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/pbCalDistGlobal/pbCalDistGlobal.c src/hg/protein/pbCalDistGlobal/pbCalDistGlobal.c
index 8b9a6ac..a8ccf63 100644
--- src/hg/protein/pbCalDistGlobal/pbCalDistGlobal.c
+++ src/hg/protein/pbCalDistGlobal/pbCalDistGlobal.c
@@ -1,299 +1,300 @@
/* pbCalDistGlobal - Create tab delimited data files to be used by Proteome Browser stamps */
/* 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 "hash.h"
#include "hCommon.h"
#include "hdb.h"
#include "spDb.h"
#include "linefile.h"
#define MAX_PROTEIN_CNT 10000000
void usage()
/* Explain usage and exit. */
{
errAbort(
"pbCalDistGlobal- Create tab delimited data files to be used by Proteome Browser stamps.\n"
"usage:\n"
" pbCalDistGlobal spDb protsDb\n"
" spDb is the name of SWISS-PROT database\n"
" protsDb is the name of proteinsXXXXXX database\n"
"Example: pbCalDistGlobal sp040915 proteins040915\n");
}
int calDist(double *measure, int nInput, int nDist, double xMin, double xDelta, char *oFileName)
/* calculate histogram distribution of a double array of nInput elements */
{
int distCnt[1000];
double xDist[1000];
FILE *o3;
int i,j;
int highestCnt, totalCnt;
int lowCnt, hiCnt;
printf("processing %s\n", oFileName);fflush(stdout);
assert(nDist < ArraySize(distCnt));
o3 = mustOpen(oFileName, "w");
for (j=0; j<=(nDist+1); j++)
{
distCnt[j] = 0;
xDist[j] = xMin + xDelta * (double)j;
}
lowCnt = 0;
hiCnt = 0;
for (i=0; i<nInput; i++)
{
/* count values below xmin */
if (measure[i] < xDist[0])
{
lowCnt++;
}
for (j=0; j<nDist; j++)
{
if ((measure[i] >= xDist[j]) && (measure[i] < xDist[j+1]))
{
distCnt[j]++;
}
}
/* count values above xmax */
if (measure[i] >= xDist[nDist])
{
hiCnt++;
}
}
highestCnt = 0;
totalCnt = 0;
for (j=0; j<nDist; j++)
{
if (distCnt[j] > highestCnt) highestCnt = distCnt[j];
totalCnt = totalCnt + distCnt[j];
}
printf("\tdisplayedCnt=%d lowCnt=%d hiCnt=%d total=%d\n", totalCnt, lowCnt, hiCnt,
totalCnt + hiCnt + lowCnt);fflush(stdout);
totalCnt = totalCnt + hiCnt + lowCnt;
if (totalCnt != nInput)
errAbort("nInput %d is not equal totalCnt %d, aborting ...\n", nInput, totalCnt);
for (j=0; j<nDist; j++)
{
fprintf(o3, "%f\t%d\n", xDist[j], distCnt[j]);
}
carefulClose(&o3);
return(highestCnt);
}
int hashCountMatches(struct hash *hash, char *key)
/* Return numbers of hits to key in hash. */
{
int count = 0;
struct hashEl *hel;
for (hel = hashLookup(hash, key); hel != NULL; hel = hashLookupNext(hel))
++count;
return count;
}
double molWt[MAX_PROTEIN_CNT];
double pI[MAX_PROTEIN_CNT];
double aaLenDouble[MAX_PROTEIN_CNT];
double avgHydro[MAX_PROTEIN_CNT];
double cCountDouble[MAX_PROTEIN_CNT];
double exonCountDouble[MAX_PROTEIN_CNT];
double pfamCountDouble[MAX_PROTEIN_CNT];
double interProCountDouble[MAX_PROTEIN_CNT];
int main(int argc, char *argv[])
{
struct sqlConnection *conn2, *conn3;
char query2[256];
struct sqlResult *sr2;
char **row2;
char *proteinDatabaseName; /* example: sp031112 */
char *protDbName; /* example: proteins031112 */
FILE *o2;
char *accession;
char *aaSeq;
char *chp;
int i, j, len;
int cCnt;
double hydroSum;
int aaResCnt[30];
double aaResCntDouble[30];
char aaAlphabet[30];
int aaResFound;
int totalResCnt;
int molWtCnt;
int pIcnt;
char *database;
int aaSize;
double aa_hydro[256];
int icnt, jExon, pcnt;
int ipcnt={0};
int interProCount;
if (argc != 3) usage();
strcpy(aaAlphabet, "WCMHYNFIDQKRTVPGEASLXZB");
/* Ala: 1.800 Arg: -4.500 Asn: -3.500 Asp: -3.500 Cys: 2.500 Gln: -3.500 */
aa_hydro['A'] = 1.800;
aa_hydro['R'] = -4.500;
aa_hydro['N'] = -3.500;
aa_hydro['D'] = -3.500;
