The R Project SVN R-packages

Rev

Rev 3457 | Rev 3473 | Go to most recent revision | Only display areas with differences | Ignore whitespace | Details | Blame | Last modification | View Log | RSS feed

Rev 3457 Rev 3471
1
#include "R.h"
1
#include "R.h"
2
#include "Rdefines.h"
2
#include "Rdefines.h"
3
#include "Rinternals.h"
3
#include "Rinternals.h"
4
#include "sqlite3.h"
4
#include "sqlite3.h"
5
 
5
 
6
#ifndef __SQLITE_DATAFRAME__
6
#ifndef __SQLITE_DATAFRAME__
7
#define __SQLITE_DATAFRAME__
7
#define __SQLITE_DATAFRAME__
8
 
8
 
9
/* # of sql buffers */
9
/* # of sql buffers */
10
#define NBUFS 4
10
#define NBUFS 4
11
 
11
 
12
#ifdef __SQLITE_WORKSPACE__
12
#ifdef __SQLITE_WORKSPACE__
13
SEXP SDF_RowNamesSymbol;
13
SEXP SDF_RowNamesSymbol;
14
SEXP SDF_VectorTypeSymbol;
14
SEXP SDF_VectorTypeSymbol;
15
SEXP SDF_DimSymbol;
15
SEXP SDF_DimSymbol;
16
SEXP SDF_DimNamesSymbol;
16
SEXP SDF_DimNamesSymbol;
17
#else 
17
#else 
18
extern SEXP SDF_RowNamesSymbol;
18
extern SEXP SDF_RowNamesSymbol;
19
extern SEXP SDF_VectorTypeSymbol;
19
extern SEXP SDF_VectorTypeSymbol;
20
extern SEXP SDF_DimSymbol;
20
extern SEXP SDF_DimSymbol;
21
extern SEXP SDF_DimNamesSymbol;
21
extern SEXP SDF_DimNamesSymbol;
22
 
22
 
23
extern sqlite3 *g_workspace;
23
extern sqlite3 *g_workspace;
24
extern char *g_sql_buf[NBUFS];
24
extern char *g_sql_buf[NBUFS];
25
extern int g_sql_buf_sz[NBUFS];
25
extern int g_sql_buf_sz[NBUFS];
26
#endif
26
#endif
27
 
27
 
28
/* sdf type attributes */
28
/* sdf type attributes */
29
#define GET_SDFVECTORTYPE(x) getAttrib(x, SDF_VectorTypeSymbol) 
29
#define GET_SDFVECTORTYPE(x) getAttrib(x, SDF_VectorTypeSymbol) 
30
#define SET_SDFVECTORTYPE(x,t) setAttrib(x, SDF_VectorTypeSymbol, t) 
30
#define SET_SDFVECTORTYPE(x,t) setAttrib(x, SDF_VectorTypeSymbol, t) 
31
#define TEST_SDFVECTORTYPE(x, t) (strcmp(CHAR(asChar(GET_SDFVECTORTYPE(x))), t) == 0)
31
#define TEST_SDFVECTORTYPE(x, t) (strcmp(CHAR(asChar(GET_SDFVECTORTYPE(x))), t) == 0)
32
#define GET_SDFROWNAMES(x) getAttrib(x, SDF_RowNamesSymbol)
32
#define GET_SDFROWNAMES(x) getAttrib(x, SDF_RowNamesSymbol)
33
#define SET_SDFROWNAMES(x, r) setAttrib(x, SDF_RowNamesSymbol, r)
33
#define SET_SDFROWNAMES(x, r) setAttrib(x, SDF_RowNamesSymbol, r)
34
 
34
 
35
#ifndef SET_ROWNAMES
35
#ifndef SET_ROWNAMES
36
#define SET_ROWNAMES(x, r) setAttrib(x, R_RowNamesSymbol, r)
36
#define SET_ROWNAMES(x, r) setAttrib(x, R_RowNamesSymbol, r)
37
#endif
37
#endif
38
 
38
 
39
#define WORKSPACE_COLUMNS 6
39
#define WORKSPACE_COLUMNS 6
40
#define MAX_ATTACHED 30     /* 31 including workspace.db */
40
#define MAX_ATTACHED 30     /* 31 including workspace.db */
41
 
41
 
42
/* utilities for checking characteristics of arg */
42
/* utilities for checking characteristics of arg */
43
int _is_r_sym(char *sym);
43
int _is_r_sym(char *sym);
44
int _file_exists(char *filename);
44
int _file_exists(char *filename);
45
int _sdf_exists2(char *iname);
45
int _sdf_exists2(char *iname);
46
 
