/*
* nbibin.c
*
* Copyright (c) Chris Putnam 2016-2018
*
* Source code released under the GPL version 2
*
*/
#include <stdio.h>
#include <stdlib.h>
#include <string.h>
#include <ctype.h>
#include "is_ws.h"
#include "str.h"
#include "str_conv.h"
#include "fields.h"
#include "name.h"
#include "title.h"
#include "url.h"
#include "serialno.h"
#include "reftypes.h"
#include "bibformats.h"
#include "generic.h"
extern variants nbib_all[];
extern int nbib_nall;
/*****************************************************
PUBLIC: void nbib_initparams()
*****************************************************/
static int nbib_readf( FILE *fp, char *buf, int bufsize, int *bufpos, str *line, str *reference, int *fcharset );
static int nbib_processf( fields *nbib, char *p, char *filename, long nref, param *pm );
static int nbib_typef( fields *nbib, char *filename, int nref, param *p );
static int nbib_convertf( fields *nbib, fields *info, int reftype, param *p );
void
nbibin_initparams( param *p, const char *progname )
{
p->readformat = BIBL_NBIBIN;
p->charsetin = BIBL_CHARSET_DEFAULT;
p->charsetin_src = BIBL_SRC_DEFAULT;
p->latexin = 0;
p->xmlin = 0;
p->utf8in = 0;
p->nosplittitle = 0;
p->verbose = 0;
p->addcount = 0;
p->output_raw = 0;
p->readf = nbib_readf;
p->processf = nbib_processf;
p->cleanf = NULL;
p->typef = nbib_typef;
p->convertf = nbib_convertf;
p->all = nbib_all;
p->nall = nbib_nall;
slist_init( &(p->asis) );
slist_init( &(p->corps) );
if ( !progname ) p->progname = NULL;
else p->progname = strdup( progname );
}
/*****************************************************
PUBLIC: int nbib_readf()
*****************************************************/
/* RIS definition of a tag is strict:
character 1 = uppercase alphabetic character
character 2 = uppercase alphabetic character
character 3 = character or space (ansi 32)
character 4 = character or space (ansi 32)
character 5 = dash (ansi 45)
character 6 = space (ansi 32)
*/
static int
is_upperchar( char c )
{
if ( c>='A' && c<='Z' ) return 1;
else return 0;
}
static int
is_upperchar_space( char c )
{
if ( c==' ' ) return 1;
if ( c>='A' && c<='Z' ) return 1;
else return 0;
}
static int
nbib_istag( char *buf )
{
if ( !is_upperchar( buf[0] ) ) return 0;
if ( !is_upperchar( buf[1] ) ) return 0;
if ( !is_upperchar_space( buf[2] ) ) return 0;
if ( !is_upperchar_space( buf[3] ) ) return 0;
if (buf[4]!='-') return 0;
if (buf[5]!=' ') return 0;
return 1;
}
static int
readmore( FILE *fp, char *buf, int bufsize, int *bufpos, str *line )
{
if ( line->len ) return 1;
else return str_fget( fp, buf, bufsize, bufpos, line );
}
static int
skip_utf8_bom( str *line, int *fcharset )
{
unsigned char *up;
if ( line->len < 3 ) return 0;
up = ( unsigned char *) str_cstr( line );
if ( up[0]==0xEF && up[1]==0xBB && up[2]==0xBF ) {
*fcharset = CHARSET_UNICODE;
return 3;
}
return 0;
}
static int
nbib_readf( FILE *fp, char *buf, int bufsize, int *bufpos, str *line, str *reference, int *fcharset )
{
int n, haveref = 0, inref = 0, readtoofar = 0;
char *p;
*fcharset = CHARSET_UNKNOWN;
while ( !haveref && readmore( fp, buf, bufsize, bufpos, line ) ) {
/* ...references are terminated by an empty line */
if ( !line->data || line->len==0 ) {
if ( reference->len ) haveref = 1;
continue;
}
/* ...recognize and skip over UTF8 BOM */
n = skip_utf8_bom( line, fcharset );
p = &( line->data[n] );
/* Each reference starts with 'PMID- ' && ends with blank line */
if ( strncmp(p,"PMID- ",6)==0 ) {
if ( !inref ) {
inref = 1;
} else {
/* we've read too far.... */
readtoofar = 1;
inref = 0;
}
}
if ( nbib_istag( p ) ) {
if ( !inref ) {
fprintf(stderr,"Warning. Tagged line not "
"in properly started reference.\n");
