+++ /dev/null
-
-/* mysql_lib.c copyright (c) 2000 William R. Pearson */
-
-/* $Name: fa_34_26_5 $ - $Id: mysql_lib.c,v 1.21 2006/04/12 18:00:02 wrp Exp $ */
-
-/* functions for opening, reading, seeking a mySQL database */
-
-/*
- For the moment, this interface assumes that the file to be searched will
- be specified in a single, long, string with 4 parts:
-
- (1) a database open string. This string has four fields, separated by
- whitespace (' \t'):
- hostname:port dbname user password
-
- '--' dashes at the beginning of lines are ignored -
- thus the first line could be:
- -- hostname:port dbname user password
-
- (2) a database query string that will return an unique ID (not
- necessarily numberic, but it must be < 12 characters as libstr[12]
- is used) and a sequence string
-
- (2a) a series of mySQL commands that do not generate results
- starting with 'DO', followed by a select() statement.
-
- (3) a database select string that will return a description
- given a unique ID
-
- (4) a database select string that well return a sequence given a
- unique ID
-
- Lines (3) and (4) are not required for pv34comp* libraries, but
- line (2) must generate a complete description as well as a sequence.
-
-
- 18-July-2001
- Additional syntax has been added to support multiline SQL queries.
-
- If the host line begins with '+', then the SQL is openned on the same
- connection as the previous SQL file.
-
- If the host line contains '-' just before the terminal ';', then
- the file will not produce any output.
-
- This string can contain "\n". ";" are used to separate the four
- functions, which must be specified in the order shown above.
- The last (fourth) query must terminate with a ';' */
-
-#include <stdio.h>
-#include <stdlib.h>
-#include <string.h>
-#include <ctype.h>
-
-#include <mysql.h>
-#define MYSQL_LIB 16
-
-#include "defs.h"
-#include "mm_file.h"
-
-#define XTERNAL
-#include "uascii.h"
-#define EOSEQ 0
-/* #include "upam.h" */
-
-#ifdef SUPERFAMNUM
-int sfnum[10], nsfnum;
-#endif
-
-int mysql_getlib(unsigned char *, int, char *, int, fseek_t *, int *, struct lmf_str *, long *);
-void mysql_ranlib(char *, int, fseek_t, char *, struct lmf_str *m_fd);
-
-#define MYSQL_BUF 4096
-
-struct lmf_str *
-mysql_openlib(char *sname, int ldnaseq, int *sascii) {
- FILE *sql_file;
- char *tmp_str, *ttmp_str;
- int tmp_str_len;
- char *bp, *bps, *bdp, *tp, tchar;
- int i, qs_len, qqs_len;
- char *sql_db, *sql_host, *sql_dbname, *sql_user, *sql_pass;
- char *sql_do;
- int sql_do_cnt;
- int sql_port;
- struct lmf_str *m_fptr;
-
- /* if (sql_reopen) return NULL; - should not be called for re-open */
-
- tmp_str_len = MYSQL_BUF;
- if ((tmp_str=(char *)calloc(tmp_str_len,sizeof(char)))==NULL) {
- fprintf(stderr,"cannot allocate %d for mySQL buffer\n",tmp_str_len);
- return NULL;
- }
-
- if (sname[0] == '%') {
- strncpy(tmp_str,sname+1,tmp_str_len);
- tmp_str[sizeof(tmp_str)-1]='\0';
- }
- else {
- if ((sql_file=fopen(sname,"r"))==NULL) {
- fprintf(stderr," cannot open mySQL file: %s\n",sname);
- return NULL;
- }
-
- if ((qs_len=fread(tmp_str,sizeof(char),tmp_str_len-1,sql_file))<=0) {
- fprintf(stderr," cannot read mySQL file: %s\n",sname);