46
 
47
/* sdf utilities */
47
/* sdf utilities */
48
int USE_SDF1(const char *iname, int exists, int protect);  /* call this before doing anything on an SDF */
48
int USE_SDF1(const char *iname, int exists, int protect);  /* call this before doing anything on an SDF */
49
int UNUSE_SDF2(const char *iname); /* somewhat like UNPROTECT */
49
int UNUSE_SDF2(const char *iname); /* somewhat like UNPROTECT */
50
SEXP _create_sdf_sexp(const char *iname);  /* create a SEXP for an SDF */
50
SEXP _create_sdf_sexp(const char *iname);  /* create a SEXP for an SDF */
51
int _add_sdf1(char *filename, char *internal_name); /* add SDF to workspace */
51
int _add_sdf1(char *filename, char *internal_name); /* add SDF to workspace */
52
void _delete_sdf2(const char *iname); /* remove SDF from workspace */
52
void _delete_sdf2(const char *iname); /* remove SDF from workspace */
53
int _get_factor_levels1(const char *iname, const char *varname, SEXP var);
53
int _get_factor_levels1(const char *iname, const char *varname, SEXP var);
54
int _get_row_count2(const char *table, int quote);
54
int _get_row_count2(const char *table, int quote);
55
SEXP _get_rownames(const char *sdf_iname);
55
SEXP _get_rownames(const char *sdf_iname);
56
char *_get_full_pathname2(char *relpath); /* get full path given relpath, used in workspace mgmt */
56
char *_get_full_pathname2(char *relpath); /* get full path given relpath, used in workspace mgmt */
57
int _is_factor2(const char *iname, const char *factor_type, const char *colname);
57
int _is_factor2(const char *iname, const char *factor_type, const char *colname);
58
SEXP _get_rownames2(const char *sdf_iname);
58
SEXP _get_rownames2(const char *sdf_iname);
59
 
59
 
60
/* utilities for creating SDF's */
60
/* utilities for creating SDF's */
61
char *_create_sdf_skeleton1(SEXP name, int *o_namelen, int protect);
61
char *_create_sdf_skeleton1(SEXP name, int *o_namelen, int protect);
62
int _copy_factor_levels2(const char *factor_type, const char *iname_src,
62
int _copy_factor_levels2(const char *factor_type, const char *iname_src,
63
        const char *colname_src, const char *iname_dst, const char *colname_dst);
63
        const char *colname_src, const char *iname_dst, const char *colname_dst);
64
int _create_factor_table2(const char *iname, const char *factor_type, 
64
int _create_factor_table2(const char *iname, const char *factor_type, 
65
        const char *colname);
65
        const char *colname);
66
char *_create_svector1(SEXP name, const char *type, int * _namelen, int protect);
66
char *_create_svector1(SEXP name, const char *type, int * _namelen, int protect);
67
 
67
 
68
/* R utilities */
68
/* R utilities */
69
SEXP _getListElement(SEXP list, char *varname);
69
SEXP _getListElement(SEXP list, char *varname);
70
SEXP _shrink_vector(SEXP vec, int len); /* shrink vector size */
70
SEXP _shrink_vector(SEXP vec, int len); /* shrink vector size */
71
 
71
 
72
/* sqlite utilities */
72
/* sqlite utilities */
73
int _empty_callback(void *data, int ncols, char **row, char **cols);
73
int _empty_callback(void *data, int ncols, char **row, char **cols);
74
int _sqlite_error_check(int res, const char *file, int line);
74
int _sqlite_error_check(int res, const char *file, int line);
75
const char *_get_column_type(const char *class, int type); /* get sqlite type corresponding to R class & type */
75
const char *_get_column_type(const char *class, int type); /* get sqlite type corresponding to R class & type */
76
sqlite3* _is_sqlitedb(char *filename);
76
sqlite3* _is_sqlitedb(char *filename);
77
 
77
 
78
/* global buffer (g_sql_buf) utilities */
78
/* global buffer (g_sql_buf) utilities */
79
int _expand_buf(int i, int size);  /* expand ith buf if size > buf[i].size */
79
int _expand_buf(int i, int size);  /* expand ith buf if size > buf[i].size */
80
 
80
 
81
 
81
 
82
/* workspace utilities */
82
/* workspace utilities */
83
int _prepare_attach2();  /* prepare workspace before attaching a sqlite db */
83
int _prepare_attach2();  /* prepare workspace before attaching a sqlite db */
84
 
