/* modi.c

   Copyright (c) 1993-2008. Free Software Foundation, Inc.

   This file is part of GNU MCSim.

   GNU MCSim  is free software; you can redistribute it and/or
   modify it under the terms of the GNU General Public License
   as published by the Free Software Foundation; either version 3
   of the License, or (at your option) any later version.

   GNU MCSim is distributed in the hope that it will be useful,
   but WITHOUT ANY WARRANTY; without even the implied warranty of
   MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
   GNU General Public License for more details.

   You should have received a copy of the GNU General Public License
   along with GNU MCSim; if not, see <http://www.gnu.org/licenses/>

   -- Revisions -----
     Logfile:  %F%
    Revision:  %I%
        Date:  %G%
     Modtime:  %U%
      Author:  @a
   -- SCCS  ---------

   Handles parsing input of the Model Definition File.
*/


#include <stdio.h>
#include <stdlib.h>
#include <string.h>
#include <ctype.h>
#include <assert.h>

#include "lexerr.h"
#include "mod.h"
#include "modd.h"
#include "modi.h"
#include "modiSBML.h"
  
/* Global Keyword Map Structure */

KM vrgkmKeywordMap[] = {
  {"States",       KM_STATES,       CN_GLOBAL},
  {"Inputs",       KM_INPUTS,       CN_GLOBAL},
  {"Outputs",      KM_OUTPUTS,      CN_GLOBAL},
  {"Compartments", KM_COMPARTMENTS, CN_GLOBAL},

  {"Dynamics",     KM_DYNAMICS,     CN_GLOBAL},
  {"Initialize",   KM_SCALE,        CN_GLOBAL},
  {"Scale",        KM_SCALE,        CN_GLOBAL}, /* obsolete */
  {"Jacobian",     KM_JACOB,        CN_GLOBAL},
  {"Jacob",        KM_JACOB,        CN_GLOBAL}, /* obsolete */
  {"CalcOutputs",  KM_CALCOUTPUTS,  CN_CALCOUTPUTS},

  /* Can be LHS only in Dynamics */
  {"dt", KM_DXDT,  CN_DYNAMICS | CN_INPUTDEF},

  {"Inline", KM_INLINE, CN_ALL},

  {"SBMLModels",  KM_SBMLMODELS,  CN_GLOBAL | CN_TEMPLATE_DEFINED},
  {"PKTemplate",  KM_PKTEMPLATE,  CN_GLOBAL},
  
  {"End", KM_END,  CN_GLOBAL | CN_TEMPLATE_DEFINED}, /* Optional End statmt */

  /* Variables names valid in all CN_ */
  {"", 0, CN_ALL} /* This marks the end of map too */
  
}; /* vrgkmKeywordMap[] */


/* ----------------------------------------------------------------------------
   GetKeyword
   
   Returns a pointer to the keyword string given the code.  If the
   code is not valid, returns empty string.
*/

PSTR GetKeyword (int iCode)
{
  PKM pkm = &vrgkmKeywordMap[0];
  
  while (*pkm->szKeyword && pkm->iKWCode != iCode)
    pkm++;
  
  return (pkm->szKeyword); /* Return Keyword Code or null str */

} /* GetKeyword */


/* ----------------------------------------------------------------------------
   GetKeywordCode
   
   Returns the code of the szKeyword given.  If the string is not
   a valid keyword or abbreviation, returns 0.
*/

int GetKeywordCode (PSTR szKeyword, PINT pfContext)
{
  PKM pkm = &vrgkmKeywordMap[0];
  
  while (*pkm->szKeyword && strcmp (szKeyword, pkm->szKeyword))
    pkm++;
  
  if (pfContext)
    *pfContext = pkm->fContext; /* Set iContext flag */

  return (pkm->iKWCode); /* Return Keyword Code or 0 */

} /* GetKeywordCode */


/* ----------------------------------------------------------------------------
   GetVarList
   
