From c07d0c2d2f6f7b0eb6e92cc6204bf05037957e82 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?J=C3=B6rg=20Frings-F=C3=BCrst?= Date: Mon, 1 Sep 2014 15:43:52 +0200 Subject: Imported Upstream version 1.6.3 --- cgats/cgats.c | 68 ++++++++++++++++++++++++++++++++++++++++++++++++----------- cgats/cgats.h | 2 +- cgats/pars.c | 30 ++++++++++++++++++++------ 3 files changed, 81 insertions(+), 19 deletions(-) (limited to 'cgats') diff --git a/cgats/cgats.c b/cgats/cgats.c index baf9992..84ff2c9 100644 --- a/cgats/cgats.c +++ b/cgats/cgats.c @@ -14,6 +14,34 @@ * see the License.txt file in this directory for licensing details. */ +/* + + Should add a function to promote a field type, ie. + promote integer to float, to avoid misrecognition + problems. + + + To make this more portable for independent use, + should save/set/restore LC_NUMERIC locale before + printf/scanf from file. e.g. + + include + char *old_locale, *saved_locale; + + old_locale = setlocale (LC_NUMERIC, NULL); + saved_locale = strdup (old_locale); + if (saved_locale == NULL) + error ("Out of memory"); + setlocale (LC_NUMERIC, "C"); + + .... read or write ... + + setlocale (LC_NUMERIC, saved_locale); + free (saved_locale); + + Also apply to pars.c + */ + #define _CGATS_C_ /* Turn on implimentation code */ #include @@ -23,8 +51,8 @@ #undef DEBUG /* Debug only in slected places */ #ifdef DEBUG -# define DBGA g_log, 0 /* First argument to DBGF() */ -# define DBGF(xx) a1logd xx +# define DBGA stderr +# define DBGF(xx) fprintf xx #else # define DBGF(xx) #endif @@ -40,7 +68,7 @@ extern void error(const char *fmt, ...), warning(const char *fmt, ...); #include "pars.h" #include "cgats.h" -#define REAL_SIGDIG 5 /* Number of significant digits in real representation */ +#define REAL_SIGDIG 6 /* Number of significant digits in real representation */ static int cgats_read(cgats *p, cgatsFile *fp); static int find_kword(cgats *p, int table, const char *ksym); @@ -374,6 +402,14 @@ cgats_read(cgats *p, cgatsFile *fp) { if (tp == NULL) break; /* EOF */ + /* This seems unlikely and will cause err() to barf */ + if (strlen(tp) > CGATS_ERRM_LENGTH/2) { + tp[CGATS_ERRM_LENGTH/2] = '\000'; + err(p,-1,"Read line got symbol '%s' that's too long\n",tp); + pp->del(pp); + return p->errc; + } + switch(rstate) { case R_IDENT: /* Expecting file identifier */ case R_KWORDS: { /* Expecting keyword, field def or data */ @@ -938,16 +974,19 @@ add_field(cgats *p, int table, const char *fsym, data_type ftype) { p->errc = 0; p->err[0] = '\000'; - if (table < 0 || table >= p->ntables) + if (table < 0 || table >= p->ntables) { return err(p,-1,"cgats.add_field(), table parameter out of range"); + } t = &p->t[table]; - if (t->nsets != 0) + if (t->nsets != 0) { return err(p,-1,"cgats.add_field(), attempt to add field to non-empty table"); + } /* Check the field name is reasonable */ - if (cs_has_ws(fsym)) + if (cs_has_ws(fsym)) { return err(p,-1,"cgats.add_kword(), field name '%s'is illegal",fsym); + } if (ftype == none_t) ftype = cs_t; /* Fudge - unknown type yet, used for reads */ @@ -956,22 +995,27 @@ add_field(cgats *p, int table, const char *fsym, data_type ftype) { st = standard_field(fsym); if (st == nqcs_t && ftype == cs_t) /* Fudge - standard type to non-quoted if normal */ ftype = nqcs_t; - if (st != none_t && st != ftype) + if (st != none_t && st != ftype) { return err(p,-1,"cgats.add_field(): unexpected data type for standard field