The R Project SVN R-packages

#include "sqlite_dataframe.h"

#include <math.h>

#include "Rmath.h"

SEXP sdf_get_variable(SEXP sdf, SEXP name) {

    if (!IS_CHARACTER(name)) {

        Rprintf("ERROR: argument is not a string.\n");

        return R_NilValue;

    }

    char *iname = SDF_INAME(sdf);

    char *varname = CHAR_ELT(name, 0);

    if (!USE_SDF(iname, TRUE)) return R_NilValue;

    /* check if sdf & varname w/in that sdf exists */

    sqlite3_stmt *stmt;

    sprintf(g_sql_buf[0], "select [%s] from [%s].sdf_data", varname, iname);

    int res = sqlite3_prepare(g_workspace, g_sql_buf[0], -1, &stmt, 0);

    if (_sqlite_error(res)) return R_NilValue;

    const char *coltype = sqlite3_column_decltype(stmt, 0);

    sqlite3_finalize(stmt);

    SEXP ret, value, class = R_NilValue; int nprotected = 0;

    PROTECT(ret = NEW_LIST(2)); nprotected++;

    /* set list names */

    PROTECT(value = NEW_CHARACTER(2)); nprotected++;

    SET_STRING_ELT(value, 0, mkChar("iname"));

    SET_STRING_ELT(value, 1, mkChar("varname"));

    SET_NAMES(ret, value);

    /* set list values */

    SET_VECTOR_ELT(ret, 0, mkString(iname));

    SET_VECTOR_ELT(ret, 1, mkString(varname));

    /* set class */

    int type = -1;

    if (strcmp(coltype, "text") == 0) class = mkChar("character");

    else if (strcmp(coltype, "double") == 0) class = mkChar("numeric");

    else if (strcmp(coltype, "bit") == 0) class = mkChar("logical");

    else if (strcmp(coltype, "integer") == 0 || strcmp(coltype, "int") == 0) {

        /* determine if int, factor or ordered */

        type = _get_factor_levels1(iname, varname, ret);

        switch(type) {

            case VAR_INTEGER: class = mkChar("integer"); break;

            case VAR_FACTOR: class = mkChar("factor"); break;

            case VAR_ORDERED: class = mkChar("ordered");

        }

    }

    if (type != VAR_ORDERED) {

        PROTECT(value = NEW_CHARACTER(2)); nprotected++;

        SET_STRING_ELT(value, 0, mkChar("sqlite.vector"));

        SET_STRING_ELT(value, 1, class);

    } else {

        PROTECT(value = NEW_CHARACTER(3)); nprotected++;

        SET_STRING_ELT(value, 0, mkChar("sqlite.vector"));

        SET_STRING_ELT(value, 1, class);

        SET_STRING_ELT(value, 2, mkChar("factor"));

    }

    SET_CLASS(ret, value);

    UNPROTECT(nprotected);

    return ret;

}

int _get_vector_index_typed_result(sqlite3_stmt *stmt, SEXP *ret, int idx_or_len) {

    int added = 1;

    if (*ret == NULL || *ret == R_NilValue) {

        const char *coltype = sqlite3_column_decltype(stmt, 0);

        if (sqlite3_column_type(stmt, 0) == SQLITE_NULL) {

            added = 0;

        }

        if (strcmp(coltype, "text") == 0) {

            PROTECT(*ret = NEW_CHARACTER(idx_or_len));

            if (added) 

                SET_STRING_ELT(*ret, 0, mkChar((char *)sqlite3_column_text(stmt, 0)));

        } else if (strcmp(coltype, "double") == 0) {

            PROTECT(*ret = NEW_NUMERIC(idx_or_len));

            if (added) REAL(*ret)[0] = sqlite3_column_double(stmt, 0);

        } else if (strcmp(coltype, "bit") == 0) {

            PROTECT(*ret = NEW_LOGICAL(idx_or_len));

            if (added) INTEGER(*ret)[0] = sqlite3_column_int(stmt, 0);

        } else if (strcmp(coltype, "integer") == 0 || 

                   strcmp(coltype, "int") == 0) {

            /* caller should just copy off the vars level attr for factors */

            PROTECT(*ret = NEW_INTEGER(idx_or_len));

            if (added) INTEGER(*ret)[0] = sqlite3_column_int(stmt, 0);