- return NULL;
- }
- else {
- tmp_str[qs_len]='\0';
- qqs_len = qs_len;
- while (qqs_len >= tmp_str_len-1) {
- tmp_str_len += MYSQL_BUF;
- if ((tmp_str=(char *)realloc(tmp_str,tmp_str_len))==NULL) {
- fprintf(stderr,
- " cannot reallocate %d for mySQL buffer\n",tmp_str_len);
- return NULL;
- }
- ttmp_str = &tmp_str[qqs_len];
- if ((qs_len=fread(ttmp_str,sizeof(char),MYSQL_BUF,sql_file))<0) {
- fprintf(stderr," cannot read mySQL file: %s\n",sname);
- return NULL;
- }
- ttmp_str[qs_len]='\0';
- qqs_len += qs_len;
- }
- }
- fclose(sql_file);
- }
-
- bps = tmp_str;
- if ((bp=strchr(bps,';'))!=NULL) {
- *bp='\0';
- if ((sql_db=calloc(strlen(bps)+1,sizeof(char)))==NULL) {
- fprintf(stderr, " cannot allocate space for database name [%d], %s\n",
- strlen(bps),bps);
- return NULL;
- }
- /* have database name, parse the fields */
- else {
- strcpy(sql_db,bps); /* strcpy OK because allocated strlen(bps) */
- bps = bp+1; /* points to next char after ';' */
- while (isspace(*bps)) bps++;
- *bp=';'; /* replace ; */
- bp = sql_db;
- while (*bp=='-') {*bp++ = ' ';}
- sql_host = strtok(bp," \t\n");
- sql_dbname = strtok(NULL," \t\n");
- sql_user = strtok(NULL," \t\n");
- sql_pass = strtok(NULL," \t\n");
- if ((tp=strchr(sql_host,':'))!=NULL) {
- *tp='\0';
- sql_port=atoi(tp+1);
- }
- else sql_port = 0;
- }
- }
- else {
- fprintf(stderr," cannot find database fields:\n%s\n",tmp_str);
- return NULL;
- }
-
- /* we have all the info we need to open a database, allocate lmf_str */
- if ((m_fptr = (struct lmf_str *)calloc(1,sizeof(struct lmf_str)))==NULL) {
- fprintf(stderr," cannot allocate lmf_str (%ld) for %s\n",
- sizeof(struct lmf_str),sname);
- return NULL;
- }
-
- /* have our struct, initialize it */
-
- strncpy(m_fptr->lb_name,sname,MAX_FN);
- m_fptr->lb_name[MAX_FN-1]='\0';
-
- m_fptr->sascii = sascii;
-
- m_fptr->sql_db = sql_db;
- m_fptr->getlib = mysql_getlib;
- m_fptr->ranlib = mysql_ranlib;
- m_fptr->mm_flg = 0;
- m_fptr->sql_reopen = 0;
- m_fptr->lb_type = MYSQL_LIB;
-
- /* now open the database, if necessary */
- if ((m_fptr->mysql_conn=mysql_init(NULL))==NULL) {
- fprintf(stderr,"*** Error - mysql_init\n");
- goto error_r;
- }
-
- if (mysql_real_connect(m_fptr->mysql_conn,
- sql_host,sql_user,sql_pass,
- sql_dbname,
- sql_port,
- NULL,
- 0)==NULL)
- {
- fprintf(stderr,"*** Error %u - could not open database:\n%s\n%s",
- mysql_errno(m_fptr->mysql_conn),tmp_str,
- mysql_error(m_fptr->mysql_conn));
- goto error_r;
- }
- else {
- fprintf(stderr," Database %s opened on %s\n",sql_dbname,sql_host);
- }
-
- /* check for 'DO' command - copy to 'DO' string */
- while (*bps == '-') { *bps++=' ';}
- if (isspace(bps[-1]) && toupper(bps[0])=='D' &&
- toupper(bps[1])=='O' && isspace(bps[2])) {
- /* have some 'DO' commands */
- /* check where the end of the last DO statement is */
-
- sql_do_cnt = 1; /* count up the number of 'DO' statements for later */
- bdp=bps+3;
- while ((bp=strchr(bdp,';'))!=NULL) {
- tp = bp+2; /* skip ;\n */
- while (isspace(*tp) || *tp == '-') {*tp++ = ' ';}
- if (toupper(*tp)=='D' && toupper(tp[1])=='O' && isspace(tp[2])) {
- sql_do_cnt++; /* count the DO statements */
