44ccfacbe3a3d4b300f80d48651c77837a4b571e
galt
Tue Apr 26 11:12:02 2022 -0700
SQL INJECTION Prevention Version 2 - this improves our methods by making subclauses of SQL that get passed around be both easy and correct to use. The way that was achieved was by getting rid of the obscure and not well used functions sqlSafefFrag and sqlDyStringPrintfFrag and replacing them with the plain versions of those functions, since these are not needed anymore. The new version checks for NOSQLINJ in unquoted %-s which is used to include SQL clauses, and will give an error the NOSQLINJ clause is not present, and this will automatically require the correct behavior by developers. sqlDyStringPrint is a very useful function, however because it was not enforced, users could use various other dyString functions and they operated without any awareness or checking for SQL correct use. Now those dyString functions are prohibited and it will produce an error if you try to use a dyString function on a SQL string, which is simply detected by the presence of the NOSQLINJ prefix.
diff --git src/hg/protein/spm6/spm6.c src/hg/protein/spm6/spm6.c
index 1b9ba1b..0f59f7c 100644
--- src/hg/protein/spm6/spm6.c
+++ src/hg/protein/spm6/spm6.c
@@ -1,293 +1,293 @@
/* spm6 - generates sorted.lis and knownGene0.tab for further KG duplicates processing */
/* Copyright (C) 2013 The Regents of the University of California
* See kent/LICENSE or http://genome.ucsc.edu/license/ for licensing information. */
#include "common.h"
#include "hCommon.h"
#include "hdb.h"
#define PDB_YES 90000
#define SWISSPROT_YES 8000
#define REFSEQREVIWED 700
#define REFSEQPROVISIONAL 60
FILE *o3, *o4, *o5;
int exStart[500], exEnd[500];
int aaStart[500], aaEnd[500];
void usage()
/* Explain usage and exit. */
{
errAbort(
"spm6 - generates sorted.lis and knownGene0.tab for further duplicates processing\n"
"usage:\n"
" spm6 xxxx db ro_db\n"
" xxxx is the release date of SWISS-PROT data\n"
" db is the genome under construction, e.g.: kgDB\n"
" ro_db is the target genome to read data from\n"
"example:\n"
" spm6 040115 kgDB hg16\n");
}
void getCDS(char *cdsStart, char *cdsEnd, char *exonCount, char *exonStarts_in, char *exonEnds_in)
{
int exCount;
char *sp, *ep;
char *chp;
int i, j;
int aalen;
int cdsS, cdsE;
int eS, eE;
int estLen;
char *exonStarts, *exonEnds;
estLen = 0;
exonStarts = strdup(exonStarts_in);
exonEnds = strdup(exonEnds_in);
sscanf(exonCount, "%d", &exCount);
sp = exonStarts;
ep = exonEnds;
sscanf(cdsStart, "%d", &cdsS);
sscanf(cdsEnd, "%d", &cdsE);
aalen = 0;
j=0;
for (i=0; i<exCount; i++)
{
chp = strstr(sp, ",");
*chp = '\0';
sscanf(sp, "%d", &(exStart[i]));
chp++;
sp = chp;
chp = strstr(ep, ",");
*chp = '\0';
sscanf(ep, "%d", &(exEnd[i]));
eS = exStart[i];
eE = exEnd[i];
if (cdsS > eS)
{
eS = cdsS;
}
if (cdsE < eE)
{
eE = cdsE;
}
if (eS > eE)
{
eS = 0;
eE = 0;
}
estLen = estLen + (eE-eS+1);
if (eS != eE)
{
aaStart[j] = aalen;
aaEnd[j] = aaStart[j] + (eE- eS +1)/3 -1;
aalen = aalen + (eE- eS +1)/3;
j++;
}
else
{
}
chp++;
ep = chp;
}
for (i=0; i<exCount; i++)
{
if (exEnd[i] < cdsS)
{
// exon is outside of CDS at right
// do nothing
}
else
{
if ((exStart[i] <= cdsS) && (cdsS <= exEnd[i]))
{
fprintf(o4, "%d,", cdsS);
}
else
{
if (exStart[i] <= cdsE)
{
fprintf(o4, "%d,", exStart[i]);
}
}
}
}