aa_hydro['C'] = 2.500;
aa_hydro['Q'] = -3.500;
/* Glu: -3.500 Gly: -0.400 His: -3.200 Ile: 4.500 Leu: 3.800 Lys: -3.900 */
aa_hydro['E'] = -3.500;
aa_hydro['G'] = -0.400;
aa_hydro['H'] = -3.200;
aa_hydro['I'] = 4.500;
aa_hydro['L'] = 3.800;
aa_hydro['K'] = -3.900;
/* Met: 1.900 Phe: 2.800 Pro: -1.600 Ser: -0.800 Thr: -0.700 Trp: -0.900 */
aa_hydro['M'] = 1.900;
aa_hydro['F'] = 2.800;
aa_hydro['P'] = -1.600;
aa_hydro['S'] = -0.800;
aa_hydro['T'] = -0.700;
aa_hydro['W'] = -0.900;
/* Tyr: -1.300 Val: 4.200 Asx: -3.500 Glx: -3.500 Xaa: -0.490 */
aa_hydro['Y'] = -1.300;
aa_hydro['V'] = 4.200;
proteinDatabaseName = argv[1];
protDbName = argv[2];
database = argv[2];
o2 = mustOpen("pepResDist.tab", "w");
conn2 = sqlConnect(database);
conn3 = sqlConnect(protDbName);
for (j=0; j<23; j++)
{
aaResCnt[j] = 0;
}
icnt = jExon = pcnt = 0;
pIcnt = 0;
molWtCnt = 0;
/* Build up hash of swInterPro accessions. We'll use this to count domains. */
struct hash *swInterProHash = hashNew(23);
{
- struct sqlResult *sr = sqlGetResult(conn3, NOSQLINJ "select accession from swInterPro");
+ sqlSafef(query2, sizeof(query2), "select accession from swInterPro");
+ struct sqlResult *sr = sqlGetResult(conn3, query2);
char **row;
while ((row = sqlNextRow(sr)) != NULL)
hashAdd(swInterProHash, row[0], NULL);
sqlFreeResult(&sr);
}
sqlSafef(query2, sizeof(query2),
"select info.acc, molWeight, aaSize, protein.val, Pi from %s.info, %s.protein, %s.pepPi where info.acc=protein.acc and pepPi.accession=protein.acc",
proteinDatabaseName, proteinDatabaseName, database);
sr2 = sqlMustGetResult(conn2, query2);
while ((molWtCnt < MAX_PROTEIN_CNT) && (row2 = sqlNextRow(sr2)) != NULL)
{
accession = row2[0];
molWt[molWtCnt] = (double)(atof(row2[1]));
molWtCnt++;
aaSize = atoi(row2[2]);
aaSeq = row2[3];
pI[pIcnt] = (double)(atof(row2[4]));
pIcnt++;
/* count InterPro domains */
int interProDomains = hashCountMatches(swInterProHash, accession);
interProCount += interProDomains;
interProCountDouble[ipcnt] = interProDomains;
++ipcnt;
len = aaSize;
chp = aaSeq;
for (i=0; i<len; i++)
{
aaResFound = 0;
for (j=0; j<23; j++)
{
if (*chp == aaAlphabet[j])
{
aaResFound = 1;
aaResCnt[j] ++;
}
}
if (!aaResFound)
{
verbose(2, "%c %d not a valid AA residue in %s:\n%s\n", *chp, *chp, accession, aaSeq);
}
chp++;
}
/* calculate hydrophobicity */
chp = aaSeq;
cCnt = 0;
hydroSum = 0;
for (i=0; i<len; i++)
{
hydroSum = hydroSum + aa_hydro[(int)(*chp)];
/* count Cysteines */
if ((*chp == 'C') || (*chp == 'c'))
{
cCnt ++;
}
chp++;
}
aaLenDouble[icnt] = len;
cCountDouble[icnt] = (double)cCnt;
avgHydro[icnt] = hydroSum/(double)len;
icnt++;
if (icnt >= MAX_PROTEIN_CNT)
errAbort("Too many proteins - please set MAX_PROTEIN_CNT to be more than %d\n", MAX_PROTEIN_CNT);
if ((icnt % 10000) == 0)
{
printf("%d done.\n", icnt);
}
}
sqlFreeResult(&sr2);
sqlDisconnect(&conn2);
sqlDisconnect(&conn3);
totalResCnt = 0;
for (i=0; i<23; i++)
{
totalResCnt = totalResCnt + aaResCnt[i];
}
/* write out residue count distribution */
for (i=0; i<20; i++)
{
aaResCntDouble[i] = ((double)aaResCnt[i])/((double)totalResCnt);
fprintf(o2, "%d\t%f\n", i+1, (float)aaResCntDouble[i]);
}
fprintf(o2, "%d\t%f\n", i+1, 0.0);
carefulClose(&o2);
/* calculate and write out various distributions */
calDist(molWt, molWtCnt, 21, 0.0, 10000.0,"pepMolWtDist.tab");
calDist(pI, pIcnt, 61, 3.0, 0.2, "pepPiDist.tab");
calDist(avgHydro, icnt, 41, -2.0, 0.1, "pepHydroDist.tab");
calDist(cCountDouble, icnt, 51, 0.0, 1.0, "pepCCntDist.tab");
calDist(interProCountDouble,ipcnt, 16, 0.0, 1.0, "pepIPCntDist.tab");
return(0);
}