   Processes a list of variables (or arrays).
*/

void GetVarList (PINPUTBUF pibIn, PSTR szLex, int iKWCode)
{
  int iLexType, iErr = 0;
  long i, iLB, iUB;
  PSTRLEX szPunct, szTmp;
         
  do { /* Read model var-list */
    NextLex (pibIn, szLex, &iLexType);

    if (iLexType & LX_IDENTIFIER) { /* identifier found */
      if (GetPunct (pibIn, szPunct, '[')) { /* array */
        GetArrayBounds (pibIn, &iLB, &iUB);
        for (i = iLB; i < iUB; i++) {
          sprintf (szTmp, "%s_%ld", szLex, i); /* create names */
          DeclareModelVar (pibIn, szTmp, iKWCode);
        }
      }
      else { /* simple var */
        DeclareModelVar (pibIn, szLex, iKWCode);
      }
    }
    else { /* not an identifier, should be ',' or '}' */
      if ((szLex[0] != ',') && (szLex[0] != CH_RBRACE))
        iErr = szPunct[1] = CH_RBRACE;
    }              
  } while ((szLex[0] != CH_RBRACE) && (!iErr));

} /* GetVarList */


/* ----------------------------------------------------------------------------
   ProcessDTStatement

   process a differential equation definition
*/

void ProcessDTStatement (PINPUTBUF pibIn, PSTR szLex, PSTR szEqn, int iKWCode)
{
  PSTRLEX szPunct, szTmp;
  PSTREQN szEqnU;
  PINPUTINFO pinfo;
  int iArgType = LX_IDENTIFIER;
  long i, iLB, iUB;

  pinfo = (PINPUTINFO) pibIn->pInfo;

  if (!GetFuncArgs (pibIn, 1, &iArgType, szLex, &iLB, &iUB))
    ReportError (pibIn, RE_BADSTATE | RE_FATAL, szLex, NULL);

  if (!GetPunct (pibIn, szPunct, '=')) { /* no assignment */
    ReportError (pibIn, RE_LEXEXPECTED, "=", NULL);
  }

  if (iUB == -1) { /* scalar */
    /* check this is a declared state */
    if (GetVarType (pinfo->pvmGloVars, szLex) != ID_STATE)
      ReportError (pibIn, RE_BADSTATE | RE_FATAL, szLex, NULL);

    /* read assignment */
    GetStatement (pibIn, szEqn);
    UnrollEquation (pibIn, 0, szEqn, szEqnU);
    DefineVariable (pibIn, szLex, szEqnU, iKWCode);
  }
  else { /* array */
    /* read assignment */
    GetStatement (pibIn, szEqn);
    for (i = iLB; i < iUB; i++) {
      sprintf (szTmp, "%s_%ld", szLex, i); /* create names */
      /* check this is a declared state */
      if (GetVarType (pinfo->pvmGloVars, szTmp) != ID_STATE) {
        sprintf (szTmp, "%s[%ld]", szLex, i); /* recreate name */
        ReportError (pibIn, RE_BADSTATE | RE_FATAL, szTmp, NULL);
      }
      UnrollEquation (pibIn, i, szEqn, szEqnU);
      DefineVariable (pibIn, szTmp, szEqnU, iKWCode);
    }
  }

  if (!GetPunct (pibIn, szLex, CH_STMTTERM))
    ReportError (pibIn, RE_EXPECTED | RE_FATAL, ";", NULL);

} /* ProcessDTStatement */


/* ----------------------------------------------------------------------------
   ProcessIdentifier
*/

void ProcessIdentifier (PINPUTBUF pibIn, PSTR szLex, PSTR szEqn, int iKWCode)
{
  PSTRLEX szPunct, szTmp;
  PSTREQN szEqnU;
  PINPUTINFO pinfo;
  long i, iLB, iUB;

  pinfo = (PINPUTINFO) pibIn->pInfo;

  /* check that szLex is less than MAX_NAME characters */
  if ((i = strlen (szLex)) > MAX_NAME)
     ReportError (pibIn, RE_NAMETOOLONG | RE_FATAL, szLex, NULL);    

  if (!GetPunct (pibIn, szPunct, '[')) { /* scalar */
    if (szPunct[0] == '=') { /* read assignment */
      GetStatement (pibIn, szEqn);
      UnrollEquation (pibIn, 0, szEqn, szEqnU);
      DefineVariable (pibIn, szLex, szEqnU, iKWCode);
      if (!GetPunct (pibIn, szLex, CH_STMTTERM))
        ReportError (pibIn, RE_EXPECTED | RE_FATAL, ";", NULL);
    }
    else if (szPunct[0] == CH_STMTTERM) { /* found a terminator */
      if (pinfo->wContext == CN_GLOBAL) {
        /* in the global section: assign 0; FB 13/6/99 */
        DefineVariable (pibIn, szLex, "0\0", iKWCode);
      }
      else
        ReportError (pibIn, RE_LEXEXPECTED | RE_FATAL, "= or [", NULL);
    }
    else /* nothing recognized: error */
      ReportError (pibIn, RE_LEXEXPECTED | RE_FATAL, "=, [ or ;", NULL);
  } /* end scalar */

