//#include <stdlib.h>

#ifndef __MSD_DEFS_H__
#include "msd_defs.h"
#endif

#include "msdsearch_soapH.h"
#ifndef __MSD_SOAP_ENABLED__
#define __MSD_SOAP_ENABLED__
#endif


//#define LPP_True_NODEFINE

//extern class ostream;

#ifndef __MSD_USER_H__
#include "msd_user.h"
#endif
#include "msdsearch_soap_service.nsmap"

#ifndef  __SRV_PXML__
#include "srv_pxml.h"
#endif

#include "expat.h"

//~~~~~~~#define LEASETERM 300

#include <sys/stat.h> // for open()
//#include <iostream>

//using std::ios;
//using std::fstream;
//using std::cout;
//#include "msd_datatypes.h"



int xml_elno=-1;
msd_xml_element * xml_inf;
//int Eventcnt = 0;
char * xml_Buff;
char * xml_txtbuff;


void default_hndl(void *data, const char *s, int len) {
  //fwrite(s, len, sizeof(char), stdout);
}  /* End default_hndl */

/****************************************************************
 ** Call from within a handler to print the currently recognized
 ** document fragment. Temporarily set the default handler and then
 ** invoke it via the the XML_DefaultCurrent call.
 */
void printcurrent(XML_Parser x_p) {
  XML_SetDefaultHandler(x_p, default_hndl);
  XML_DefaultCurrent(x_p);
  XML_SetDefaultHandler(x_p, (XML_DefaultHandler) 0);
}  /* End printcurrent */




void start_hndl(void *data, const char *el, const char **attr) {
  
xml_elno++;

xml_inf[xml_elno].tag=(char *)malloc(strlen(el)+1);
 
sprintf(xml_inf[xml_elno].tag,"%s",el);
xml_inf[xml_elno].data=(char *)malloc(strlen(xml_txtbuff)+1);
sprintf(xml_inf[xml_elno].data,"%s","");
sprintf(xml_txtbuff,"%s", "");  //NULL

 
 // printf("\n%4d: Start tag %s - ", Eventcnt++, el);

  printcurrent((XML_Parser) data);
}  /* End of start_hndl */


void end_hndl(void *data, const char *el) {
 
 sprintf(xml_inf[xml_elno].data,"%s",xml_txtbuff);
 
 //printf("\n%4d: End tag %s -\n", Eventcnt++, el);
}  /* End of end_hndl */

void char_hndl(void *data, const char *txt, int txtlen) {
 
 char* xbuf;
 xbuf=(char*)malloc(strlen(txt)+1);
 sprintf(xbuf,"%s","");
 //strncpy(xbuf,txt,txtlen);
 strcpy(xbuf,txt);
 xbuf[txtlen]='\0';
 //trimspace(xbuf);
 sprintf(xml_txtbuff,"%s%s", xml_txtbuff, xbuf);
 //free(xbuf);
 
  //printf("\n%4d: Text - ", Eventcnt++);
  //fwrite(txt, txtlen, sizeof(char), stdout);
 //if (xml_txtbuff)
// {printf("\n%4d: Text - ", Eventcnt++);
//  fwrite(xml_txtbuff, strlen(xml_txtbuff), sizeof(char), stdout);
// }
  
  
  
 
}  /* End char_hndl */

void proc_hndl(void *data, const char *target, const char *pidata) {
  //printf("\n%4d: Processing Instruction - ", Eventcnt++);
  printcurrent((XML_Parser) data);
 // elno++;
}  /* End proc_hndl */


 
  /* Notice that the default handler is not set at this point */

  
 





//const char msd_soap_service[] = "http://phoenix.ebi.ac.uk:8099/cgi-bin/msdsearch_soap_service.cgi";
const char msdsearch_soap_service[] = "http://www.ebi.ac.uk/msd-srv/ssm/cgi-bin/ws/msdsearch_soap_service.cgi";

int main(int argc, char **argv)
{  
   
   
   int m, s;
   struct soap soap;
   soap_init(&soap);
   //soap.user = (void*)&conn;          // associate factory with run-time
   
   //~~~soap.accept_timeout = LEASETERM;        // term before leases runs out is used as a rate to purge objects
   
   
   //soap.cookie_domain = "http://www.ebi.ac.uk/msd-srv/ssm/cgi-bin/ws/"; 
   //soap.cookie_path = "/ebi/msd/ssm/cgi-bin/ws"; // the path which is used to filter/set cookies with this destination 
   //int cookie_max =64;
   
   //soap_set_recv_logfile(&soap, "/ebi/msd/ssm/cgi-bin/ws/work/msd_ws_recv.log"); // append all messages received in /logs/recv/service12.log 
   //soap_set_sent_logfile(&soap, "/ebi/msd/ssm/cgi-bin/ws/work/msd_ws_sent.log"); // append all messages sent in /logs/sent/service12.log 
   //soap_set_test_logfile(&soap, "/ebi/msd/ssm/cgi-bin/ws/work/msd_ws_test.log"); //  NULL no file name: do not save debug messages 
   
