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SASxport.c

/*
 *
 *  Read SAS transport data set format
 *
 *  Copyright 1999-1999 Douglas M. Bates <bates@stat.wisc.edu>,
 *                      Saikat DebRoy <saikat@stat.wisc.edu>
 *
 *  This program 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 2 of the License, or
 *  (at your option) any later version.
 *
 *  This program 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 this program; if not, write to the Free
 *  Software Foundation, Inc., 51 Franklin Street, Fifth Floor,
 *  Boston, MA 02110-1301  USA
 *
 */

#include <stdio.h>
#include <string.h>
#include <R.h>
#include <Rinternals.h>
#include "foreign.h"
#include "SASxport.h"

#define HEADER_BEG "HEADER RECORD*******"
#define HEADER_TYPE_LIBRARY "LIBRARY "
#define HEADER_TYPE_MEMBER "MEMBER  "
#define HEADER_TYPE_DSCRPTR "DSCRPTR "
#define HEADER_TYPE_NAMESTR "NAMESTR "
#define HEADER_TYPE_OBS "OBS     "
#define HEADER_END "HEADER RECORD!!!!!!!000000000000000000000000000000  "

#define LIB_HEADER HEADER_BEG HEADER_TYPE_LIBRARY HEADER_END
#define MEM_HEADER HEADER_BEG HEADER_TYPE_MEMBER \
                   "HEADER RECORD!!!!!!!000000000000000001600000000"
#define DSC_HEADER HEADER_BEG HEADER_TYPE_DSCRPTR HEADER_END
#define NAM_HEADER HEADER_BEG HEADER_TYPE_NAMESTR \
                   "HEADER RECORD!!!!!!!000000"
#define OBS_HEADER HEADER_BEG HEADER_TYPE_OBS HEADER_END
#define BLANK24 "                        "

#define GET_RECORD(rec, fp, len) \
          fread((rec), sizeof(char), (size_t) (len), (fp))

#define IS_SASNA_CHAR(c) ((c) == 0x5f || (c) == 0x2e || \
                          (0x41 <= (c) && (c) <= 0x5a))

#ifndef NULL
#define NULL ((void *) 0)
#endif


#define Two32 4294967296.0

static double get_IBM_double(char* c, size_t len)
{
                        /* Conversion from IBM 360 format to double */
/*
 * IBM format:
 * 6       5                 0
 * 3       1                 0
 *
 * SEEEEEEEMMMM ......... MMMM
 *
 * Sign bit, 7 bit exponent, 56 bit fraction. Exponent is
 * excess 64. The fraction is multiplied by a power of 16 of
 * the actual exponent. Normalized floating point numbers are
 * represented with the radix point immediately to the left of
 * the high order hex fraction digit.
 */
    unsigned int i, upper, lower;
                        /* exponent is expressed here as
                           excess 70 (=64+6) to accomodate
                           integer conversion of c[1] to c[4] */
    char negative = c[0] & 0x80, exponent = (c[0] & 0x7f) - 70, buf[4];
    double value; 
    char ibuf[8];

    if (len < 2 || len > 8) 
      error(_("invalid field length in numeric variable"));

    /* this effectively zero-pads c: */
    memset(ibuf, 0, (size_t) 8);
    memcpy(ibuf, c, len);
    c = ibuf;
    /* check for missing value */
    /* This isn't really right: NAs are ' ',  '.', A-Z plus zero fill */
    if (c[1] == '\0' && c[0] != '\0') return R_NaReal;
    /* convert c[1] to c[3] to an int */
    buf[0] = '\0';
    for (i = 1; i < 4; i++) buf[i] = c[i];
    char_to_uint(buf, upper);
    /* convert c[4] to c[7] to an int */
    for (i = 0; i < 4; i++) buf[i] = c[i + 4];
    char_to_uint(buf, lower);
    /* initialize the constant if needed */
    value = ((double) upper + ((double) lower)/Two32) *
      pow(16., (double) exponent);
    if (negative) value = -value;
    return value;
}

static int
get_nam_header(FILE *fp, struct SAS_XPORT_namestr *namestr, int length)
{
    char record[141];
    int n;

    record[length] = '\0';
    n = GET_RECORD(record, fp, length);
    if(n != length)
      return 0;