        } else added = 0;

        UNPROTECT(1);

    } else {

        const char *coltype = sqlite3_column_decltype(stmt, 0);

        if (sqlite3_column_type(stmt, 0) == SQLITE_NULL) {

            added = 0;

        } else if (strcmp(coltype, "text") == 0) {

            SET_STRING_ELT(*ret, idx_or_len, 

                    mkChar((char *)sqlite3_column_text(stmt, 0)));

        } else if (strcmp(coltype, "double") == 0) {

            REAL(*ret)[idx_or_len] = sqlite3_column_double(stmt, 0);

        } else if (strcmp(coltype, "bit") == 0) {

            INTEGER(*ret)[idx_or_len] = sqlite3_column_int(stmt, 0);

        } else if (strcmp(coltype, "integer") == 0 ||

                   strcmp(coltype, "int") == 0) {

            /* caller should just copy off the vars level attr for factors */

            INTEGER(*ret)[idx_or_len] = sqlite3_column_int(stmt, 0);

        } else added = 0;

    }

    return added;

}

SEXP sdf_get_variable_length(SEXP svec) {

    char *iname = SDF_INAME(svec);

    if (!USE_SDF(iname, TRUE)) return R_NilValue;

    sprintf(g_sql_buf[0], "[%s].sdf_data", iname);

    SEXP ret;

    PROTECT(ret = NEW_INTEGER(1));

    INTEGER(ret)[0] = _get_row_count2(g_sql_buf[0]);

    UNPROTECT(1);

    return ret;

}

SEXP sdf_get_variable_index(SEXP svec, SEXP idx) {

    SEXP ret = R_NilValue, tmp;

    char *iname = SDF_INAME(svec), *varname = SVEC_VARNAME(svec);

    int index, idxlen, i, retlen=0, res;

    if (!USE_SDF(iname, TRUE)) return R_NilValue;

    /* check if sdf exists */

    sqlite3_stmt *stmt;

    sprintf(g_sql_buf[0], "select [%s] from [%s].sdf_data", varname, iname);

    res = sqlite3_prepare(g_workspace, g_sql_buf[0], -1, &stmt, 0);

    sqlite3_finalize(stmt);

    if (_sqlite_error(res)) { return ret; }

    idxlen = LENGTH(idx);

    if (idxlen < 1) return ret;

    sprintf(g_sql_buf[0], "select [%s] from [%s].sdf_data limit ?,1",

            varname, iname);

    res = sqlite3_prepare(g_workspace, g_sql_buf[0], -1, &stmt, 0);

    /* get data based on index */

    if (IS_NUMERIC(idx)) {

        index = ((int) REAL(idx)[0]) - 1;

        if (index < 0 && idxlen == 1) return ret;

        if (index >= 0) {

            sqlite3_bind_int(stmt, 1, index);

            res = sqlite3_step(stmt);

            if (res == SQLITE_ROW) { 

                retlen = _get_vector_index_typed_result(stmt, &ret, idxlen);

            } 

        } 

        if (index < 0 || res != SQLITE_ROW) {

            /* something wrong w/ 1st idx, and it is quietly ignored. we make 

             * a "dummy" call to setup the SEXP */

            sqlite3_bind_int(stmt, 1, 0);

            _get_vector_index_typed_result(stmt, &ret, idxlen - 1);

            retlen = 0;

        }

        if (idxlen > 1) {

            for (i = 1; i < idxlen; i++) {

                index = ((int) REAL(idx)[i]) - 1;

                if (index < 0) continue;

                sqlite3_reset(stmt);

                sqlite3_bind_int(stmt, 1, index);

                res = sqlite3_step(stmt);

                if (res == SQLITE_ROW)

                    retlen += _get_vector_index_typed_result(stmt, &ret, retlen); 

            }

        }

    } else if (IS_INTEGER(idx)) {

        /* similar to REAL (IS_NUMERIC) above, except that we don't have

         * to cast idx to int. can't refactor this out, sucks. */

        index = INTEGER(idx)[0] - 1;

        if (index < 0 && idxlen == 1) return ret;

        if (index >= 0) {

            sqlite3_bind_int(stmt, 1, index);

            res = sqlite3_step(stmt);

            if (res == SQLITE_ROW) { 

                retlen = _get_vector_index_typed_result(stmt, &ret, idxlen);