   
   
   if (argc < 3)
        {
          // soap_getenv_cookies(&soap); // CGI app: grab cookies from 'HTTP_COOKIE' env var 
           soap_serve(&soap); // run as CGI application over the Web
    }
  else // run as stand-alone server on machine given by argv[1] listening to port argv[2]
  { m = soap_bind(&soap, argv[1], atoi(argv[2]), 100);
    if (m < 0)
    { soap_print_fault(&soap, stderr);
      exit(-1);
    }
    fprintf(stderr, "Socket connection successful: master socket = %d\n", m);
    for (int i = 1; ; i++)
    { s = soap_accept(&soap);
      if (s < 0)
      { soap_print_fault(&soap, stderr);
        exit(-1);
      }
      fprintf(stderr, "%d: accepted connection from IP = %d.%d.%d.%d socket = %d ... ", i, (int)(soap.ip>>24)&0xFF, (int)(soap.ip>>16)&0xFF, (int)(soap.ip>>8)&0xFF, (int)soap.ip&0xFF, s);
      soap_serve(&soap);                // process request
      fprintf(stderr, "request served\n");
      soap_destroy(&soap);      // delete class instances
      soap_end(&soap);          // clean up everything and close socket
         // soap_free_cookies(&soap); // remove all old cookies from database so no interference occurs with the arrival of new cookies 
    }
  }
  //soap_dealloc(&soap, NULL); 
  soap_destroy(&soap);
  soap_end(&soap);
  //free(&soap);
  return 0;
}


 int ns__msdSSM(struct soap *soap,int numofpars, array *inparams, int &result){
 char* xmlstr = (char*)soap_malloc(soap,4096);
 char* xmlstrn = (char*)soap_malloc(soap,4096);
 char* infname = (char*)soap_malloc(soap,256);
 char* outfname = (char*)soap_malloc(soap,256);
 inparams->__size=numofpars;
 sprintf(xmlstr,"%s",(*inparams)[0]->__item);

 
char * pch;
  pch = strtok (xmlstr,">");
  sprintf (xmlstrn,"%s", "");
  while (pch != NULL){
        //int i=1;
    if (pch[0]==' ' || pch[0]=='\n')
    { while (pch[0]==' ' || pch[0]=='\n'){ 
           pch++;
      }
          sprintf (xmlstrn,"%s%s>",xmlstrn, pch);
    }else{
        sprintf (xmlstrn,"%s%s>",xmlstrn, pch);}
        pch = strtok (NULL, ">");
  }
  sprintf (xmlstr, "%s",xmlstrn);
  pch = strtok (xmlstr,">");
  sprintf (xmlstrn,"%s", "");
  while (pch != NULL)
  { if (pch[0]=='<' )
    {sprintf (xmlstrn,"%s\n%s>",xmlstrn, pch);
    }else{
        sprintf (xmlstrn,"%s%s>",xmlstrn, pch);}
        pch = strtok (NULL, ">\n");
  }
sprintf (xmlstrn,"%s\n",xmlstrn);

sprintf(infname,"/ebi/msd/ssm/cgi-bin/ws/work/%s_in.xml",(*inparams)[1]->__item);
 FILE * pfile;
 pfile = fopen (infname,"w+t");
   if (pfile==NULL)
   {cerr << "error: could not create " << infname  << endl;
    exit(1);}
 fwrite (xmlstrn , 1 , strlen(xmlstrn), pfile);
 //fputs (xmlstrn,pfile);
 fclose (pfile);
 pfile=NULL;
 sprintf(outfname,"/ebi/msd/ssm/cgi-bin/ws/work/%s_out.xml",(*inparams)[1]->__item);
 char* buff;
 char* syscall;
 size_t buffsize=0;
 
// msd_anyType* tmp[5];
// //tmp[0]=new msd_string("bsub -q extsrv_interactive -R msd_ssm -o /ebi/msd/ssm/cgi-bin/ws/work/ssmws.log"); // -o outfname
// tmp[0]=new msd_string("/ebi/msd/ssm/cgi-bin/ssmserver -offline");
// tmp[1]=new msd_string(infname);
// tmp[2]=new msd_string(outfname);
// tmp[3]=new msd_string("/ebi/msd/ssm/ssmdata/ssm_webservice.conf");
// tmp[4]=new msd_string("> /ebi/msd/ssm/cgi-bin/ws/work/ssmws.log"); // should change according session
// 
// for (int i=0;i<5 ;i++ )
// {buffsize = buffsize + strlen(tmp[i]->msd_item)+1;
// }
//  buff=(char *)soap_malloc(soap, buffsize);
// sprintf(buff,"%s",tmp[0]->msd_item);
// for (int i=1;i<5 ;i++ )
// {sprintf(buff,"%s %s",buff,tmp[i]->msd_item);
// }
// for (int i = 0; i < 5; i++){
//        delete tmp[i];
// }
 char ** tmp = (char**)soap_malloc(soap,5*256);
 for (int i=0;i<5 ;i++ ){
 tmp[i]= (char*)soap_malloc(soap,256);
 } 
 sprintf(tmp[0],"%s","/ebi/msd/ssm/cgi-bin/ssmserver -offline");
 sprintf(tmp[1],"%s",infname);
 sprintf(tmp[2],"%s",outfname);
 sprintf(tmp[3],"%s","/ebi/msd/ssm/ssmdata/ssm_webservice.conf");
 sprintf(tmp[4]," > /ebi/msd/ssm/cgi-bin/ws/work/%s_ssmws.log", (*inparams)[1]->__item);
 buff=(char *)soap_malloc(soap, 5*(256+1));
 sprintf(buff,"%s",tmp[0]);
 for (int i=1;i<5 ;i++ )
 {sprintf(buff,"%s %s",buff,tmp[i]);
 }
 
 

 syscall = (char*)soap_malloc(soap, strlen(buff)+1);
 sprintf(syscall,"%s", buff);
 pfile=fopen (infname,"rt");
 if (pfile)
 {fclose (pfile);
  pfile=NULL;
  result = system(syscall);
 }
 
 if (result < 0){
         result = errno;         
 }
 //soap_unlink(soap, (void*)xmlstr);
 //soap_unlink(soap, (void*)xmlstrn);
 //soap_unlink(soap, (void*)buff);
 //soap_unlink(soap, (void*)syscall);
 return SOAP_OK;
 }          