- bdp = tp+3; /* move to the next DO statement */
- }
- else break;
- }
- if (bp != NULL) { /* end of the last DO, begin of select */
- tchar = *(bp+1);
- *(bp+1)='\0'; /* terminate DO strings */
- if ((sql_do = calloc(strlen(bps)+1, sizeof(char)))==NULL) {
- fprintf(stderr," cannot allocate %d for sql_do\n",strlen(bps));
- goto error_r;
- }
- else {
- strcpy(sql_do,bps);
- *(bp+1)=tchar; /* replace missing ';' */
- }
- bps = bp+1;
- while (isspace(*bps)) bps++;
- }
- else {
- fprintf(stderr," terminal ';' not found: %s\n",bps);
- goto error_r;
- }
- /* all the DO commands are in m_fptr->sql_do in the form:
- DO command1; DO command2; DO command3; */
- bdp = sql_do;
- while (sql_do_cnt-- && (bp=strchr(bdp,';'))!=NULL) {
- /* do the mysql statement on bdp+3 */
- /* check for error */
- *bp='\0';
- if (mysql_query(m_fptr->mysql_conn,bdp+3)) {
- fprintf(stderr,"*** Error %u - query failed:\n%s\n%s\n",
- mysql_errno(m_fptr->mysql_conn), bdp+3, mysql_error(m_fptr->mysql_conn));
- goto error_r;
- }
- *bp=';';
- bdp = bp+1;
- while (isspace(*bdp)) bdp++;
- }
- }
-
- /* copy 1st query field */
- if ((bp=strchr(bps,';'))!=NULL) {
- *bp='\0';
- if ((m_fptr->sql_query=calloc(strlen(bps)+1,sizeof(char)))==NULL) {
- fprintf(stderr, " cannot allocate space for query string [%d], %s\n",
- strlen(bps),bps);
- goto error_r;
- }
- /* have query, copy it */
- else {
- strcpy(m_fptr->sql_query,bps);
- *bp=';'; /* replace ; */
- bps = bp+1;
- while(isspace(*bps)) bps++;
- }
- }
- else {
- fprintf(stderr," cannot find database query field:\n%s\n",tmp_str);
- goto error_r;
- }
-
- /* copy get_desc field */
- if ((bp=strchr(bps,';'))!=NULL) {
- *bp='\0';
- if ((m_fptr->sql_getdesc=calloc(strlen(bps)+1,sizeof(char)))==NULL) {
- fprintf(stderr, " cannot allocate space for database name [%d], %s\n",
- strlen(bps),bps);
- goto error_r;
- }
- /* have get_desc, copy it */
- else {
- strcpy(m_fptr->sql_getdesc,bps);
- *bp=';'; /* replace ; */
- bps = bp+1;
- while(isspace(*bps)) bps++;
- }
- }
- else {
- fprintf(stderr," cannot find getdesc field:\n%s\n",tmp_str);
- goto error_r;
- }
-
- if ((bp=strchr(bps,';'))!=NULL) { *bp='\0';}
-
- if ((m_fptr->sql_getseq=calloc(strlen(bps)+1,sizeof(char)))==NULL) {
- fprintf(stderr, " cannot allocate space for database name [%d], %s\n",
- strlen(bps),bps);
- goto error_r;
- }
-
- if (strlen(bps) > 0) {
- strcpy(m_fptr->sql_getseq,bps);
- }
- else {
- fprintf(stderr," cannot find getseq field:\n%s\n",tmp_str);
- return 0;
- }
- if (bp!=NULL) *bp=';';
-
- /* now do the query */
-
- if (mysql_query(m_fptr->mysql_conn,m_fptr->sql_query)) {
- fprintf(stderr,"*** Error %u - query failed:\n%s\n%s\n",
- mysql_errno(m_fptr->mysql_conn), m_fptr->sql_query, mysql_error(m_fptr->mysql_conn));
- goto error_r;
- }
-
- if ((m_fptr->mysql_res = mysql_use_result(m_fptr->mysql_conn)) == NULL) {
- fprintf(stderr,"*** Error = use result failed\n%s\n",
- mysql_error(m_fptr->mysql_conn));
- goto error_r;
- }
- return m_fptr;
-
- error_r:
- free(m_fptr->sql_getseq);
- free(m_fptr->sql_getdesc);
- free(m_fptr->sql_query);
- free(m_fptr);
- free(sql_db);
- return NULL;
-}
-
-struct lmf_str *
-mysql_reopen(struct lmf_str *m_fptr) {
- m_fptr->sql_reopen = 1;