  else { /* array */
    GetArrayBounds (pibIn, &iLB, &iUB);
    if (GetPunct (pibIn, szPunct, '=')) { /* read assignment */
      GetStatement (pibIn, szEqn);
      for (i = iLB; i < iUB; i++) {
        sprintf (szTmp, "%s_%ld", szLex, i); /* create names */
        UnrollEquation (pibIn, i, szEqn, szEqnU);
        DefineVariable (pibIn, szTmp, szEqnU, iKWCode);
      }
      if (!GetPunct (pibIn, szLex, CH_STMTTERM))
        ReportError (pibIn, RE_EXPECTED | RE_FATAL, ";", NULL);
    }
    else if (szPunct[0] == CH_STMTTERM) { /* found a terminator */
      if (pinfo->wContext == CN_GLOBAL) { /* in global section assign 0 */
        for (i = iLB; i < iUB; i++) {
          sprintf (szTmp, "%s_%ld", szLex, i); /* create names */
          DefineVariable (pibIn, szTmp, "0\0", iKWCode);
        }
      }
      else
        ReportError (pibIn, RE_LEXEXPECTED | RE_FATAL, "= or [", NULL);
    }
    else /* nothing recognized: error */
      ReportError (pibIn, RE_LEXEXPECTED | RE_FATAL, "= or ;", NULL);
  } /* end array */

} /* ProcessIdentifier */


/* ----------------------------------------------------------------------------
   ProcessInlineStatement
*/

void ProcessInlineStatement (PINPUTBUF pibIn, PSTR szLex, PSTR szEqn, 
                             int iKWCode)
{
  PINPUTINFO pinfo;

  pinfo = (PINPUTINFO) pibIn->pInfo;

  GetStatement (pibIn, szEqn);
  /* remove leading parenthesis */
  szEqn = szEqn + 1;
  /* remove ending parenthesis */
  szEqn[strlen(szEqn) - 1] = '\0';
  DefineVariable (pibIn, szLex, szEqn, iKWCode);

  if (!GetPunct (pibIn, szLex, CH_STMTTERM))
    ReportError (pibIn, RE_EXPECTED | RE_FATAL, ";", NULL);

} /* ProcessInlineStatement */


/* ----------------------------------------------------------------------------
   ProcessWord
   
   Processes the word szLex.
*/

void ProcessWord (PINPUTBUF pibIn, PSTR szLex, PSTR szEqn)
{
  int iErr = 0;
  int iKWCode, fContext;
  PSTRLEX szPunct;
  PINPUTINFO pinfo;
  
  if (!pibIn || !szLex || !szLex[0] || !szEqn)
    return;

  pinfo = (PINPUTINFO) pibIn->pInfo;

  iKWCode = GetKeywordCode (szLex, &fContext);

  assert (pinfo->wContext != CN_END);

  if ((pinfo->wContext == CN_END) ||   /* Beyond valid input ! */
      (iKWCode &&                      /* Is a keyword */
       !(fContext & pinfo->wContext))) /* In a valid context */
    ReportError (pibIn, RE_BADCONTEXT | RE_FATAL, szLex, NULL);

  else {
    switch (iKWCode) {
      case KM_END:
        pinfo->wContext = CN_END;
        break;
      
      case KM_STATES:
      case KM_INPUTS:
      case KM_OUTPUTS:
      case KM_COMPARTMENTS:
        if (GetPunct (pibIn, szPunct, '=')) {
          if (GetPunct (pibIn, szPunct, CH_LBRACE))
            GetVarList(pibIn, szLex, iKWCode);
          else
            ReportError (pibIn, RE_EXPECTED | RE_FATAL, "{", NULL);
        }
        else
          ReportError (pibIn, RE_EXPECTED | RE_FATAL, "=", NULL);
        break;
      