fprintf(stderr,"Ignored: '%s'\n", p );
} else if ( !strncmp(p,"ER -",5) ) {
inref = 0;
} else {
str_addchar( reference, '\n' );
str_strcatc( reference, p );
}
}
/* not a tag, but we'll append to last values ...*/
else if ( inref && strlen( p ) >= 6 ) {
str_strcatc( reference, p+5 );
}
if ( !readtoofar ) str_empty( line );
}
if ( inref ) haveref = 1;
return haveref;
}
/*****************************************************
PUBLIC: int nbib_processf()
*****************************************************/
static char*
process_line2( str *tag, str *data, char *p )
{
while ( *p==' ' || *p=='\t' ) p++;
while ( *p && *p!='\r' && *p!='\n' )
str_addchar( data, *p++ );
while ( *p=='\r' || *p=='\n' ) p++;
return p;
}
static char*
process_line( str *tag, str *data, char *p )
{
int i;
i = 0;
while ( i<6 && *p ) {
if ( *p!=' ' && *p!='-' ) str_addchar( tag, *p );
p++;
i++;
}
while ( *p==' ' || *p=='\t' ) p++;
while ( *p && *p!='\r' && *p!='\n' )
str_addchar( data, *p++ );
str_trimendingws( data );
while ( *p=='\n' || *p=='\r' ) p++;
return p;
}
static int
nbib_processf( fields *nbib, char *p, char *filename, long nref, param *pm )
{
str tag, data;
int status, n;
strs_init( &tag, &data, NULL );
while ( *p ) {
if ( nbib_istag( p ) )
p = process_line( &tag, &data, p );
/* no anonymous fields allowed */
if ( str_has_value( &tag ) ) {
status = fields_add( nbib, str_cstr( &tag ), str_cstr( &data ), 0 );
if ( status!=FIELDS_OK ) return 0;
} else {
p = process_line2( &tag, &data, p );
n = fields_num( nbib );
if ( data.len && n>0 ) {
str *od;
od = fields_value( nbib, n-1, FIELDS_STRP );
str_addchar( od, ' ' );
str_strcat( od, &data );
}
}
strs_empty( &tag, &data, NULL );
}
strs_free( &tag, &data, NULL );
return 1;
}
/*****************************************************
PUBLIC: int nbib_typef()
*****************************************************/
/*
* PT - Case Reports
* PT - Journal Article
* PT - Research Support, N.I.H., Extramural
* PT - Review
*/
static int
nbib_typef( fields *nbib, char *filename, int nref, param *p )
{
int reftype, nrefname, is_default;
char *typename, *refname = "";
vplist_index i;
vplist a;
nrefname = fields_find( nbib, "PMID", LEVEL_MAIN );
if ( nrefname!=FIELDS_NOTFOUND ) refname = fields_value( nbib, nrefname, FIELDS_CHRP_NOUSE );
vplist_init( &a );
fields_findv_each( nbib, LEVEL_MAIN, FIELDS_CHRP_NOUSE, &a, "PT" );
is_default = 1;
for ( i=0; i<a.n; ++i ) {
typename = vplist_get( &a, i );
reftype = get_reftype( typename, nref, p->progname, p->all, p->nall, refname, &is_default, REFTYPE_SILENT );
if ( !is_default ) break;
}
if ( a.n==0 )
reftype = get_reftype( "", nref, p->progname, p->all, p->nall, refname, &is_default, REFTYPE_CHATTY );
else if ( is_default ) {
if ( p->progname ) fprintf( stderr, "%s: ", p->progname );
fprintf( stderr, "Did not recognize type of refnum %d (%s).\n"
"\tDefaulting to %s.\n", nref, refname, p->all[0].type );
}
vplist_free( &a );
return reftype;
}
/*****************************************************
PUBLIC: int nbib_convertf()
*****************************************************/
/* PB - 2016 May 7 */
static int
nbibin_date( fields *bibin, int n, str *intag, str *invalue, int level, param *pm, char *outtag, fields *bibout )
{
int fstatus, status = BIBL_OK;
str s;
char *p;
p = str_cstr( invalue );
if ( !p ) return status;
str_init( &s );
/* ...handle year */
while ( *p && !is_ws( *p ) ) {
str_addchar( &s, *p );
p++;
}
if ( str_memerr( &s ) ) {
status = BIBL_ERR_MEMERR;
goto out;
}
if ( str_has_value( &s ) ) {
fstatus = fields_add( bibout, "DATE:YEAR", str_cstr( &s ), LEVEL_MAIN );
if ( fstatus!=FIELDS_OK ) {
status = BIBL_ERR_MEMERR;
goto out;
}
}
/* ...handle month */
str_empty( &s );