84
 
85
/* misc utilities */
85
/* misc utilities */
86
char *_r2iname(char *internal_name, char *filename);
86
char *_r2iname(char *internal_name, char *filename);
87
char *_fixname(char *rname);
87
char *_fixname(char *rname);
88
char *_str_tolower(char *out, const char *ref);
88
char *_str_tolower(char *out, const char *ref);
89
 
89
 
90
/* register functions to sqlite */
90
/* register functions to sqlite */
91
void __register_vector_math();
91
void __register_vector_math();
92
 
92
 
93
#define _sqlite_exec(sql) sqlite3_exec(g_workspace, sql, _empty_callback, NULL, NULL)
93
#define _sqlite_exec(sql) sqlite3_exec(g_workspace, sql, _empty_callback, NULL, NULL)
94
#define _sqlite_error(res) _sqlite_error_check((res), __FILE__, __LINE__)
94
#define _sqlite_error(res) _sqlite_error_check((res), __FILE__, __LINE__)
95
 
95
 
96
#ifdef __SQLITE_DEBUG__
96
#ifdef __SQLITE_DEBUG__
97
#define _sqlite_begin  { _sqlite_error(_sqlite_exec("begin")); Rprintf("begin at "  __FILE__  " line %d\n",  __LINE__); }
97
#define _sqlite_begin  { _sqlite_error(_sqlite_exec("begin")); Rprintf("begin at "  __FILE__  " line %d\n",  __LINE__); }
98
#define _sqlite_commit  { _sqlite_error(_sqlite_exec("commit")); Rprintf("commit at "  __FILE__  " line %d\n",  __LINE__); }
98
#define _sqlite_commit  { _sqlite_error(_sqlite_exec("commit")); Rprintf("commit at "  __FILE__  " line %d\n",  __LINE__); }
99
#else
99
#else
100
#define _sqlite_begin  _sqlite_error(_sqlite_exec("begin")) 
100
#define _sqlite_begin  _sqlite_error(_sqlite_exec("begin")) 
101
#define _sqlite_commit _sqlite_error(_sqlite_exec("commit"))
101
#define _sqlite_commit _sqlite_error(_sqlite_exec("commit"))
102
#endif
102
#endif
103
 
103
 
104
/* R object accessors shortcuts */
104
/* R object accessors shortcuts */
105
#define CHAR_ELT(str, i) CHAR(STRING_ELT(str,i))
105
#define CHAR_ELT(str, i) CHAR(STRING_ELT(str,i))
106
 
106
 
107
/* SDF object accessors shortcuts */
107
/* SDF object accessors shortcuts */
108
#define SDF_INAME(sdf) CHAR(STRING_ELT(_getListElement(sdf, "iname"),0))
108
#define SDF_INAME(sdf) CHAR(STRING_ELT(_getListElement(sdf, "iname"),0))
109
#define SVEC_VARNAME(sdf) CHAR(STRING_ELT(_getListElement(sdf, "varname"),0))
109
#define SVEC_VARNAME(sdf) CHAR(STRING_ELT(_getListElement(sdf, "varname"),0))
110
 
110
 
111
/* possible var types when stored in sqlite as integer */
111
/* possible var types when stored in sqlite as integer */
112
#define VAR_INTEGER 0
112
#define VAR_INTEGER 0
113
#define VAR_FACTOR  1
113
#define VAR_FACTOR  1
114
#define VAR_ORDERED 2
114
#define VAR_ORDERED 2
115
 
115
 
116
/* detail constants (see _get_sdf_detail2 in sqlite_workspace.c) */
116
/* detail constants (see _get_sdf_detail2 in sqlite_workspace.c) */
117
#define SDF_DETAIL_EXISTS 0
117
#define SDF_DETAIL_EXISTS 0
118
#define SDF_DETAIL_FULLFILENAME 1
118
#define SDF_DETAIL_FULLFILENAME 1
119
 
119
 
120
/* R SXP type constants */
120
/* R SXP type constants */
121
#define FACTORSXP 11
121
#define FACTORSXP 11
122
#define ORDEREDSXP 12
122
#define ORDEREDSXP 12
123
 