 int ns__msdSSMParser(struct soap *soap, char* sessionid, char* dbserver, int &result){
 char* xmlfn = (char*)soap_malloc(soap,256);
 char* session = (char*)soap_malloc(soap,64);
 char* db_server= (char*)soap_malloc(soap,32);
 char* login_string = (char*)soap_malloc(soap,64);
 char* syscall = (char*)soap_malloc(soap,256);
 char* loginstr;
 char* fname = (char*)soap_malloc(soap,512);
 char* ofname = (char*)soap_malloc(soap,512);
 int out_file_ok=1;
 char* tmp = (char*)soap_malloc(soap,64);
 //session_id = (char*)soap_malloc(soap, strlen(sessionid)+1);
 sprintf(session,"%s",sessionid);
 sprintf(db_server,"%s",dbserver);
 sprintf(login_string,"search/search55@%s",db_server);
 loginstr = (char*)malloc(strlen(login_string)+1);
 strcpy(loginstr, login_string);
 sprintf(xmlfn,"/ebi/msd/ssm/cgi-bin/ws/work/%s_out.xml",session);
 sprintf(fname,"/ebi/msd/ssm/cgi-bin/ws/work/%s_in.xml",session);
 sprintf(ofname,"/ebi/msd/ssm/cgi-bin/ws/work/%s_log.txt",session);
 char write_line[1024];

 //sprintf(table_exists_stm,"select o.object_name as table_name,o.owner as owner " 
 //"from all_objects o where o.object_name like 'SSM_OUT_TAB' and o.owner = 'search'");
 
  char* stmnt = (char*)soap_malloc(soap,512);
  int j=0;
  wait(30);
  while(j<12*15) // up to 15 minutes wait for result
  { if (fileexists(xmlfn))
          { out_file_ok=0;
            break;}else 
          {wait(5);} // wait 5 seconds and retry again
        j++;
  } // end while
 if (out_file_ok!=0)
   {cerr << "error: SSM's xml output file: "  << xmlfn << " does not exists! " << endl;
    result = -2;
        exit(1);}
 
 PCSSMXML SSMXML;
 char*  queryID = (char*)soap_malloc(soap,500);
 char*  targetID = (char*)soap_malloc(soap,500);
 char*  queryCh = (char*)soap_malloc(soap,10);
 char*  targetCh = (char*)soap_malloc(soap,10);
 mat44    RT;
 int      rc, nMatches;
 //  1.  Make routine initializations, which must always be done
 //      before working with MMDB
 InitMatType();
 //  2.  Create an instance of XML object
 SSMXML = new CSSMXML();

 //sprintf (write_line, "%s", "Before SSM XML file read\n");
 //fputs (write_line,pfile);

 //  3.  Read XML file.
 rc = SSMXML->readSSMXML ( xmlfn );
 //sprintf (write_line, "  SSM XML file read rc=%i\n",rc );
 //fputs (write_line,pfile);
 if (rc) {
 result=rc;
 //return SOAP_FAULT;
 }
 

//ofstream outfile;
//outfile.open(ofname);


//FILE * pfile;
//pfile = fopen (ofname,"w+t");
// if (pfile==NULL)
// {
//  cerr << "error: could not open " << ofname  << endl;
// exit(1); 
// }


 
 nMatches = SSMXML->getNofMatches();
  sprintf (write_line, "  Total %i matches\n",nMatches );
  //fputs (write_line,pfile);
  //outfile << write_line;
  if (nMatches<=0){
          result=2;
          //return SOAP_FAULT; 
          }
  //fclose (pfile);
  //exit(1);
  char* insert_stm = (char*)soap_malloc(soap,4096);
  
  sprintf(stmnt, "insert into ssm_out_tab values ('%s' ", session); 
  




  
  
  rc = SSMXML->getQueryID ( queryID );
  
//~~~~~~~~~  FILE * pfile;
//~~~~~~~~~  pfile = fopen (fname,"w+t");
//~~~~~~~~~   if (pfile==NULL)
//~~~~~~~~~   {
//~~~~~~~~~    cerr << "error: could not open " << fname  << endl;
//~~~~~~~~~    exit(1); 
//~~~~~~~~~   }
 char*  table_exists_stm = (char*)soap_malloc(soap,3072);
 int n;
 char* create_table_stm="create table ssm_out_tab(session_id varchar2(64), query_id varchar2(10), target_id  varchar2(10), query_chain varchar2(6), target_chain  varchar2(6),"
 "p_score number, z_score number, rmsd number, r_xx number, r_xy number, r_xz number, r_yx number, r_yy number, r_yz number, r_zx number, r_zy number, r_zz number,"
 "t_x number, t_y number, t_z number, pair_query_start varchar2(10), pair_query_end varchar2(10),pair_target_chain varchar2(6), pair_target_start varchar2(6),pair_target_end varchar2(6),querydate varchar2(32) DEFAULT TO_CHAR(SYSDATE, 'MM-DD-YYYY HH24:MI:SS'))";
 sprintf(table_exists_stm, "select count(*) " 
 "from all_objects o where o.object_name like 'SSM_OUT_TAB' and o.owner = 'SEARCH'");
 msdbConnect db;
 msdbConnect::msdbInit(); // initialize OCI environment
 try{
  db.rlogon(loginstr); // connect to Oracle
 // otl_cursor::direct_exec(db,"drop table ssm_out_tab",
 //   msdbException::disabled // disable OTL exceptions
 //  ); // drop table
 msdbStream i(1, table_exists_stm, db);
 i >> n;
 if (n==0)
 {otl_cursor::direct_exec(db,create_table_stm);  // create table
 }
 
  
 } //try
 catch(msdbException& p){ // intercept OTL exceptions
  cerr<<p.msg<<endl; // print out error message
  cerr<<p.stm_text<<endl; // print out SQL that caused the error
  cerr<<p.var_info<<endl; // print out the variable that caused the error
  //outfile <<p.msg<<endl; // print out error message                          
  //outfile <<p.stm_text<<endl; // print out SQL that caused the error         
  //outfile <<p.var_info<<endl; // print out the variable that caused the error
 
 
 }
 if (rc==query_pdbentry)  {
          sprintf(stmnt, "%s, '%s'",stmnt,queryID);
          //sprintf(tmp, "'%s'",queryID);
          //sprintf (write_line, "  Query: PDB code %s\n",queryID );
     