    char_to_short(record, namestr->ntype);
    char_to_short(record+2, namestr->nhfun);
    char_to_short(record+4, namestr->nlng);
    char_to_short(record+6, namestr->nvar0);
    memcpy(namestr->nname, record + 8, 8);
    memcpy(namestr->nlabel, record + 16, 40);
    memcpy(namestr->nform, record + 56, 8);
    char_to_short(record+64, namestr->nfl);
    char_to_short(record+66, namestr->nfd);
    char_to_short(record+68, namestr->nfj);
    memcpy(namestr->nfill, record + 70, 2);
    memcpy(namestr->niform, record + 72, 8);
    char_to_short(record+80, namestr->nifl);
    char_to_short(record+82, namestr->nifd);
    char_to_int(record+84, namestr->npos);
    return 1;
}

static int
get_lib_header(FILE *fp, struct SAS_XPORT_header *head)
{
    char record[81];
    int n;

    n = GET_RECORD(record, fp, 80);
    if(n == 80 && strncmp(LIB_HEADER, record, 80) != 0)
      error(_("file not in SAS transfer format"));
  
    n = GET_RECORD(record, fp, 80);
    if(n != 80)
      return 0;
    record[80] = '\0';
    memcpy(head->sas_symbol[0], record, 8);
    memcpy(head->sas_symbol[1], record+8, 8);
    memcpy(head->saslib, record+16, 8);
    memcpy(head->sasver, record+24, 8);
    memcpy(head->sas_os, record+32, 8);
    if((strrchr(record+40, ' ') - record) != 63)
      return 0;
    memcpy(head->sas_create, record+64, 16);

    n = GET_RECORD(record, fp, 80);
    if(n != 80)
      return 0;
    record[80] = '\0';
    memcpy(head->sas_mod, record, 16);
    if((strrchr(record+16, ' ') - record) != 79)
      return 0;
    return 1;
}
  
static int
get_mem_header(FILE *fp, struct SAS_XPORT_member *member)
{
    char record[81];
    int n;

    n = GET_RECORD(record, fp, 80);
    if(n != 80 || strncmp(DSC_HEADER, record, 80) != 0)
      error(_("file not in SAS transfer format"));
  
    n = GET_RECORD(record, fp, 80);
    if(n != 80)
      return 0;
    record[80] = '\0';
    memcpy(member->sas_symbol, record, 8);
    memcpy(member->sas_dsname, record+8, 8);
    memcpy(member->sasdata, record+16, 8);
    memcpy(member->sasver, record+24, 8);
    memcpy(member->sas_osname, record+32, 8);
    if((strrchr(record+40, ' ') - record) != 63)
      return 0;
    memcpy(member->sas_create, record+64, 16);

    n = GET_RECORD(record, fp, 80);
    if(n != 80)
      return 0;
    memcpy(member->sas_mod, record, 16);
    if((strrchr(record+16, ' ') - record) != 79)
      return 0;
    return 1;
}

static int
init_xport_info(FILE *fp)
{
    char record[81];
    int n;
    int namestr_length;

    struct SAS_XPORT_header *lib_head;

    lib_head = Calloc(1, struct SAS_XPORT_header);

    if(!get_lib_header(fp, lib_head)) {
      Free(lib_head);
      error(_("SAS transfer file has incorrect library header"));
    }

    Free(lib_head);

    n = GET_RECORD(record, fp, 80);
    if(n != 80 || strncmp(MEM_HEADER, record, 75) != 0 ||
       strncmp("  ", record+78, 2) != 0)
      error(_("file not in SAS transfer format"));
    record[78] = '\0';
    sscanf(record+75, "%d", &namestr_length);

    return namestr_length;
}

static int
init_mem_info(FILE *fp, char *name)
{
    int length, n;
    char record[81];
    char *tmp;
    struct SAS_XPORT_member  *mem_head;

    mem_head = Calloc(1, struct SAS_XPORT_member);
    if(!get_mem_header(fp, mem_head)) {
      Free(mem_head);
      error(_("SAS transfer file has incorrect member header"));
    }

    n = GET_RECORD(record, fp, 80);
    record[80] = '\0';
    if(n != 80 || strncmp(NAM_HEADER, record, 54) != 0 ||
       (strrchr(record+58, ' ') - record) != 79) {
      Free(mem_head);
      error(_("file not in SAS transfer format"));
    }
    record[58] = '\0';
    sscanf(record+54, "%d", &length);

    tmp = strchr(mem_head->sas_dsname, ' ');
    n = tmp - mem_head->sas_dsname;
    if(n > 0) {
      if (n > 8)
          n = 8;
      strncpy(name, mem_head->sas_dsname, n);
      name[n] = '\0';
    } else name[0] = '\0';

