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/pbCalDist/pbCalDist.c src/hg/protein/pbCalDist/pbCalDist.c index 99c1e10..6a64676 100644 --- src/hg/protein/pbCalDist/pbCalDist.c +++ src/hg/protein/pbCalDist/pbCalDist.c @@ -1,331 +1,331 @@ /* pbCalDist - 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 "hCommon.h" #include "hdb.h" #include "spDb.h" void usage() /* Explain usage and exit. */ { errAbort( "pbCalDist- Create tab delimited data files to be used by Proteome Browser stamps.\n" "usage:\n" " pbCalDist spDb protsDb taxn gnDb\n" " spDb is the name of SWISS-PROT database\n" " protsDb is the name of proteinsXXXXXX database\n" " taxn is the taxnomy number of the Taxonomy ID\n" " gnDb is the genome database name\n" "Example: pbCalDist sp031112 proteins031112 9606 hg16\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; 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]; } 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 main(int argc, char *argv[]) { struct sqlConnection *conn, *conn2; char query2[256]; struct sqlResult *sr2; char **row2; char cond_str[255]; char *proteinDatabaseName; /* example: sp031112 */ char *protDbName; /* example: proteins031112 */ char emptyStr[1] = {""}; FILE *o2; char *accession; char *aaSeq; char *chp; int i, j, len; int cCnt; char *answer, *answer2; double hydroSum; char *protDisplayId; int aaResCnt[30]; double aaResCntDouble[30]; char aaAlphabet[30]; int aaResFound; int totalResCnt; int molWtCnt; double molWt[100000]; int pIcnt; double pI[100000]; double aa_hydro[256]; int icnt, jExon, pcnt, ipcnt = 0; double aaLenDouble[100000]; double avgHydro[100000]; double cCountDouble[100000]; double exonCountDouble[100000]; double interProCountDouble[100000]; char *taxon; char *database; char *exonCnt; int interProCount; char *kgId; if (argc != 5) 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]; taxon = argv[3]; database = argv[4]; o2 = mustOpen("pepResDist.tab", "w"); conn = hAllocConn(database); conn2 = hAllocConn(database); for (j=0; j<23; j++) { aaResCnt[j] = 0; } icnt = jExon = pcnt = 0; pIcnt = 0; molWtCnt = 0; sqlSafef(query2, sizeof(query2), "select acc from %s.accToTaxon where taxon=%s;", proteinDatabaseName, taxon); sr2 = sqlMustGetResult(conn2, query2); row2 = sqlNextRow(sr2); while (row2 != NULL) { accession = row2[0]; - sqlSafefFrag(cond_str, sizeof(cond_str), "acc='%s'", accession); + sqlSafef(cond_str, sizeof(cond_str), "acc='%s'", accession); protDisplayId = sqlGetField(proteinDatabaseName, "displayId", "val", cond_str); - sqlSafefFrag(cond_str, sizeof(cond_str), "proteinID='%s'", protDisplayId); + sqlSafef(cond_str, sizeof(cond_str), "proteinID='%s'", protDisplayId); answer = sqlGetField(database, "knownGene", "name", cond_str); /* count InterPro domains */ if (answer != NULL) { - sqlSafefFrag(cond_str, sizeof(cond_str), "accession='%s'", accession); + sqlSafef(cond_str, sizeof(cond_str), "accession='%s'", accession); answer2 = sqlGetField(protDbName, "swInterPro", "count(*)", cond_str); if (answer2 != NULL) { interProCount = interProCount + atoi(answer2); interProCountDouble[ipcnt] = (double)(atoi(answer2)); ipcnt++; } else { printf("%s is not in InterPro DB.\n", accession);fflush(stdout); } } /* count exons, using coding exons from kgProtMap2 (KG-III) table */ - sqlSafefFrag(cond_str, sizeof(cond_str), "spID='%s'", accession); + sqlSafef(cond_str, sizeof(cond_str), "spID='%s'", accession); kgId = sqlGetField(database, "kgXref", "kgID", cond_str); - sqlSafefFrag(cond_str, sizeof(cond_str), "qName='%s'", kgId); + sqlSafef(cond_str, sizeof(cond_str), "qName='%s'", kgId); answer2 = sqlGetField(database, "kgProtMap2", "blockCount", cond_str); if (answer2 != NULL) { exonCnt = strdup(answer2); if (atoi(exonCnt) == 0) { errAbort("%s %s has 0 block count\n", accession, protDisplayId); } exonCountDouble[jExon] = (double)(atoi(exonCnt)); jExon++; } else { exonCnt = emptyStr; } /* process Mol Wt */ - sqlSafefFrag(cond_str, sizeof(cond_str), "accession='%s'", accession); + sqlSafef(cond_str, sizeof(cond_str), "accession='%s'", accession); answer2 = sqlGetField(database, "pepMwAa", "molWeight", cond_str); if (answer2 != NULL) { molWt[molWtCnt] = (double)(atof(answer2)); molWtCnt++; } /* process pI */ - sqlSafefFrag(cond_str, sizeof(cond_str), "accession='%s'", accession); + sqlSafef(cond_str, sizeof(cond_str), "accession='%s'", accession); answer2 = sqlGetField(database, "pepPi", "pI", cond_str); if (answer2 != NULL) { pI[pIcnt] = (double)(atof(answer2)); pIcnt++; } - sqlSafefFrag(cond_str, sizeof(cond_str), "acc='%s'", accession); + sqlSafef(cond_str, sizeof(cond_str), "acc='%s'", accession); aaSeq = sqlGetField(proteinDatabaseName, "protein", "val", cond_str); if (aaSeq == NULL) { errAbort("%s does not have protein sequence data in %s, aborting ...\n", accession, proteinDatabaseName); } len = strlen(aaSeq); 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) { warn("%c %d not a valid AA residue in %s:\n%s", *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++; row2 = sqlNextRow(sr2); } 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(exonCountDouble, jExon, 31, 0.0, 1.0, "pepExonCntDist.tab"); calDist(interProCountDouble, ipcnt, 16, 0.0, 1.0, "pepIPCntDist.tab"); sqlFreeResult(&sr2); hFreeConn(&conn); hFreeConn(&conn2); return(0); }