          //fwrite (write_line, 1 , strlen(write_line), pfile);
         
          }
  else if (rc==query_file) {
          sprintf(stmnt, "%s, '%s'",stmnt,queryID);
          //sprintf(tmp, "'%s'",queryID);
          //sprintf (write_line,"  Query: coordinate file %s\n",queryID );
          
          //fwrite (write_line, 1 , strlen(write_line), pfile);
         
          }
                      else {
                                                  sprintf(stmnt, "%s, NULL",stmnt);
                                                  //sprintf (write_line, "  Error retrieving query ID #%i\n",rc );
                                                  
                                                  //fwrite (write_line, 1 , strlen(write_line), pfile);
                                                
                                                  }

  
  
  
  
  
  for (int i=1;i<=nMatches;i++)  { //nMatches
    sprintf (insert_stm,"%s",stmnt);
    //sprintf (write_line, "\n  MATCH #%i\n",i );
   
        //fwrite (write_line, 1 , strlen(write_line), pfile);
    rc = SSMXML->getTargetID ( targetID,i );
    switch (rc)  {
      case target_pdbentry   :
        {//sprintf (write_line, "  Target: PDB code %s\n" ,targetID );
            sprintf(insert_stm, "%s, '%s'",insert_stm,targetID);
                //sprintf(tmp, "'%s'",targetID);
                }
                break;
      case target_file       :
        {//sprintf (write_line, "  Target: file %s\n"     ,targetID );
             sprintf(insert_stm, "%s, '%s'",insert_stm,targetID);
                 //sprintf(tmp, "'%s'",targetID);
                 } 
           break;
      case target_pdb        :
        {//sprintf (write_line, "  Target: PDB entry %s\n",targetID );
            sprintf(insert_stm, "%s, '%s'",insert_stm,targetID);
                //sprintf(tmp, "'%s'",targetID);
                }
                break;
      case target_scop       :
        {//sprintf (write_line, "  Target: SCOP entry %s\n",targetID );
            sprintf(insert_stm, "%s, '%s'",insert_stm,targetID);
                //sprintf(tmp, "'%s'",targetID);
                }
                break;
      case target_scopsubset :
        {//sprintf (write_line, "  Target: SCOP subset entry %s\n",targetID );
            sprintf(insert_stm, "%s, '%s'",insert_stm,targetID);
                //sprintf(tmp, "'%s'",targetID);
                }
                break;
      default :
        {//sprintf (write_line, "  Error retrueving target ID #%i\n",rc );
                 sprintf(insert_stm, "%s, NULL",insert_stm);}
    } // end switch
    //outfile << queryID << endl;
        //outfile << targetID << endl;
        //fwrite (write_line, 1 , strlen(write_line), pfile);
    SSMXML->getQueryChain  ( queryCh ,i );
    SSMXML->getTargetChain ( targetCh,i );
    //sprintf (write_line, "          query  chain '%s'\n"
    //         "          target chain '%s'\n", queryCh,targetCh );
    
        if (!queryCh || strlen(queryCh)==0 || queryCh==NULL)
     {sprintf(insert_stm, "%s, NULL",insert_stm);}
          else
         {sprintf(insert_stm, "%s, '%s'",insert_stm,queryCh);
          //sprintf(tmp, "'%s'",queryCh);
          }
        if (!targetCh || strlen(targetCh)==0 || targetCh==NULL)
     {sprintf(insert_stm, "%s, NULL",insert_stm);}
          else
         {sprintf(insert_stm, "%s, '%s'",insert_stm,targetCh);
         //sprintf(tmp, "'%s'",targetCh);
         }
    
        //outfile << "\nHere I am\n";
    
        //fwrite (write_line, 1 , strlen(write_line), pfile);
    //sprintf (write_line, "          P-score %11.4f, Z-score %11.4f, RPDBe %11.4f\n",
    //         SSMXML->getPScore(i),SSMXML->getZScore(i),SSMXML->getRMSD(i) );
    sprintf(insert_stm, "%s, %11.4f",insert_stm,SSMXML->getPScore(i));
        
        sprintf(insert_stm, "%s, %11.4f",insert_stm,SSMXML->getZScore(i));
        
        sprintf(insert_stm, "%s, %11.4f",insert_stm,SSMXML->getRMSD(i));
        
        
        //fwrite (write_line, 1 , strlen(write_line), pfile);
    rc = SSMXML->getRTMatrix ( RT,i );
    if (rc)  {
      //sprintf (write_line, "          Error #%i at retrieving RT-matrix.\n",rc );
          for (int x=0;x<3 ;x++ )
   {for (int y=0;y<4 ;y++ )
    {sprintf(insert_stm, "%s, NULL",insert_stm);}
   }
          
         
          //fwrite (write_line, 1 , strlen(write_line), pfile);
          sprintf(insert_stm, "%s )",insert_stm);
      //fwrite (insert_stm, 1 , strlen(insert_stm), pfile);
      //fclose (pfile);
      break;
    }
    //sprintf (write_line, "          RT-matrix: %10.3f %10.3f %10.3f   %10.3f\n"
    //         "                     %10.3f %10.3f %10.3f   %10.3f\n"
    //         "                     %10.3f %10.3f %10.3f   %10.3f\n",
    //         RT[0][0], RT[0][1], RT[0][2], RT[0][3],
    //         RT[1][0], RT[1][1], RT[1][2], RT[1][3],
    //         RT[2][0], RT[2][1], RT[2][2], RT[2][3] );
   for (int x=0;x<3 ;x++ )
   {for (int y=0;y<4 ;y++ )
    {sprintf(insert_stm, "%s, %10.3f",insert_stm, RT[x][y]);}
   }
   sprintf(insert_stm, "%s, NULL, NULL, NULL, NULL, NULL, TO_CHAR(SYSDATE, 'MM-DD-YYYY HH24:MI:SS'))",insert_stm);
   