- return m_fptr;
-}
-
-void
-mysql_closelib(struct lmf_str *m_fptr) {
-
- if (m_fptr == NULL) return;
- if (m_fptr->mysql_res != NULL)
- mysql_free_result(m_fptr->mysql_res);
- mysql_close(m_fptr->mysql_conn);
- m_fptr->sql_reopen=0;
-}
-
-/*
-static char *sql_seq = NULL, *sql_seqp;
-static int sql_seq_len;
-static MYSQL_ROW sql_row;
-*/
-
-int
-mysql_getlib( unsigned char *seq,
- int maxs,
- char *libstr,
- int n_libstr,
- fseek_t *libpos,
- int *lcont,
- struct lmf_str *lm_fd,
- long *l_off)
-{
- register unsigned char *cp, *seqp;
- register int *ap;
- unsigned char *seqm, *seqm1;
- char *bp;
- /* int l_start, l_stop, len; */
-
- seqp = seq;
- seqm = &seq[maxs-9];
- seqm1 = seqm-1;
-
- ap = lm_fd->sascii;
-
-#ifdef SUPERFAMNUM
- sfnum[0]=nsfnum = 0;
-#endif
-
- if (*lcont==0) {
- /* get a row, with UID, sequence */
- *l_off = 1;
- if ((lm_fd->mysql_row =mysql_fetch_row(lm_fd->mysql_res))!=NULL) {
- *libpos=(fseek_t)atol(lm_fd->mysql_row[0]);
-
- /* for @P:1-n removed */
- /*
- if ((bp=strchr(lm_fd->mysql_row[2],'@'))!=NULL &&
- !strncmp(bp+1,"P:",2)) {
- sscanf(bp+3,"%d-%d",&l_start,&l_stop)
- l_start--;
- if (l_start < 0) l_start=0;
- if (l_stop > (len=strlen(lm_fd->mysql_row[1]))) l_stop= len-1;
- lm_fd->sql_seqp = lm_fd->mysql_row[1];
- lm_fd->sql_seqp[l_stop]='\0';
- lm_fd->sql_seqp += l_start;
- */
-
- if (lm_fd->mysql_row[2] == NULL) {
- fprintf(stderr," NULL comment at: [%s] %ld\n",
- lm_fd->mysql_row[0],*libpos);
- }
- else if ((bp=strchr(lm_fd->mysql_row[2],'@'))!=NULL &&
- !strncmp(bp+1,"C:",2)) sscanf(bp+3,"%ld",l_off);
- else *l_off = 1;
-
- lm_fd->sql_seqp = lm_fd->mysql_row[1];
-
- /* because of changes in mysql_ranlib(), it is essential that
- libstr return the unique identifier; thus we must use
- sql_row[0], not sql_row[2]. Using libstr as the UID allows
- one to use any UID, not just numeric ones. *libpos is not
- used for mysql libraries.
- */
-
- if (n_libstr <= MAX_UID) {
- /* the normal case returns only GID/sequence */
- strncpy(libstr,lm_fd->mysql_row[0],MAX_UID-1);
- libstr[MAX_UID-1]='\0';
- }
- else {
- /* here we do not use the UID in libstr, because we are not
- going back into the db */
- /* the PVM case also returns a long description */
- if (lm_fd->mysql_row[2]!=NULL) {
- strncpy(libstr,lm_fd->mysql_row[2],n_libstr-1);
- }
- else {
- strncpy(libstr,lm_fd->mysql_row[0],n_libstr-1);
- }
- libstr[n_libstr-1]='\0';
- }
- }
- else {
- mysql_free_result(lm_fd->mysql_res);
- lm_fd->mysql_res=NULL;
- *lcont = 0;
- *seqp = EOSEQ;
- return -1;
- }
- }
-
- for (cp=(unsigned char *)lm_fd->sql_seqp; seqp<seqm1 && *cp; ) {
- if ((*seqp++=ap[*cp++])<NA &&
- (*seqp++=ap[*cp++])<NA &&
- (*seqp++=ap[*cp++])<NA &&
- (*seqp++=ap[*cp++])<NA &&
- (*seqp++=ap[*cp++])<NA &&
- (*seqp++=ap[*cp++])<NA &&
- (*seqp++=ap[*cp++])<NA &&
- (*seqp++=ap[*cp++])<NA &&
- (*seqp++=ap[*cp++])<NA &&
- (*seqp++=ap[*cp++])<NA) continue;
- --seqp;
- if (*(cp-1)==0) break;
- }
- lm_fd->sql_seqp = (char *)cp;
-
- if (seqp>=seqm1) (*lcont)++;
- else {
- *lcont=0;
- if (lm_fd->sql_reopen) {
- mysql_free_result(lm_fd->mysql_res);
- lm_fd->mysql_res = NULL;
- }
- }
-
- *seqp = EOSEQ;
- /* if ((int)(seqp-seq)==0) return 1; */