name"); + } } t->nfields++; if (t->nfields > t->nfieldsa) { - /* Allocate fields in groups of 4 */ - t->nfieldsa += 4; - if ((t->fsym = (char **)al->realloc(al, t->fsym, t->nfieldsa * sizeof(char *))) == NULL) + /* Allocate fields in groups of 32 */ + t->nfieldsa += 32; + if ((t->fsym = (char **)al->realloc(al, t->fsym, t->nfieldsa * sizeof(char *))) == NULL) { return err(p,-2,"cgats.add_field(), realloc failed!"); + } if ((t->ftype = (data_type *)al->realloc(al, t->ftype, t->nfieldsa * sizeof(data_type))) - == NULL) + == NULL) { return err(p,-2,"cgats.add_field(), realloc failed!"); + } } - if ((t->fsym[t->nfields-1] = (char *)alloc_copy_data_type(al, cs_t, (void *)fsym)) == NULL) + if ((t->fsym[t->nfields-1] = (char *)alloc_copy_data_type(al, cs_t, (void *)fsym)) == NULL) { return err(p,-2,"cgats.alloc_copy_data_type() malloc fail"); + } + t->ftype[t->nfields-1] = ftype; return t->nfields-1; diff --git a/cgats/cgats.h b/cgats/cgats.h index 2a6b1fd..7537a48 100644 --- a/cgats/cgats.h +++ b/cgats/cgats.h @@ -20,7 +20,7 @@ #define CGATSLIB_VERSION 0x020005 #define CGATSLIB_VERSION_STR "2.05" -#define CGATS_ERRM_LENGTH 200 +#define CGATS_ERRM_LENGTH 2000 #ifdef __cplusplus extern "C" { diff --git a/cgats/pars.c b/cgats/pars.c index 606957c..a0e694c 100644 --- a/cgats/pars.c +++ b/cgats/pars.c @@ -41,6 +41,8 @@ extern void error(const char *fmt, ...), warning(const char *fmt, ...); #include "pars.h" +#undef DEBUG /* Print each token returned */ + static void del_parse(parse *p); static int read_line(parse *p); static void reset_del(parse *p); @@ -420,6 +422,9 @@ read_line(parse *p) { if ((c = p->fp->getch(p->fp)) == EOF) { if (p->bo == 0) { /* If there is nothing in the buffer */ p->line = 0; +#ifdef DEBUG + printf("pars: read_line() got EOF\n"); +#endif return 0; } c = 0; /* Finish the line */ @@ -443,16 +448,16 @@ read_line(parse *p) { } if (c == '\r') { - p->line++; /* Increment line number */ + p->line++; /* Increment line number */ p->ltflag = 1; /* Remember to allow 1 of '\n' before next line */ if (p->q == 0) - c = 0; /* Finish the line */ + c = 0; /* Finish the line */ } else if (p->q == 0 && (p->delf[c] & PARS_COMM) != 0) { /* Hit a comment */ - p->line++; /* Increment line number */ + p->line++; /* Increment line number */ p->ltflag = 2; /* Remember to flush all chars up to end of line */ - c = 0; /* Finish the line */ + c = 0; /* Finish the line */ } else if (c == '\n') { - p->line++; /* Increment line number */ + p->line++; /* Increment line number */ if (p->q == 0) c = 0; /* Finish the the line */ } @@ -477,6 +482,9 @@ read_line(parse *p) { } while (c != 0); /* Null means we've done the end of the line */ p->to = 0; /* Reset token pointer to the start of the line buffer */ p->q = 0; /* Reset quoted flag */ +#ifdef DEBUG + printf("pars: read_line() got buffer '%s'\n",p->b); +#endif return 1; } @@ -525,8 +533,12 @@ get_token(parse *p) { p->errc = 0; /* Reset error status */ p->err[0] = '\000'; - if (p->b == NULL) + if (p->b == NULL) { +#ifdef DEBUG + printf("pars: read_token() NULL buffe\n"); +#endif return NULL; + } p->token++; /* Increment token number */ p->q = 0; do { @@ -566,8 +578,14 @@ get_token(parse *p) { p->q = 0; if (tbo <= 1) { p->token = 0; +#ifdef DEBUG + printf("pars: read_token() got nothing useful\n"); +#endif return NULL; /* Haven't read anything useful */ } +#ifdef DEBUG + printf("pars: read_token() returning '%s'\n",p->tb); +#endif return p->tb; } -- cgit v1.2.3