   //TO_DATE(TO_CHAR(SYSDATE, 'MM-DD-YYYY HH24:MI:SS'),'MM-DD-YYYY HH24:MI:SS')
   //~*******sprintf(insert_stm, "%s )",insert_stm);
   //fwrite (insert_stm, 1 , strlen(insert_stm), pfile);
   //fclose (pfile);
   //fwrite (write_line, 1 , strlen(write_line), pfile);
  
   //fwrite (insert_stm, 1 , strlen(insert_stm), pfile);
   try
  {
        otl_cursor::direct_exec(db,insert_stm);
  }
   catch(msdbException& p){ // intercept OTL exceptions
   cerr<<p.msg<<endl; // print out error message
   cerr<<p.stm_text<<endl; // print out SQL that caused the error
   cerr<<p.var_info<<endl; // print out the variable that caused the error
   //outfile <<p.msg<<endl; // print out error message                          
   //outfile <<p.stm_text<<endl; // print out SQL that caused the error         
   //outfile <<p.var_info<<endl; // print out the variable that caused the error
  }

  } // for loop
 
 
 //outfile.close();

 

//~***********  fwrite (insert_stm, 1 , strlen(insert_stm), pfile);
//~***********  
  //fclose (pfile);
  db.logoff(); // disconnect from Oracle 
  
  sprintf(syscall, "rm -f %s %s", fname,xmlfn);
  result = system(syscall); // syscall to delete files 
  if (result < 0){
          result = errno;
  }else{
          result=0;
  }
  
  
  
  //msdbStream o(50, // buffer size
  //            "insert into test_tab values(12345678900000000+:f1<int>,:f11<int>,:f2<char[31]>, SYSDATE)", 
  //               // SQL statement
  //            db // connect object
  //           );
 
 return SOAP_OK;
 }           


int ns__msdAppServer(struct soap *soap, int numofpars, array *inparams,  int &result){
 inparams->__size=numofpars;
 size_t buffsize=0;
 char* syscall;
 char * buff;
 for (int i=0;i<numofpars ;i++ )
 {buffsize = buffsize + strlen((*inparams)[i]->__item)+1;
 }
 buff=(char *)soap_malloc(soap, buffsize);
 sprintf(buff,"%s",(*inparams)[0]->__item);
 for (int i=1;i<numofpars ;i++ )
 {sprintf(buff,"%s %s",buff,(*inparams)[i]->__item);
 }
 syscall = (char*)soap_malloc(soap, strlen(buff)+1);
 sprintf(syscall,"%s", buff);
 result = system(syscall); // syscall
 if (result < 0)
 {result = errno;
 }
  return SOAP_OK;
}       



//char* instr ="<fatsa>"
// "<sequence>VMVSPMASIRSDEGMPIFVGDRSNVQDGVVLHALETINEEGEPIEDNI</sequence>"
// "<evalue>1e-10</evalue>"
//" <library>PDB</library>"
//"</fatsa>";














int ns__msdFasta(struct soap *soap, int numofpars, array *inparams,  int &result){
 char* xmlstr=(char*)soap_malloc(soap,4096); //4096
 char* xmlstrn=(char*)soap_malloc(soap,4096);
 char* infname=(char*)soap_malloc(soap,256);
 char* outfname=(char*)soap_malloc(soap,256);
 char* sessionid=(char*)soap_malloc(soap,64);
 char* sequence=(char*)soap_malloc(soap,3072);
 char* evalue=(char*)soap_malloc(soap,256);
 char* library=(char*)soap_malloc(soap,256);
 char* libref=(char*)soap_malloc(soap,8);
 
 //char xml_txtbuff[256];
 //char * xml_Buff;
 //int xml_elno=-1;
 //msd_xml_element * xml_inf=new msd_xml_element[10];
 
 inparams->__size=numofpars;
 size_t buffsize=0;
 sprintf(xmlstr,"%s",(*inparams)[0]->__item);
 //~~~~trimcr(xmlstr);
 xml_Buff=(char*)soap_malloc(soap,strlen(xmlstr)+1);
 sprintf(xml_Buff,"%s",xmlstr);
 sprintf(sessionid,"%s",(*inparams)[1]->__item);
 sprintf(infname,"/ebi/msd/ssm/cgi-bin/ws/work/%s_in.fasta",sessionid);
 sprintf(outfname,"/ebi/msd/ssm/cgi-bin/ws/work/%s_out.fasta",sessionid);
 
 xml_inf = (msd_xml_element *) soap_malloc(soap, sizeof(msd_xml_element)*10);
 xml_txtbuff = (char*)soap_malloc(soap, 3072);
 
    
 
 XML_Parser xp = XML_ParserCreate(NULL);
 XML_Parser * pxp;
  if (! xp) {
    fprintf(stderr, "Couldn't allocate memory for parser\n");
    exit(-1);
  } else {
   pxp=(XML_Parser *)soap_malloc(soap, sizeof(XML_Parser));
   pxp=&xp;
  }
 

  //xml_elements * info;
 
  //XML_SetUserData(*pxp, soap);

  XML_UseParserAsHandlerArg(*pxp);
  XML_SetElementHandler(*pxp, start_hndl, end_hndl);
  XML_SetCharacterDataHandler(*pxp, char_hndl);
  XML_SetProcessingInstructionHandler(*pxp, proc_hndl);
if (! XML_Parse(*pxp, xml_Buff, strlen(xml_Buff), true)) {
        fprintf(stderr, "Parse error at line %d:\n%s\n",
              XML_GetCurrentLineNumber(*pxp),
              XML_ErrorString(XML_GetErrorCode(*pxp)));
      exit(-1);
    }
        