            } 

        } 

        if (index < 0 || res != SQLITE_ROW) {

            /* something wrong w/ 1st idx, and it is quietly ignored. we make 

             * a "dummy" call to setup the SEXP */

            sqlite3_bind_int(stmt, 1, 0);

            _get_vector_index_typed_result(stmt, &ret, idxlen - 1);

            retlen = 0;

        }

        if (idxlen > 1) {

            for (i = 1; i < idxlen; i++) {

                index = INTEGER(idx)[i] - 1;

                if (index < 0) continue;

                sqlite3_reset(stmt);

                sqlite3_bind_int(stmt, 1, index);

                sqlite3_step(stmt);

                retlen += _get_vector_index_typed_result(stmt, &ret, retlen); 

            }

        }

    } else if (IS_LOGICAL(idx)) {

        /* have to deal with recycling */

        sprintf(g_sql_buf[0], "[%s].sdf_data", iname);

        int veclen = _get_row_count2(g_sql_buf[0]);

        /* find if there is any TRUE element in the vector */

        for (i = 0; i < idxlen && i < veclen; i++) {

            if (LOGICAL(idx)[i]) {

                sqlite3_bind_int(stmt, 1, i);

                sqlite3_step(stmt);

                /* there are at least (idxlen-i) TRUE per cycle of the LOGICAL

                 * index. there are at least (veclen/idxlen) cycles (int div).

                 * at the last cycle, if (veclen%idxlen > 0), there will be

                 * at least (veclen%idxlen - i) if veclen%idxlen > i */

                retlen = (idxlen-i) * (veclen/idxlen);

                if (veclen%idxlen > i) retlen += (veclen%idxlen - i);

                /* create the vector */

                retlen = _get_vector_index_typed_result(stmt, &ret, retlen);

                break;

            }

        }

        if (i < idxlen && i < veclen) {

            for (i++; i < veclen; i++) {

                if (LOGICAL(idx)[i%idxlen]) {

                    sqlite3_reset(stmt);

                    sqlite3_bind_int(stmt, 1, i);

                    sqlite3_step(stmt);

                    retlen += _get_vector_index_typed_result(stmt, &ret, retlen);

                }

            }

        }

    }

    sqlite3_finalize(stmt);

    if (ret != R_NilValue) {

        ret = _shrink_vector(ret, retlen);

        tmp = GET_LEVELS(svec);

        if (tmp != R_NilValue) {

            SET_LEVELS(ret, duplicate(tmp));

            if (LENGTH(GET_CLASS(svec)) == 2) {

                SET_CLASS(ret, mkString("factor"));

            } else {

                PROTECT(tmp = NEW_CHARACTER(2));

                SET_STRING_ELT(tmp, 0, mkChar("ordered"));

                SET_STRING_ELT(tmp, 1, mkChar("factor"));

                UNPROTECT(1);

            }

        }

    }

    return ret;

}

/* the global accumulator should be safe if we only do 1 cummulative or

 * aggregate at any time. it won't work for stuffs like "select max(col)-min(col)

 * from sdf_data". */

static double g_accumulator = 0.0; /* accumulator var for cumsum, cumprod, etc. */

static int g_start = 0;            /* flag for start of cummulation */

static int g_narm = 0;             /* for Summary group */

SEXP sdf_do_variable_math(SEXP func, SEXP vector, SEXP extra_args, SEXP _nargs) {

    char *iname, *iname_src, *varname_src, *funcname;

    int namelen, res, nargs;

    sqlite3_stmt *stmt;

    /* get data from arguments (function name and sqlite.vector stuffs) */

    funcname = CHAR_ELT(func, 0);

    iname_src = SDF_INAME(vector);

    varname_src = SVEC_VARNAME(vector);

    nargs = INTEGER(_nargs)[0];

    if (!USE_SDF(iname_src, TRUE)) return R_NilValue;

    /* check nargs */

    if (nargs > 2) {

        Rprintf("Error: Don't know how to handle Math functions w/ more than 2 args\n");

        return R_NilValue;

    }

    /* create a new sdf, with 1 column named V1 */

    iname = _create_sdf_skeleton2(R_NilValue, &namelen);

    if (iname == NULL) return R_NilValue;

    sprintf(g_sql_buf[0], "create table [%s].sdf_data ([row name] text, "