    Free(mem_head);

    return length;
}

static int
next_xport_info(FILE *fp, int namestr_length, int nvars, int *headpad,
            int *tailpad, int *length, int *ntype, int *nlng,
            int *nvar0, SEXP nname, SEXP nlabel, SEXP nform, int *npos)
{
    char *tmp;
    char record[81];
    int i, n, nbytes, totwidth, nlength, restOfCard;
    struct SAS_XPORT_namestr *nam_head;

    nam_head = Calloc(nvars, struct SAS_XPORT_namestr);

    for(i = 0; i < nvars; i++) {
      if(!get_nam_header(fp, nam_head+i, namestr_length)) {
          Free(nam_head);
          error(_("SAS transfer file has incorrect library header"));
      }
    }

    *headpad = 480 + nvars * namestr_length;
    i = *headpad % 80;
    if(i > 0) {
      i = 80 - i;
      if (fseek(fp, i, SEEK_CUR) != 0) {
          Free(nam_head);
          error(_("file not in SAS transfer format"));
      }
      (*headpad) += i;
    }
    
    n = GET_RECORD(record, fp, 80);
    if(n != 80 || strncmp(OBS_HEADER, record, 80) != 0) {
      Free(nam_head);
      error(_("file not in SAS transfer format"));
    }
  
    for(i = 0; i < nvars; i++) {
      int nname_len = 0, nlabel_len = 0, nform_len = 0;
      char tmpname[41];

      ntype[i] = (int) ((nam_head[i].ntype == 1) ? REALSXP : STRSXP);
      nlng[i]  = nam_head[i].nlng;
      nvar0[i] = nam_head[i].nvar0;
      npos[i]  = nam_head[i].npos;

      /* Variable name */
      nname_len = 8;
      while (nname_len && nam_head[i].nname[nname_len-1] == ' ')
          nname_len--;
      strncpy(tmpname, nam_head[i].nname, nname_len);
      tmpname[nname_len] = '\0';
      SET_STRING_ELT(nname, i, mkChar(tmpname));

      /* Variable label */
      nlabel_len = 40;
      while (nlabel_len && nam_head[i].nlabel[nlabel_len-1] == ' ')
          nlabel_len--;
      strncpy(tmpname, nam_head[i].nlabel, nlabel_len);
      tmpname[nlabel_len] = '\0';
      SET_STRING_ELT(nlabel, i, mkChar(tmpname));

      /* Variable format name */
      nform_len = 8;
      while (nform_len && nam_head[i].nform[nform_len-1] == ' ')
          nform_len--;
      strncpy(tmpname, nam_head[i].nform, nform_len);
      tmpname[nform_len] = '\0';
      SET_STRING_ELT(nform, i, mkChar(tmpname));
    }

    Free(nam_head);

    totwidth = 0;
    for(i = 0; i < nvars; i++)
      totwidth += nlng[i];

    nbytes = 0;
    nlength = 0;
/*      tmp = (char *) R_alloc(totwidth+1, sizeof(char)); */
    tmp = CHAR(PROTECT(allocVector(CHARSXP, (totwidth<=80?81:(totwidth+1)) * 
                           sizeof(char))));
    restOfCard = 0;
    *tailpad = 0;
    while(!feof(fp)) {
      int allSpace = 1;
      fpos_t currentPos;