123
 
124
 
124
 
125
 
125
 
126
/* top level functions */
126
/* top level functions */
127
/* sqlite_workspace.c */
127
/* sqlite_workspace.c */
128
SEXP sdf_init_workspace();
128
SEXP sdf_init_workspace();
129
SEXP sdf_finalize_workspace();
129
SEXP sdf_finalize_workspace();
130
SEXP sdf_list_sdfs(SEXP pattern);
130
SEXP sdf_list_sdfs(SEXP pattern);
131
SEXP sdf_get_sdf(SEXP name);
131
SEXP sdf_get_sdf(SEXP name);
132
SEXP sdf_attach_sdf(SEXP filename, SEXP internal_name);
132
SEXP sdf_attach_sdf(SEXP filename, SEXP internal_name);
133
SEXP sdf_detach_sdf(SEXP internal_name);
133
SEXP sdf_detach_sdf(SEXP internal_name);
134
SEXP sdf_rename_sdf(SEXP sdf, SEXP name);
134
SEXP sdf_rename_sdf(SEXP sdf, SEXP name);
135
 
135
 
136
/* sqlite_dataframe.c */
136
/* sqlite_dataframe.c */
137
SEXP sdf_create_sdf(SEXP df, SEXP name);
137
SEXP sdf_create_sdf(SEXP df, SEXP name);
138
SEXP sdf_get_names(SEXP sdf);
138
SEXP sdf_get_names(SEXP sdf);
139
SEXP sdf_get_length(SEXP sdf);
139
SEXP sdf_get_length(SEXP sdf);
140
SEXP sdf_get_row_count(SEXP sdf);
140
SEXP sdf_get_row_count(SEXP sdf);
141
SEXP sdf_import_table(SEXP _filename, SEXP _name, SEXP _sep, SEXP _quote, 
141
SEXP sdf_import_table(SEXP _filename, SEXP _name, SEXP _sep, SEXP _quote, 
142
        SEXP _rownames, SEXP _colnames);
142
        SEXP _rownames, SEXP _colnames);
143
SEXP sdf_get_index(SEXP sdf, SEXP row, SEXP col);
143
SEXP sdf_get_index(SEXP sdf, SEXP row, SEXP col, SEXP new_sdf);
144
SEXP sdf_rbind(SEXP sdf, SEXP data);
144
SEXP sdf_rbind(SEXP sdf, SEXP data);
145
SEXP sdf_get_iname(SEXP sdf);
145
SEXP sdf_get_iname(SEXP sdf);
146
 
146
 
147
/* sqlite_vector.c */
147
/* sqlite_vector.c */
148
SEXP sdf_get_variable(SEXP sdf, SEXP name);
148
SEXP sdf_get_variable(SEXP sdf, SEXP name);
149
SEXP sdf_get_variable_length(SEXP svec);
149
SEXP sdf_get_variable_length(SEXP svec);
150
SEXP sdf_get_variable_index(SEXP svec, SEXP idx);
150
SEXP sdf_get_variable_index(SEXP svec, SEXP idx);
151
/* SEXP sdf_set_variable_index(SEXP svec, SEXP idx, SEXP value); */
151
/* SEXP sdf_set_variable_index(SEXP svec, SEXP idx, SEXP value); */
152
SEXP sdf_variable_summary(SEXP svec, SEXP maxsum);
152
SEXP sdf_variable_summary(SEXP svec, SEXP maxsum);
153
SEXP sdf_do_variable_math(SEXP func, SEXP vector, SEXP other_args);
153
SEXP sdf_do_variable_math(SEXP func, SEXP vector, SEXP other_args);
154
SEXP sdf_do_variable_op(SEXP func, SEXP vector, SEXP op2, SEXP arg_reversed);
154
SEXP sdf_do_variable_op(SEXP func, SEXP vector, SEXP op2, SEXP arg_reversed);
155
SEXP sdf_do_variable_summary(SEXP func, SEXP vector, SEXP na_rm);
155
SEXP sdf_do_variable_summary(SEXP func, SEXP vector, SEXP na_rm);
156
SEXP sdf_sort_variable(SEXP svec, SEXP decreasing);
156
SEXP sdf_sort_variable(SEXP svec, SEXP decreasing);
157
 
157
 
158
/* sqlite_external.c */
158
/* sqlite_external.c */
159
SEXP sdf_import_sqlite_table(SEXP _dbfilename, SEXP _tblname, SEXP _sdfiname);
159
SEXP sdf_import_sqlite_table(SEXP _dbfilename, SEXP _tblname, SEXP _sdfiname);
160
 
160
 
161
/* sqlite_matrix.c */
161
/* sqlite_matrix.c */
162
SEXP sdf_as_matrix(SEXP sdf, SEXP name);
162
SEXP sdf_as_matrix(SEXP sdf, SEXP name);
163
#endif
163
#endif