        XML_ParserFree(xp);
        //printf("\nNumber of objects created: %d \n",elno);
        //for (int i=0;i<=elno ;i++ )
        //{printf("\nValue of tag %s :",inf[i].tag);
        // printf("%s\n",inf[i].data);
        //}
for (int i=0;i<=xml_elno ;i++ ){
        if (strcmp(xml_inf[i].tag,"evalue")==0)
        {sprintf(evalue,"%s",xml_inf[i].data);}else if (strcmp(xml_inf[i].tag,"sequence")==0)
        {removena(xml_inf[i].data);
         sprintf(sequence,">Q\n%s\n",xml_inf[i].data);}else if (strcmp(xml_inf[i].tag,"library")==0)
        {sprintf(libref,"%s",xml_inf[i].data);}
} //end for


//~~~~sprintf(sequence,">Q\n%s\n",inf[1].data);
//~~~~sprintf(evalue,"%s",inf[2].data);
//~~~~sprintf(libref,"%s",inf[3].data);

FILE * pfile;
 pfile = fopen (infname,"w+t");
   if (pfile==NULL)
   {cerr << "error: could not create " << infname  << endl;
    exit(1);}
 fwrite (sequence , 1 , strlen(sequence), pfile);
 //pfile << sequence << endl;
 //pfile.close();
 //pfile << evalue << endl;
 //pfile << library << endl;
 //fwrite (xmlstr , 1 , strlen(xmlstr), pfile);
 //fwrite (evalue , 1 , strlen(evalue), pfile);
 //fwrite (library , 1 , strlen(library), pfile);

         //fputs (xmlstrn,pfile);
// pfile.close();

fclose (pfile);
pfile=NULL; 




lcase(libref);
if (strcmp(libref, "pdb")==0) // strcmp((*inparams)[3]->__item 
{sprintf(library,"/ebi/msd/ssm/cgi-bin/ws/fasta/pdb_aa.fasta"); // /ebi/ftp/pub/databases/msd/pdb_aa.fasta
} //     /ebi/msd/srchsrv/fastalib/pdb_aa.fasta
 
 
 //ofstream pfile;
 //pfile.open(infname);
 
 


 //for (int i = 0; i < 10; i++){
//      free(xml_inf[i].data); 
//      free(xml_inf[i].tag);
 //}
 
 //delete [] xml_Buff;
 //delete [] xml_txtbuff;
 
 //free(xml_Buff);
 //free(xml_txtbuff);
 
 xml_elno = -1;
 char* buff;
 char* syscall;
 
 
//~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 
//Try this first:
//system("/bin/sh -c bsub ...")
//other choices:
//". /etc/profile.d/lsf.sh ; bsub ..."
//for tcsh
//"source /etc/profile.d/lsf.csh ; bsub ..."
 
//bsub -q extsrv_interactive -R msd_ssm -o /ebi/msd/work/siamak/apache/htdocs/23f5a66ec9c2091bea3b8f7fb82b4864_out.fasta /ebi/msd/work/siamak/msd_api/fasta/bin/fasta -Q -H -E 1e-10 /ebi/msd/work/siamak/apache/htdocs/23f5a66ec9c2091bea3b8f7fb82b4864_in.fasta /ebi/msd/srchsrv/fastalib/pdb_aa.fasta
 int noarr = 8;
 char ** tmp = (char**)soap_malloc(soap,noarr*256);
 for (int i=0;i<noarr ;i++ ){
 tmp[i]= (char*)soap_malloc(soap,256);
 } 
 sprintf(tmp[0],"%s","bsub -q extsrv_interactive -R msd_ssm -o");
 sprintf(tmp[1],"%s",outfname);
 sprintf(tmp[2],"%s","/ebi/msd/ssm/cgi-bin/ws/fasta/bin/fasta -Q -H -E ");
 sprintf(tmp[3],"%s",evalue);
 sprintf(tmp[4],"%s",infname);
 sprintf(tmp[5],"%s",library);
 sprintf(tmp[6],"%s",">");
 sprintf(tmp[7],"%s",outfname);

 buff=(char *)soap_malloc(soap, noarr*(256+1));
 sprintf(buff,"%s",tmp[0]);
 for (int i=1;i<noarr ;i++ )
 {sprintf(buff,"%s %s",buff,tmp[i]);
 }
 
 
 
 
 
 
// xsd__anyType* tmp[8];
// tmp[0]=new xsd__string("bsub -q extsrv_interactive -R msd_ssm -o"); // -o outfname
// tmp[1]=new xsd__string(outfname);
// tmp[2]=new xsd__string("/ebi/msd/ssm/cgi-bin/ws/fasta/bin/fasta -Q -H -E ");
// tmp[3]=new xsd__string(evalue);
// tmp[4]=new xsd__string(infname);
// tmp[5]=new xsd__string(library);
// tmp[6]=new xsd__string(">"); 
// tmp[7]=new xsd__string(outfname);
//  
// 
// for (int i=0;i<8 ;i++ ) //6
// {buffsize = buffsize + strlen(tmp[i]->__item)+1;
// }
//buff=(char *)soap_malloc(soap, buffsize);
 sprintf(buff,"%s",tmp[0]);
 for (int i=1;i<noarr ;i++ ) 
 {sprintf(buff,"%s %s",buff,tmp[i]);
 }
 
 //for (int i = 0; i < 8; i++){
 //       delete tmp[i];
 //}

 syscall = (char*)soap_malloc(soap, strlen(buff)+1);
 sprintf(syscall,"%s", buff);
 //pfile << syscall << endl;
 //pfile = fopen (infname,"a");
 //fwrite (syscall, 1 , strlen(syscall), pfile);
 //fwrite (library , 1 , strlen(library), pfile);
 //fwrite (evalue , 1 , strlen(evalue), pfile);
 //fclose (pfile);
 //pfile=NULL;
 //int j=0;
 //while(!fileexists(infname) && j<12*15) // fileexists --- up to 15 minutes wait for result
 // { wait(5); // wait 5 seconds and retry again
 //     j++;
 // } // end while
 


 
 pfile=fopen (infname,"r+t");
 if (pfile)
 { //fwrite (syscall, 1 , strlen(syscall), pfile);
  fclose (pfile);
  pfile=NULL;
  
  result = system(syscall);
  