            "V1 double)", iname);

    res = _sqlite_exec(g_sql_buf[0]);

    _sqlite_error(res);

    /* insert into <newsdf>.col, row.names select func(col), rownames */

    sprintf(g_sql_buf[0], "insert into [%s].sdf_data([row name], V1) "

            "select [row name], %s([%s]) from [%s].sdf_data", iname, funcname,

            varname_src, iname_src);

    res = sqlite3_prepare(g_workspace, g_sql_buf[0], -1, &stmt, 0); 

    if (_sqlite_error(res)) {

        sprintf(g_sql_buf[0], "detach %s", iname);

        _sqlite_exec(g_sql_buf[0]);

        /* we will return a string with the file name, and do file.remove

         * at R */

        iname[namelen] = '.';

        return mkString(iname);

    }

    g_accumulator = 0.0;   /* initialize accumulator */

    g_start = 1;           /* flag that we are at start of accumulating */

    sqlite3_step(stmt);

    sqlite3_finalize(stmt);

    /* create sqlite.vector sexp */

    SEXP ret, value; int nprotected = 0;

    PROTECT(ret = NEW_LIST(2)); nprotected++;

    /* set list names */

    PROTECT(value = NEW_CHARACTER(2)); nprotected++;

    SET_STRING_ELT(value, 0, mkChar("iname"));

    SET_STRING_ELT(value, 1, mkChar("varname"));

    SET_NAMES(ret, value);

    /* set list values */

    SET_VECTOR_ELT(ret, 0, mkString(iname));

    SET_VECTOR_ELT(ret, 1, mkString("V1"));

    /* set sexp class */

    PROTECT(value = NEW_CHARACTER(2)); nprotected++;

    SET_VECTOR_ELT(value, 0, mkChar("sqlite.vector"));

    SET_VECTOR_ELT(value, 1, mkChar("numeric"));

    SET_CLASS(ret, value);

    UNPROTECT(nprotected);

    return ret;

}

SEXP sdf_do_variable_summary(SEXP func, SEXP vector, SEXP na_rm) {

    char *iname_src, *varname_src, *funcname;

    int res;

    sqlite3_stmt *stmt;

    double _ret = NA_REAL; SEXP ret;

    /* get data from arguments (function name and sqlite.vector stuffs) */

    funcname = CHAR_ELT(func, 0);

    iname_src = SDF_INAME(vector);

    varname_src = SVEC_VARNAME(vector);

    if (!USE_SDF(iname_src, TRUE)) return R_NilValue;

    g_narm = LOGICAL(na_rm)[0];

    if (strcmp(funcname, "range") == 0) {

        /* special handling for range. use min then max */

        g_start = 1;

        g_accumulator = 0.0;

        sprintf(g_sql_buf[0], "select min_df([%s]) from [%s].sdf_data", varname_src, iname_src);

        res = sqlite3_prepare(g_workspace, g_sql_buf[0], -1, &stmt, NULL);

        if (_sqlite_error(res)) return R_NilValue;

        sqlite3_step(stmt); sqlite3_finalize(stmt);

        _ret = g_accumulator;

        if (R_IsNA(_ret) && !g_narm) {

            PROTECT(ret = NEW_NUMERIC(2));

            REAL(ret)[0] = REAL(ret)[1] = R_NaReal;

            goto __sdf_do_variable_summary_out;

        }

        g_start = 1;

        g_accumulator = 0.0;

        sprintf(g_sql_buf[0], "select max_df([%s]) from [%s].sdf_data", varname_src, iname_src);

        res = sqlite3_prepare(g_workspace, g_sql_buf[0], -1, &stmt, NULL);

        if (_sqlite_error(res)) return R_NilValue;

        sqlite3_step(stmt); sqlite3_finalize(stmt);

        /* if there is NA, then the if above should have caught it already */

        PROTECT(ret = NEW_NUMERIC(2));

        REAL(ret)[0] = _ret;

        REAL(ret)[1] = g_accumulator;