while ( is_ws( *p ) ) p++;
while ( *p && !is_ws( *p ) ) {
str_addchar( &s, *p );
p++;
}
if ( str_memerr( &s ) ) {
status = BIBL_ERR_MEMERR;
goto out;
}
if ( str_has_value( &s ) ) {
fstatus = fields_add( bibout, "DATE:MONTH", str_cstr( &s ), LEVEL_MAIN );
if ( fstatus!=FIELDS_OK ) {
status = BIBL_ERR_MEMERR;
goto out;
}
}
/* ...handle day */
str_empty( &s );
while ( is_ws( *p ) ) p++;
while ( *p && !is_ws( *p ) ) {
str_addchar( &s, *p );
p++;
}
if ( str_memerr( &s ) ) {
status = BIBL_ERR_MEMERR;
goto out;
}
if ( str_has_value( &s ) ) {
fstatus = fields_add( bibout, "DATE:DAY", str_cstr( &s ), LEVEL_MAIN );
if ( fstatus!=FIELDS_OK ) {
status = BIBL_ERR_MEMERR;
goto out;
}
}
out:
str_free( &s );
return status;
}
/* the LID and AID fields that can be doi's or pii's */
static int
nbibin_doi( fields *bibin, int n, str *intag, str *invalue, int level, param *pm, char *outtag, fields *bibout )
{
int fstatus, sstatus, status = BIBL_OK;
char *id, *type, *usetag="";
slist tokens;
slist_init( &tokens );
sstatus = slist_tokenize( &tokens, invalue, " ", 1 );
if ( sstatus!=SLIST_OK ) {
status = BIBL_ERR_MEMERR;
goto out;
}
if ( tokens.n == 2 ) {
id = slist_cstr( &tokens, 0 );
type = slist_cstr( &tokens, 1 );
if ( !strcmp( type, "[doi]" ) ) usetag = "DOI";
else if ( !strcmp( type, "[pii]" ) ) usetag = "PII";
if ( strlen( outtag ) > 0 ) {
fstatus = fields_add( bibout, usetag, id, LEVEL_MAIN );
if ( fstatus!=FIELDS_OK ) {
status = BIBL_ERR_MEMERR;
goto out;
}
}
}
out:
slist_free( &tokens );
return status;
}
static int
nbibin_pages( fields *bibin, int n, str *intag, str *invalue, int level, param *pm, char *outtag, fields *bibout )
{
int fstatus, status = BIBL_OK;
str sp, tmp, ep;
char *p;
int i;
p = str_cstr( invalue );
if ( !p ) return BIBL_OK;
strs_init( &sp, &tmp, &ep, NULL );
while ( *p && *p!='-' ) {
str_addchar( &sp, *p );
p++;
}
if ( str_memerr( &sp ) ) {
status = BIBL_ERR_MEMERR;
goto out;
}
while ( *p=='-' ) p++;
while ( *p ) {
str_addchar( &tmp, *p );
p++;
}
if ( sp.len ) {
fstatus = fields_add( bibout, "PAGES:START", str_cstr( &sp ), LEVEL_MAIN );
if ( fstatus!=FIELDS_OK ) {
status = BIBL_ERR_MEMERR;
goto out;
}
}
if ( tmp.len ) {
for ( i=0; i<sp.len - tmp.len; ++i )
str_addchar( &ep, sp.data[i] );
str_strcat( &ep, &tmp );
fstatus = fields_add( bibout, "PAGES:STOP", str_cstr( &ep ), LEVEL_MAIN );
if ( fstatus!=FIELDS_OK ) {
status = BIBL_ERR_MEMERR;
goto out;
}
}
out:
strs_free( &sp, &tmp, &ep, NULL );
return status;
}
static void
nbib_report_notag( param *p, char *tag )
{
if ( p->verbose && strcmp( tag, "TY" ) ) {
if ( p->progname ) fprintf( stderr, "%s: ", p->progname );
fprintf( stderr, "Did not identify NBIB tag '%s'\n", tag );
}
}
static int
nbib_convertf( fields *bibin, fields *bibout, int reftype, param *p )
{
static int (*convertfns[NUM_REFTYPES])(fields *, int i, str *, str *, int, param *, char *, fields *) = {
[ 0 ... NUM_REFTYPES-1 ] = generic_null,
[ SIMPLE ] = generic_simple,
[ TITLE ] = generic_title,
[ PERSON ] = generic_person,
[ SKIP ] = generic_skip,
[ DATE ] = nbibin_date,
[ PAGES ] = nbibin_pages,
[ DOI ] = nbibin_doi,
};
int process, level, i, nfields, status = BIBL_OK;
str *intag, *invalue;
char *outtag;
nfields = fields_num( bibin );
for ( i=0; i<nfields; ++i ) {
intag = fields_tag( bibin, i, FIELDS_STRP );
if ( !translate_oldtag( intag->data, reftype, p->all, p->nall, &process, &level, &outtag ) ) {
nbib_report_notag( p, intag->data );
continue;
}
invalue = fields_value( bibin, i, FIELDS_STRP );
status = convertfns[ process ] ( bibin, i, intag, invalue, level, p, outtag, bibout );
if ( status!=BIBL_OK ) return status;
}
if ( status==BIBL_OK && p->verbose ) fields_report( bibout, stderr );
return status;
}