  //result = system("/ebi/msd/work/siamak/apache/cgi-bin/msd_main > /ebi/msd/ssm/cgi-bin/ws/work/appserv.txt");
  //system(syscall);
  //result = 0;
 } 
  //wait(5);
  
  if (result < 0)
  {result = errno;         
  }


 //int j=0;
  //wait(5);
  //while(!fileexists(outfname) && j<12*15) // up to 15 minutes wait for result
 // { wait(5); // wait 5 seconds and retry again
 //     j++;
 // }
 
 //delete [] buff;
 //delete [] syscall;
 
 //soap_dealloc(soap, (void*)buff);
 //soap_dealloc(soap,(void*)syscall);
 //soap_dealloc(soap,(void*)xml_Buff);

 soap_dealloc(soap, (void*)xmlstr);
 soap_dealloc(soap, (void*)xmlstrn);
 soap_dealloc(soap, (void*)xml_Buff);
 soap_dealloc(soap, (void*)xml_txtbuff);
 soap_dealloc(soap, (void*)sequence);
 
 
 soap_unlink(soap, (void*)xmlstr);
 soap_unlink(soap, (void*)xmlstrn);
 soap_unlink(soap, (void*)xml_Buff);
 soap_unlink(soap, (void*)xml_txtbuff);
 soap_unlink(soap, (void*)sequence);
 
 //soap_unlink(soap, (void*)buff);
 //soap_unlink(soap, (void*)syscall);

 return SOAP_OK;
}       





int ns__msdFastaParser (struct soap *soap, char* sessionid, char* dbserver, int &result){
 char* fastafn = (char*)soap_malloc(soap,256);
 char* session_id;
 char* login_string = (char*)soap_malloc(soap,64);
 char* loginstr;
 char* fasta_parser = (char*)soap_malloc(soap,256);
 char* syscall = (char*)soap_malloc(soap,256);
 session_id=(char*)soap_malloc(soap, strlen(sessionid)+1);
 //sprintf(session_id,"%s",sessionid);
 strcpy(session_id,sessionid);
 sprintf(login_string,"search/search55@%s",dbserver);
 loginstr = (char*)soap_malloc(soap,strlen(login_string)+1);
 strcpy(loginstr, login_string);
 sprintf(fastafn,"/ebi/msd/ssm/cgi-bin/ws/work/%s_out.fasta",session_id);
 sprintf(fasta_parser,"/ebi/msd/ssm/cgi-bin/ws/work/%s_in.fasta",session_id);
 
 char* read_line = (char*)soap_malloc(soap,1024);
 char* stmnt = (char*)soap_malloc(soap,256);
  int j=0;
  //wait(5);
  while(!lsf_file_completed(fastafn) && j<12*15) // fileexists --- up to 15 minutes wait for result
  { wait(5); // wait 5 seconds and retry again
        j++;
  } // end while
  
  
  //~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
    ifstream infile;
        infile.open(fastafn);
        //ofstream outfile;
        //outfile.open(fasta_parser);
        
        char * search = ">>";
        char * replace = "Record No.";
        char * linebuf = (char*)soap_malloc(soap,256);
        char * tempbuf = (char*)soap_malloc(soap,256);
        char * lastTok = (char*)soap_malloc(soap,256);
        char * record = (char*)soap_malloc(soap,7000);
    char * tmprec = (char*)soap_malloc(soap,7000);
    char * evalue_result = (char*)soap_malloc(soap,16);
        char * id_chain = (char*)soap_malloc(soap,16);
        char * id = (char*)soap_malloc(soap,12);
        char * chain = (char*)soap_malloc(soap,4);
        char * alignment = (char*)soap_malloc(soap,6000);
        char*  midbuf = (char*)soap_malloc(soap,12);
        char* tmp = (char*)soap_malloc(soap,16);
        char * outBuf = (char*)soap_malloc(soap,6000);
        // char tokbuf[100]= "";
    char * pchs;
        char * pche;
        //char * pche;
        char * per;
        char * tok;
        char * pid;
        char * pch;
        char * token = (char*)soap_malloc(soap,16);
        int start,end,len,newrecord,recno;
        newrecord=0;
        char* insert_stm = (char*)soap_malloc(soap,4096);
    sprintf(stmnt, "insert into ssm_out_tab values ('%s' ", session_id);   
        char* table_exists_stm = (char*)soap_malloc(soap,3072);
 int n;
 char* create_table_stm="create table fasta_out_tab(session_id varchar2(64), e_value_result varchar2(16), lib_id_and_chain varchar2(16), lib_id varchar2(12), chain  varchar2(4),"
 "alignment blob, querydate varchar2(32) DEFAULT TO_CHAR(SYSDATE, 'MM-DD-YYYY HH24:MI:SS'))";
 sprintf(table_exists_stm, "select count(*) " 
 "from all_objects o where o.object_name like 'FASTA_OUT_TAB' and o.owner = 'SEARCH'");
 msdbConnect db;
 msdbConnect::msdbInit(); // initialize OCI environment
 try{
  db.rlogon(loginstr); // connect to Oracle
 // otl_cursor::direct_exec(db,"drop table ssm_out_tab",
 //   msdbException::disabled // disable OTL exceptions
 //  ); // drop table
 
 otl_long_string alignment_blob(6000); // define long string variable for blob
 db.set_max_long_size(6000); // set maximum long string size for connect object
 msdbStream i(1, table_exists_stm, db);
 i >> n;
 if (n==0)
 {otl_cursor::direct_exec(db,create_table_stm);  // create table
 }
 //otl_cursor::direct_exec(db,insert_stm);
 //} //------------> try
// catch(msdbException& p){ // intercept OTL exceptions
//  cerr<<p.msg<<endl; // print out error message
//  cerr<<p.stm_text<<endl; // print out SQL that caused the error
//  cerr<<p.var_info<<endl; // print out the variable that caused the error
// }
        