    } else {

        g_start = 1;  /* we'll use these instead of sqlite3_aggregate_context */

        g_accumulator = 0.0;

        sprintf(g_sql_buf[0], "select %s_df([%s]) from [%s].sdf_data", funcname, varname_src, iname_src);

        res = sqlite3_prepare(g_workspace, g_sql_buf[0], -1, &stmt, NULL);

        if (_sqlite_error(res)) return R_NilValue;

        res = sqlite3_step(stmt); sqlite3_finalize(stmt);

        if (strcmp(funcname, "all") == 0 || strcmp(funcname, "any") == 0) {

            PROTECT(ret = NEW_LOGICAL(1));

            if (R_IsNA(g_accumulator)) LOGICAL(ret)[0] = NA_INTEGER;

            else LOGICAL(ret)[0] = !(g_accumulator == 0);

        } else {

            PROTECT(ret = NEW_NUMERIC(1));

            REAL(ret)[0] = g_accumulator;

        }

    }

__sdf_do_variable_summary_out:

    UNPROTECT(1);

    return ret;

}

/****************************************************************************

 * VECTOR MATH/OPS/GROUP OPERATIONS

 ****************************************************************************/

int __vecmath_checkarg(sqlite3_context *ctx, sqlite3_value *arg, double *value) {

    int ret = 1;

    if (sqlite3_value_type(arg) == SQLITE_NULL) { 

        sqlite3_result_null(ctx); 

        ret = 0;

    } else {

        if (sqlite3_value_type(arg) == SQLITE_INTEGER) 

            *value = sqlite3_value_int(arg); 

        else *value = sqlite3_value_double(arg); 

    }

    return ret;

}

#define SQLITE_MATH_FUNC1(name, func) static void __vecmath_ ## name(\

        sqlite3_context *ctx, int argc, sqlite3_value **argv) { \

    double value; \

    if (__vecmath_checkarg(ctx, argv[0], &value)) { \

        sqlite3_result_double(ctx, func(value)); \

    }  \

}

#define SQLITE_MATH_FUNC_CUM(name, func) static void __vecmath_ ## name(\

        sqlite3_context *ctx, int argc, sqlite3_value **argv) { \

    double value; \

    if (__vecmath_checkarg(ctx, argv[0], &value)) { \

        if (g_start) { g_start = 0; g_accumulator = value; } \

        else g_accumulator = func(g_accumulator, value); \

        sqlite3_result_double(ctx, g_accumulator); \

    }  \

}

/* SQLITE_MATH_FUNC1(abs, abs)   in SQLite */

SQLITE_MATH_FUNC1(sign, sign)   /* in R */

SQLITE_MATH_FUNC1(sqrt, sqrt)

SQLITE_MATH_FUNC1(floor, floor)

SQLITE_MATH_FUNC1(ceiling, ceil)

SQLITE_MATH_FUNC1(trunc, ftrunc) /* in R */

/* SQLITE_MATH_FUNC1(round, )   in SQLite */

/* SQLITE_MATH_FUNC1(signif, ) 2 arg */

SQLITE_MATH_FUNC1(exp, exp)

/* SQLITE_MATH_FUNC1(log, ) 2 arg */

SQLITE_MATH_FUNC1(cos, cos)

SQLITE_MATH_FUNC1(sin, sin)

SQLITE_MATH_FUNC1(tan, tan)

SQLITE_MATH_FUNC1(acos, acos)

SQLITE_MATH_FUNC1(asin, asin)

SQLITE_MATH_FUNC1(atan, atan)

SQLITE_MATH_FUNC1(cosh, cosh)

SQLITE_MATH_FUNC1(sinh, sinh)

SQLITE_MATH_FUNC1(tanh, tanh)

SQLITE_MATH_FUNC1(acosh, acosh)  /* nowhere in include?? */

SQLITE_MATH_FUNC1(asinh, asinh)  /* nowhere in include?? */

SQLITE_MATH_FUNC1(atanh, atanh)  /* nowhere in include?? */

SQLITE_MATH_FUNC1(lgamma, lgammafn) /* in R */

SQLITE_MATH_FUNC1(gamma, gammafn) /* in R */

/* SQLITE_MATH_FUNC1(gammaCody, gammaCody)   * in R ?? */

SQLITE_MATH_FUNC1(digamma, digamma) /* in R */    

SQLITE_MATH_FUNC1(trigamma, trigamma) /* in R */

#define SUM(a, b)  (a) + (b)

#define PROD(a, b) (a) * (b)

#define MIN(a, b) ((a) <= (b)) ? (a) : (b)