- return (int)(seqp-seq);
-}
-
-void
-mysql_ranlib(char *str,
- int cnt,
- fseek_t libpos,
- char *libstr,
- struct lmf_str *lm_fd
- )
-{
- char tmp_query[1024], tmp_val[20];
- char *bp;
-
- str[0]='\0';
-
- /* put the UID into the query string - cannot use sprintf because of
- "%' etc */
-
- /* sprintf(tmp_query,lm_fd->sql_getdesc,libpos); */
-
- if ((bp=strchr(lm_fd->sql_getdesc,'#'))==NULL) {
- fprintf(stderr, "no GID position in %s\n",lm_fd->sql_getdesc);
- goto next1;
- }
- else {
- *bp = '\0';
- strncpy(tmp_query,lm_fd->sql_getdesc,sizeof(tmp_query));
- tmp_query[sizeof(tmp_query)-1]='\0';
- /* sprintf(tmp_val,"%ld",(long)libpos); */
- strncat(tmp_query,libstr,sizeof(tmp_query)-1);
- strncat(tmp_query,bp+1,sizeof(tmp_query)-1);
- *bp='#';
- lm_fd->lpos = libpos;
- }
-
- /* fprintf(stderr," requesting: %s\n",tmp_query); */
-
- if (lm_fd->mysql_res !=NULL) {
- mysql_free_result(lm_fd->mysql_res);
- lm_fd->mysql_res = NULL;
- }
-
- if (mysql_query(lm_fd->mysql_conn,tmp_query)) {
- fprintf(stderr,"*** Error - query failed:\n%s\n%s\n",tmp_query,
- mysql_error(lm_fd->mysql_conn));
- sprintf(str,"gi|%ld ***Error - query failed***",(long)libpos);
- goto next1;
- }
-
- if ((lm_fd->mysql_res = mysql_use_result(lm_fd->mysql_conn)) == NULL) {
-/* fprintf(stderr,"*** Error = use result failed\n%s\n",
- mysql_error(lm_fd->mysql_conn)); */
- sprintf(str,"gi|%ld ***use result failed***",(long)libpos);
- goto next0;
- }
-
- /* have the description */
- if ((lm_fd->mysql_row = mysql_fetch_row(lm_fd->mysql_res))==NULL) {
- /* fprintf(stderr," cannot fetch description: %s\n",tmp_query); */
- sprintf(str,"gi|%ld ***cannot fetch description***",(long)libpos);
- goto next0;
- }
-
- if (lm_fd->mysql_row[1] != NULL) strncpy(str,lm_fd->mysql_row[1],cnt-1);
- else strncpy(str,lm_fd->mysql_row[0],cnt-1);
- str[cnt-1]='\0';
- while (strlen(str) < cnt-1 &&
- (lm_fd->mysql_row = mysql_fetch_row(lm_fd->mysql_res))!=NULL) {
- strncat(str," ",cnt-2-strlen(str));
- if (lm_fd->mysql_row[1]!=NULL)
- strncat(str,lm_fd->mysql_row[1],cnt-2-strlen(str));
- else break;
- }
-
- str[cnt-1]='\0';
- if ((bp = strchr(str,'\r'))!=NULL) *bp='\0';
- if ((bp = strchr(str,'\n'))!=NULL) *bp='\0';
-
- next0:
- mysql_free_result(lm_fd->mysql_res);
- next1:
- lm_fd->mysql_res = NULL;
-
- /* get the sequence, set up for mysql_getseq() */
- /* put the UID into the query string */
-
- if ((bp=strchr(lm_fd->sql_getseq,'#'))==NULL) {
- fprintf(stderr, "no GID position in %s\n",lm_fd->sql_getseq);
- return;
- }
- else {
- *bp = '\0';
- strncpy(tmp_query,lm_fd->sql_getseq,sizeof(tmp_query));
- tmp_query[sizeof(tmp_query)-1]='\0';
- /* sprintf(tmp_val,"%ld",(long)libpos); */
- strncat(tmp_query,libstr,sizeof(tmp_query));
- strncat(tmp_query,bp+1,sizeof(tmp_query));
- *bp='#';
- }
-
- if (mysql_query(lm_fd->mysql_conn,tmp_query)) {
- fprintf(stderr,"*** Error - query failed:\n%s\n%s\n",tmp_query,
- mysql_error(lm_fd->mysql_conn));
- }
-
- if ((lm_fd->mysql_res = mysql_use_result(lm_fd->mysql_conn)) == NULL) {
- fprintf(stderr,"*** Error = use result failed\n%s\n",
- mysql_error(lm_fd->mysql_conn));
- }
-}
git://source.jalview.org / jabaws.git / blobdiff