 
 msdbStream o(1, // buffer size has to be set to 1 for operations with LOBs
 "insert into fasta_out_tab values(:session_id<char[64]>,:e_value_result<char[16]>,:lib_id_and_chain<char[16]>, "
 ":lib_id<char[12]>,:chain<char[4]>,empty_blob(),TO_CHAR(SYSDATE, 'MM-DD-YYYY HH24:MI:SS')) returning alignment into :alignment<blob> ",
 db );  
 recno=0;
        do {      //newrecord=0;
                      infile.getline(linebuf, 256);
                      if(linebuf != NULL)
                                { strcpy(tempbuf, linebuf);
                                  pchs = strstr (tempbuf, ">>");
                                  pche = strstr (tempbuf, "Library scan:");
                  if ((pchs != NULL) || (newrecord == 1) || (pche != NULL))
                    {   
                                          sprintf(record,"%s%s\n",record, linebuf);
                                          do {
                                                 infile.getline(linebuf, 256);
                                                 if(linebuf != NULL)
                                          {strcpy(tempbuf, linebuf);
                                                   pchs = strstr (tempbuf, ">>");
                                                   pche = strstr (tempbuf, "Library scan:");
                                                   if ((pchs == NULL) && (pche == NULL)){
                                                    sprintf(record,"%s%s\n",record, linebuf);
                                                        }else{
                                                                //recore has been completed and should be processed

                                                                sprintf(tmprec,"%s",record);
                                                    per = strstr (tmprec,":");
                                                tok = strtok (tmprec," ");
                                                sprintf(token,"%s", tok);
                                len=strlen(token);
                                                    start=per-tok+1;
                                                    end=len;
                                                    midcopy(token,midbuf,start,end);
                                                    sprintf(id_chain,"%s",midbuf);
                                                                sprintf(tmp,"%s",id_chain);
                                                                pid = strtok (tmp,"_");
                                                                sprintf(id,"%s",pid);
                                                                start=strlen(id)+1;
                                                                end=strlen(id_chain);
                                                                if (start != end)
                                                                {midcopy(id_chain,chain,start,end);
                                                                }else sprintf(chain,"%s","");
                                                                
                                                                sprintf(tmprec,"%s",record);
                                per = strstr (tmprec,"E():");
                                                                tok = strtok(per,"\n");
                                                                sprintf(token,"%s", tok);
                                                                start=per-tok+5;
                                                    end=strlen(token);
                                                                midcopy(token,midbuf,start,end);
                                                    sprintf(evalue_result,"%s",midbuf);
                                                                sprintf(tmprec,"%s",record);
                                                                per = strstr (tmprec,"Q   ");
                                                                sprintf(alignment,"%s",per-68);

//~~~~~~~~~                                      outfile << session_id <<endl;
//~~~~~~~~~                                      outfile << record <<endl;
//~~~~~~~~~                  outfile << id_chain <<endl;
//~~~~~~~~~                                      outfile << id <<endl;
//~~~~~~~~~                                      outfile << chain <<endl;
//~~~~~~~~~                                      outfile << evalue_result << endl;
//~~~~~~~~~                  outfile << alignment << endl;
//~~~~~~~~~                                      outfile << "Record finished~~~~~~~~" << endl;
                                         
                                         recno++;
                                         len=strlen(alignment);
                                         
                     for (int i=0;i< len ;i++ )
                     {alignment_blob[i] = alignment[i];
                     }
                                         alignment_blob.set_len(len+1); 
                                          o << session_id << evalue_result << id_chain << id << chain << alignment_blob;         
                                                                sprintf(record,"%s","");
                                                                sprintf(record,"%s\n", linebuf);
                                                                newrecord=1; // new record starts
                                                                //pchs=NULL;
                                                                } 
                                                  }
                                                 } while ((pchs == NULL) && !infile.eof() && (pche == NULL));
                                    }
                                  }
                        else linebuf[0] = '0';
                        
                 } while ( ! infile.eof());
 
 
//--- otl_long_string blob_result(4000); // define long string variable
//--- db.set_max_long_size(4000); // set maximum long string size for connect object
//---
//--- msdbStream si(10, // buffer size. To read BLOBs, it can be set to a size greater than 1
//---              "select alignment from fasta_out_tab",
//---                 // SELECT statement
//---              db // connect object
//---             ); 
//--- while(!si.eof()){ // while not end-of-data
//---  si>>blob_result;
//---  outfile <<"blob_result="<<blob_result[0]<<blob_result[blob_result.len()-1]<<", len="<<blob_result.len()<<endl;
//--- } // end while
 
 
 } // try
 catch(msdbException& p){ // intercept OTL exceptions
  cerr<<p.msg<<endl; // print out error message
  cerr<<p.stm_text<<endl; // print out SQL that caused the error
  cerr<<p.var_info<<endl; // print out the variable that caused the error
//~~~~~~~  outfile <<p.msg<<endl; // print out error message
//~~~~~~~  outfile <<p.stm_text<<endl; // print out SQL that caused the error
//~~~~~~~  outfile <<p.var_info<<endl; // print out the variable that caused the error
 }
//~~~~~~~  outfile << "Total Records: " << recno <<endl;
    db.logoff();        
        infile.close();
        //~~~~~~~ outfile.close();
        sprintf(syscall, "rm -f %s %s", fasta_parser,fastafn);
    result = system(syscall); // syscall
   if (result < 0){
          result = errno;
   }else{
          result=0;
   }
        
        
        
//      delete linebuf;
//      delete tempbuf;
//      delete lastTok;
//      delete record;
//      delete tmprec;
//      delete outBuf;
//      delete alignment;
  //outfile << outBuf <<endl;
  
  return SOAP_OK;
}

---