      case KM_CALCOUTPUTS:
      case KM_JACOB:
      case KM_SCALE:
      case KM_DYNAMICS:
        if (!GetPunct (pibIn, szPunct, CH_LBRACE)) {
          szPunct[1] = CH_LBRACE;
          ReportError (pibIn, RE_EXPECTED | RE_FATAL, szPunct,
                       "* Section must be delimited by curly braces.");
        }
        else
          pinfo->wContext = KM_TO_CN(iKWCode);
        break;
      
      case KM_DXDT: /* State equation definition */    
        ProcessDTStatement (pibIn, szLex, szEqn, iKWCode);
        break;

      case KM_INLINE: /* Inline statement definition */    
        ProcessInlineStatement (pibIn, szLex, szEqn, iKWCode);
        break;

      case KM_SBMLMODELS:
        if (GetPunct (pibIn, szPunct, '=')) {
          if (GetPunct (pibIn, szPunct, CH_LBRACE)) {
            ReadSBMLModels (pibIn);
          }
          else
            ReportError (pibIn, RE_EXPECTED | RE_FATAL, "{", NULL);
        }
        else
          ReportError (pibIn, RE_EXPECTED | RE_FATAL, "=", NULL);
        break;

      case KM_PKTEMPLATE:
        if (GetPunct (pibIn, szPunct, '=')) {
          if (GetPunct (pibIn, szPunct, CH_LBRACE)) {
            printf ("\nreading pharmacokinetic template "); 
            ReadPKTemplate (pibIn);
          }
          else
            ReportError (pibIn, RE_EXPECTED | RE_FATAL, "{", NULL);
        }
        else
          ReportError (pibIn, RE_EXPECTED | RE_FATAL, "=", NULL);
        break;

      default: /* Not a keyword, process identifier */
        ProcessIdentifier (pibIn, szLex, szEqn, iKWCode);
        break;

    } /* switch */

    if (iErr)
      EatStatement (pibIn); /* Err in statement, eat to terminator */

  } /* else */

} /* ProcessWord */


/* ----------------------------------------------------------------------------
   ReadModel
   
   Read the model definition in the given szFullPathname according to
   the syntax described above and in the documentation.
*/

void ReadModel (PINPUTINFO pinfo, PINPUTINFO ptempinfo, PSTR szFileIn)
{
  INPUTBUF ibIn;
  PSTRLEX szLex; /* Lex elem of MAX_LEX length */
  PSTREQN szEqn; /* Equation buffer of MAX_EQN length */
  int iLexType;

  if (!InitBuffer (&ibIn, BUFFER_SIZE, szFileIn))
    ReportError (&ibIn, RE_INIT | RE_FATAL, "ReadModel", NULL);

  /* Attach info records to input buffer */
  ibIn.pInfo = (PVOID) pinfo;
  ibIn.pTempInfo = (PVOID) ptempinfo;

  do { /* State machine for parsing syntax */
    NextLex (&ibIn, szLex, &iLexType);
    switch (iLexType) {
      case LX_NULL:
        pinfo->wContext = CN_END;
        break;

      case LX_IDENTIFIER:
        ProcessWord (&ibIn, szLex, szEqn);
        break;
 
      case LX_PUNCT: case LX_EQNPUNCT:
        if (szLex[0] == CH_STMTTERM) {
          break;
        }
        else {
          if (szLex[0] == CH_RBRACE && 
             (pinfo->wContext & (CN_DYNAMICS | CN_JACOB | CN_SCALE))) {
            pinfo->wContext = CN_GLOBAL;
            break;
          }
          else {
            if (szLex[0] == CH_COMMENT) {
              SkipComment (&ibIn);
              break;
            }
            /* else: fall through! */
          }
        }

      default:
        ReportError (&ibIn, RE_UNEXPECTED, szLex, "* Ignoring");
        break;
 
      case LX_INTEGER:
      case LX_FLOAT:
        ReportError (&ibIn, RE_UNEXPNUMBER, szLex, "* Ignoring");
        break; 
 
    } /* switch */

  } while (pinfo->wContext != CN_END && 
           (*ibIn.pbufCur || FillBuffer (&ibIn, BUFFER_SIZE) != EOF));

  pinfo->wContext = CN_END; 
  fclose (ibIn.pfileIn);

} /* ReadModel */