/*    restOfCard = 80 - (ftell(fp) % 80); */
      if (fgetpos(fp, &currentPos)) {
          error(_("problem accessing SAS XPORT file"));
      }

      n = GET_RECORD(tmp, fp, restOfCard);
      if (n != restOfCard) {
          allSpace = 0;
      } else {
          for (i = 0; i < restOfCard; i++) {
            if (tmp[i] != ' ') {
                allSpace = 0;
                break;
            }
          }
      }
      if (allSpace) {
          n = GET_RECORD(record, fp, 80);
          if (n < 1) {
            *tailpad = restOfCard;
            break;
          }
          if(n == 80 && strncmp(MEM_HEADER, record, 75) == 0 &&
             strncmp("  ", record+78, 2) == 0) {
            *tailpad = restOfCard;
            record[78] = '\0';
            sscanf(record+75, "%d", &namestr_length);
            break;
          }
      }
      if (fsetpos(fp, &currentPos)) {
          error(_("problem accessing SAS XPORT file"));
      }

      n = GET_RECORD(tmp, fp, totwidth);
      if (n != totwidth) {
          if (!feof(fp)) {
            error(_("problem accessing SAS XPORT file"));
          }
          *tailpad = n;
          break;
      }
      restOfCard = (restOfCard >= totwidth)?
          (restOfCard - totwidth):
          (80 - (totwidth - restOfCard)%80);
      nlength++;
    }
    *length = nlength;
    UNPROTECT(1);

    return (feof(fp)?-1:namestr_length);
}

/*
 * get the list element named str.
 */

static SEXP
getListElement(SEXP list, char *str) {
    SEXP names;
    SEXP elmt = (SEXP) NULL;
    char *tempChar;
    int i;

    names = getAttrib(list, R_NamesSymbol);

    for (i = 0; i < LENGTH(list); i++) {
      tempChar = CHAR(STRING_ELT(names, i));
      if( strcmp(tempChar,str) == 0) {
          elmt = VECTOR_ELT(list, i);
          break;
      }
    }
    return elmt;
}

#define VAR_INFO_LENGTH 11

const char *cVarInfoNames[] = {
    "headpad",
    "type",
    "width",
    "index",
    "position",
    "name",
    "label",
    "format",
    "sexptype",
    "tailpad",
    "length"
};

#define XPORT_VAR_HEADPAD(varinfo)   VECTOR_ELT(varinfo, 0)
#define XPORT_VAR_TYPE(varinfo)      VECTOR_ELT(varinfo, 1)
#define XPORT_VAR_WIDTH(varinfo)     VECTOR_ELT(varinfo, 2)
#define XPORT_VAR_INDEX(varinfo)     VECTOR_ELT(varinfo, 3)
#define XPORT_VAR_POSITION(varinfo)  VECTOR_ELT(varinfo, 4)
#define XPORT_VAR_NAME(varinfo)      VECTOR_ELT(varinfo, 5)
#define XPORT_VAR_LABEL(varinfo)     VECTOR_ELT(varinfo, 6)
#define XPORT_VAR_FORM(varinfo)      VECTOR_ELT(varinfo, 7)
#define XPORT_VAR_SEXPTYPE(varinfo)  VECTOR_ELT(varinfo, 8)
#define XPORT_VAR_TAILPAD(varinfo)   VECTOR_ELT(varinfo, 9)
#define XPORT_VAR_LENGTH(varinfo)    VECTOR_ELT(varinfo, 10)

#define SET_XPORT_VAR_HEADPAD(varinfo, val)   SET_VECTOR_ELT(varinfo, 0, val)
#define SET_XPORT_VAR_TYPE(varinfo, val)      SET_VECTOR_ELT(varinfo, 1, val)
#define SET_XPORT_VAR_WIDTH(varinfo, val)     SET_VECTOR_ELT(varinfo, 2, val)
#define SET_XPORT_VAR_INDEX(varinfo, val)     SET_VECTOR_ELT(varinfo, 3, val)
#define SET_XPORT_VAR_POSITION(varinfo, val)  SET_VECTOR_ELT(varinfo, 4, val)
#define SET_XPORT_VAR_NAME(varinfo, val)      SET_VECTOR_ELT(varinfo, 5, val)
#define SET_XPORT_VAR_LABEL(varinfo, val)     SET_VECTOR_ELT(varinfo, 6, val)
#define SET_XPORT_VAR_FORM(varinfo, val)      SET_VECTOR_ELT(varinfo, 7, val)
#define SET_XPORT_VAR_SEXPTYPE(varinfo, val)  SET_VECTOR_ELT(varinfo, 8, val)
#define SET_XPORT_VAR_TAILPAD(varinfo, val)   SET_VECTOR_ELT(varinfo, 9, val)
#define SET_XPORT_VAR_LENGTH(varinfo, val)    SET_VECTOR_ELT(varinfo, 10, val)