fprintf(o4, "\t");
for (i=0; i<exCount; i++)
{
if (exEnd[i] < cdsS)
{
// exon is outside of CDS at right
// do nothing
}
else
{
if ((exStart[i] <= cdsE) && (cdsE <= exEnd[i]))
{
fprintf(o4, "%d,", cdsE);
}
else
{
if (cdsE > exEnd[i])
{
fprintf(o4, "%d,", exEnd[i]);
}
}
}
}
fprintf(o4, "\t");
}
int main(int argc, char *argv[])
{
struct sqlConnection *conn2;
char proteinName[40], mrnaName[40];
char query2[256];
char cond_str[500];
FILE *inf;
char line[1000];
int alignmentID;
struct sqlResult *sr2;
char **row2;
char *name, *chrom, *strand, *txStart, *txEnd, *cdsStart, *cdsEnd,
*exonCount, *exonStarts, *exonEnds;
char *mrnaDate;
char *pdbID;
char *genomeDBname;
char *genomeReadOnly;
char *proteinDataDate;
char proteinsDB[40];
char *proteinDbSource;
int itxStart, itxEnd;
int transcriptLength;
int priority;
if (argc != 4) usage();
proteinDataDate = argv[1];
genomeDBname = argv[2];
genomeReadOnly = argv[3];
o3 = fopen("j.dat", "w");
o4 = fopen("jj.dat", "w");
o5 = fopen("align.lis", "w");
conn2= hAllocConn(genomeReadOnly);
inf = mustOpen("best.lis", "r");
alignmentID = 0;
while (fgets(line, 1000, inf) != NULL)
{
sscanf(line, "%s\t%s", proteinName, mrnaName);
priority = 0;
- sqlSafefFrag(cond_str, sizeof cond_str, "sp='%s'", proteinName);
+ sqlSafef(cond_str, sizeof cond_str, "sp='%s'", proteinName);
sprintf(proteinsDB, "proteins%s", proteinDataDate);
pdbID= sqlGetField(proteinsDB, "pdbSP", "pdb", cond_str);
if (pdbID != NULL)
{
priority = priority + PDB_YES;
}
- sqlSafefFrag(cond_str, sizeof cond_str, "displayID='%s'", proteinName);
+ sqlSafef(cond_str, sizeof cond_str, "displayID='%s'", proteinName);
proteinDbSource = sqlGetField(proteinsDB, "spXref2", "biodatabaseID", cond_str);
if (proteinDbSource == NULL)
{
printf("No proteinDbSource found for %s, skipping it ... \n", proteinName);
break;
}
if (strcmp(proteinDbSource, "1") == 0)
{
priority = priority + SWISSPROT_YES;
}
// get mRNA date
if ((mrnaDate = hGenbankModDate(mrnaName, conn2)) == NULL)
{
fprintf(stderr, "%s could not be found!!!\n", mrnaName);
exit(1);
}
sqlSafef(query2, sizeof query2, "select * from %sTemp.mrnaGene where name='%s';", genomeDBname, mrnaName);
sr2 = sqlMustGetResult(conn2, query2);
row2 = sqlNextRow(sr2);
while (row2 != NULL)
{
name = row2[0];
chrom = row2[1];
strand = row2[2];
txStart = row2[3];
txEnd = row2[4];
cdsStart= row2[5];
cdsEnd = row2[6];
exonCount = row2[7];
exonStarts= row2[8];
exonEnds = row2[9];
fprintf(o4, "%s\t", chrom);
getCDS(cdsStart, cdsEnd, exonCount, exonStarts, exonEnds);
sscanf(txStart, "%d", &itxStart);
sscanf(txEnd, "%d", &itxEnd);
transcriptLength = itxEnd - itxStart;
fprintf(o4, "%d\t%010d\t%s\t%s\t%s\t%d\n",
priority, transcriptLength, mrnaDate, name, proteinName, alignmentID);
fprintf(o5, "%d\t%d\t%s\t%s\t%s\n",
alignmentID, priority, name, proteinName, proteinDbSource);
fprintf(o3,"%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%d\n",
name,
chrom,
strand,
txStart,
txEnd,
cdsStart,
cdsEnd,
exonCount,
exonStarts,
exonEnds,
proteinName,
alignmentID);
alignmentID++;
row2 = sqlNextRow(sr2);
}
sqlFreeResult(&sr2);
}
hFreeConn(&conn2);
fclose(o3);
fclose(o4);
fclose(o5);
mustSystem("cat j.dat|sort|uniq >knownGene0.tab");
mustSystem("rm j.dat");
mustSystem("cat jj.dat|sort -r |uniq >sorted.lis");
mustSystem("rm jj.dat");
return(0);
}