#define MAX(a, b) ((a) >= (b)) ? (a) : (b)

#define ALL(a, b) (((a) == 0) || ((b) == 0)) ? 0 : 1

#define ANY(a, b) (((a) == 0) && ((b) == 0)) ? 0 : 1

SQLITE_MATH_FUNC_CUM(cumsum, SUM)

SQLITE_MATH_FUNC_CUM(cumprod, PROD)

SQLITE_MATH_FUNC_CUM(cummin, MIN)

SQLITE_MATH_FUNC_CUM(cummax, MAX)

#define SQLITE_SUMMARY_FUNC(name, func) static void __vecsummary_ ## name(\

        sqlite3_context *ctx, int argc, sqlite3_value **argv) { \

    double value; \

    if (!g_narm && R_IsNA(g_accumulator)) return; /* NA if na.rm=F & NA found */ \

    if (sqlite3_value_type(argv[0]) != SQLITE_NULL) {  \

        if (sqlite3_value_type(argv[0]) == SQLITE_INTEGER) {  \

            int tmp = sqlite3_value_int(argv[0]); \

            value = (tmp == NA_INTEGER) ? R_NaReal : tmp; \

        } else value = sqlite3_value_double(argv[0]);  \

        if (R_IsNA(value)) { \

            if (!g_narm) g_accumulator = value; return; \

        } else if (g_start) { g_start = 0; g_accumulator = value; } \

        else g_accumulator = func(g_accumulator, value); \

    } \

}

SQLITE_SUMMARY_FUNC(all_df, ALL)

SQLITE_SUMMARY_FUNC(any_df, ANY)

SQLITE_SUMMARY_FUNC(sum_df, SUM)

SQLITE_SUMMARY_FUNC(prod_df, PROD)

SQLITE_SUMMARY_FUNC(min_df, MIN)

SQLITE_SUMMARY_FUNC(max_df, MAX)

static void __vecsummary_finalize(sqlite3_context *ctx) {

    /* g_accumulator already summarizes it. just return that */

    sqlite3_result_double(ctx, g_accumulator);

}

#define VMENTRY1(func)  {#func, __vecmath_ ## func}

#define VSENTRY1(func)  {#func, __vecsummary_ ## func}

void __register_vector_math() {

    int i, res;

    static const struct {

        char *name;

        void (*func)(sqlite3_context*, int, sqlite3_value**);

    } arr_func1[] = {

        VMENTRY1(sign),

        VMENTRY1(sqrt),

        VMENTRY1(floor),

        VMENTRY1(ceiling),

        VMENTRY1(trunc),

        VMENTRY1(exp),

        VMENTRY1(cos),

        VMENTRY1(sin),

        VMENTRY1(tan),

        VMENTRY1(acos),

        VMENTRY1(asin),

        VMENTRY1(atan),

        VMENTRY1(cosh),

        VMENTRY1(sinh),

        VMENTRY1(tanh),

        VMENTRY1(acosh),

        VMENTRY1(asinh),

        VMENTRY1(atanh),

        VMENTRY1(lgamma),

        VMENTRY1(gamma),

        VMENTRY1(digamma),

        VMENTRY1(trigamma),

        VMENTRY1(cumsum),

        VMENTRY1(cumprod),

        VMENTRY1(cummin),

        VMENTRY1(cummax)

    }, arr_sum1[] = {

        VSENTRY1(all_df),  /* can't override sum, min, max */

        VSENTRY1(any_df),

        VSENTRY1(sum_df),

        VSENTRY1(prod_df),

        VSENTRY1(min_df),

        VSENTRY1(max_df)

    };

    int len = sizeof(arr_func1) / sizeof(arr_func1[0]);

    for (i = 0; i < len; i++) {

        res = sqlite3_create_function(g_workspace, arr_func1[i].name, 1, 

                SQLITE_ANY, NULL, arr_func1[i].func, NULL, NULL);

        _sqlite_error(res);

    }

    len = sizeof(arr_sum1) / sizeof(arr_sum1[0]);

    for (i = 0; i < len; i++) {

        res = sqlite3_create_function(g_workspace, arr_sum1[i].name, 1, 

                SQLITE_ANY, NULL, NULL, arr_sum1[i].func, __vecsummary_finalize);

        _sqlite_error(res);

    }

}