SEXP
xport_info(SEXP xportFile)
{
    FILE *fp;
    int i, namestrLength, memLength, ansLength;
    char dsname[9];
    SEXP ans, ansNames, varInfoNames, varInfo;
    SEXP char_numeric, char_character;

    PROTECT(varInfoNames = allocVector(STRSXP, VAR_INFO_LENGTH));
    for(i = 0; i < VAR_INFO_LENGTH; i++)
      SET_STRING_ELT(varInfoNames, i, mkChar(cVarInfoNames[i]));

    PROTECT(char_numeric   = mkChar("numeric"));
    PROTECT(char_character = mkChar("character"));

    if(!isValidString(xportFile))
      error(_("first argument must be a file name"));
    fp = fopen(R_ExpandFileName(CHAR(STRING_ELT(xportFile, 0))), "rb");
    if (!fp)
      error(_("unable to open file"));
    namestrLength = init_xport_info(fp);

    ansLength = 0;
    PROTECT(ans = allocVector(VECSXP, 0));
    PROTECT(ansNames = allocVector(STRSXP, 0));

    while(namestrLength > 0 && (memLength = init_mem_info(fp, dsname)) > 0) {

      PROTECT(varInfo = allocVector(VECSXP, VAR_INFO_LENGTH));
      setAttrib(varInfo, R_NamesSymbol, varInfoNames);

      SET_XPORT_VAR_TYPE(varInfo, allocVector(STRSXP, memLength));
      SET_XPORT_VAR_WIDTH(varInfo, allocVector(INTSXP, memLength));
      SET_XPORT_VAR_INDEX(varInfo, allocVector(INTSXP, memLength));
      SET_XPORT_VAR_POSITION(varInfo, allocVector(INTSXP, memLength));
      SET_XPORT_VAR_NAME(varInfo, allocVector(STRSXP, memLength));
      SET_XPORT_VAR_LABEL(varInfo, allocVector(STRSXP, memLength));
      SET_XPORT_VAR_FORM(varInfo, allocVector(STRSXP, memLength));
      SET_XPORT_VAR_SEXPTYPE(varInfo, allocVector(INTSXP, memLength));
      SET_XPORT_VAR_HEADPAD(varInfo, allocVector(INTSXP, 1));
      SET_XPORT_VAR_TAILPAD(varInfo, allocVector(INTSXP, 1));
      SET_XPORT_VAR_LENGTH(varInfo, allocVector(INTSXP, 1));

      namestrLength =
          next_xport_info(fp, namestrLength, memLength,
                      INTEGER(XPORT_VAR_HEADPAD(varInfo)),
                      INTEGER(XPORT_VAR_TAILPAD(varInfo)),
                      INTEGER(XPORT_VAR_LENGTH(varInfo)),
                      INTEGER(XPORT_VAR_SEXPTYPE(varInfo)),
                      INTEGER(XPORT_VAR_WIDTH(varInfo)),
                      INTEGER(XPORT_VAR_INDEX(varInfo)),
                      XPORT_VAR_NAME(varInfo),
                      XPORT_VAR_LABEL(varInfo),
                      XPORT_VAR_FORM(varInfo),
                      INTEGER(XPORT_VAR_POSITION(varInfo)));

      for(i = 0; i < memLength; i++) {
          int *ntype = INTEGER(XPORT_VAR_SEXPTYPE(varInfo));
          SET_STRING_ELT(XPORT_VAR_TYPE(varInfo), i,
                     (ntype[i] == REALSXP) ? char_numeric :
                     char_character);
      }
      PROTECT(ans = lengthgets(ans, ansLength+1));
      PROTECT(ansNames = lengthgets(ansNames, ansLength+1));
/*    PROTECT(newAns = allocVector(VECSXP, ansLength+1)); */
/*    PROTECT(newAnsNames = allocVector(STRSXP, ansLength+1)); */

/*    for(i = 0; i < ansLength; i++) { */
/*        SET_VECTOR_ELT(newAns, i, VECTOR_ELT(ans, i)); */
/*        SET_STRING_ELT(newAnsNames, i, STRING_ELT(ansNames, i)); */
/*    } */
/*    ans = newAns; */
/*    ansNames = newAnsNames; */

      SET_STRING_ELT(ansNames, ansLength, mkChar(dsname));
      SET_VECTOR_ELT(ans, ansLength, varInfo);
      ansLength++;
 
      UNPROTECT(5);
      PROTECT(ans);
      PROTECT(ansNames);
    }

    setAttrib(ans, R_NamesSymbol, ansNames);  
    UNPROTECT(5);
    fclose(fp);
    return ans;
}

SEXP
xport_read(SEXP xportFile, SEXP xportInfo)
{
    int i, j, k, n;
    int nvar;
    int ansLength, dataLength, totalWidth;
    int dataHeadPad, dataTailPad;
    int *dataWidth;
    int *dataPosition;
    SEXPTYPE *dataType;
    char *record, *tmpchar, *c;
    FILE *fp;
    SEXP ans, names, data, dataInfo, dataName;

    ansLength = LENGTH(xportInfo);
    PROTECT(ans = allocVector(VECSXP, ansLength));
    names = getAttrib(xportInfo, R_NamesSymbol);
    setAttrib(ans, R_NamesSymbol, names);

    if(!isValidString(xportFile))
      error(_("first argument must be a file name"));
    fp = fopen(R_ExpandFileName(CHAR(STRING_ELT(xportFile, 0))), "rb");
    if (!fp)
      error(_("unable to open file"));
    if (fseek(fp, 240, SEEK_SET) != 0)
      error(_("problem reading SAS XPORT file '%s'"),
            CHAR(STRING_ELT(xportFile, 0)));

    for(i = 0; i < ansLength; i++) {
      dataInfo = VECTOR_ELT(xportInfo, i);
      dataName = getListElement(dataInfo, "name");
      nvar = LENGTH(dataName);
      dataLength = asInteger(getListElement(dataInfo, "length"));
      SET_VECTOR_ELT(ans, i, data = allocVector(VECSXP, nvar));
      setAttrib(data, R_NamesSymbol, dataName);
      dataType = (SEXPTYPE *) INTEGER(getListElement(dataInfo, "sexptype"));
      for(j = 0; j < nvar; j++)
          SET_VECTOR_ELT(data, j, allocVector(dataType[j], dataLength));

      dataWidth = INTEGER(getListElement(dataInfo, "width"));
      dataPosition = INTEGER(getListElement(dataInfo, "position"));

      totalWidth = 0;
      for(j = 0; j < nvar; j++)
          totalWidth += dataWidth[j];
/*    record = (char *) R_alloc(totalWidth + 1, sizeof (char)); */
      record = CHAR(PROTECT(allocVector(CHARSXP,
                                (totalWidth+1) * sizeof(char))));

      dataHeadPad = asInteger(getListElement(dataInfo, "headpad"));
      dataTailPad = asInteger(getListElement(dataInfo, "tailpad"));
      fseek(fp, dataHeadPad, SEEK_CUR);

      for(j = 0; j < dataLength; j++) {
          n = GET_RECORD(record, fp, totalWidth);
          if(n != totalWidth) {
            error(_("problem reading SAS transport file"));
          }

          for(k = nvar-1; k >= 0; k--) {
            tmpchar = record + dataPosition[k];
            if(dataType[k] == REALSXP) {
                REAL(VECTOR_ELT(data, k))[j] = 
                  get_IBM_double(tmpchar, dataWidth[k]);
            } else {
                tmpchar[dataWidth[k]] = '\0';
                /* strip trailing blanks */
                c = tmpchar + dataWidth[k];
                while (c-- > tmpchar && *c == ' ')
                  *c ='\0';

                SET_STRING_ELT(VECTOR_ELT(data, k), j,
                           (c < tmpchar) ? R_BlankString :
                           mkChar(tmpchar));
            }
          }
      }

      fseek(fp, dataTailPad, SEEK_CUR);
      
      UNPROTECT(1);
    }
    UNPROTECT(1);
    fclose(fp);
    return ans;
}

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