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/makeDb/outside/hgJaxQtl/hgJaxQtl.c src/hg/makeDb/outside/hgJaxQtl/hgJaxQtl.c index acdadb1..0c307e8 100644 --- src/hg/makeDb/outside/hgJaxQtl/hgJaxQtl.c +++ src/hg/makeDb/outside/hgJaxQtl/hgJaxQtl.c @@ -1,251 +1,251 @@ /* hgJaxQtl - generate the bed file for jaxQTL3 table using the mySQL table jaxQtlRaw as input. */ /* 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" void usage() /* Explain usage and exit. */ { errAbort( "hgJaxQtl - generate bed file for jaxQTL3 table \n" " using the table jaxQtlRaw as input\n" " output file is jaxQTL3.tab.\n" "usage:\n" " hgJaxQtl xxxx\n" " xxxx is the database\n" "example: hgJaxQtl mm5\n"); } /* get valid identNo from stsMapMouseNew table, return NULL if not found */ char *getStsId(struct sqlConnection *conn3, char *database, char *stsName) { char cond_str[255]; char *identNo; -sqlSafefFrag(cond_str, sizeof(cond_str), "name='%s'", stsName); +sqlSafef(cond_str, sizeof(cond_str), "name='%s'", stsName); identNo = sqlGetField(database, "stsMapMouseNew", "identNo", cond_str); if (identNo == NULL) { /* check to see if stsAlias has it */ - sqlSafefFrag(cond_str, sizeof(cond_str), "alias='%s'", stsName); + sqlSafef(cond_str, sizeof(cond_str), "alias='%s'", stsName); identNo = sqlGetField(database, "stsAlias", "identNo", cond_str); /* now make sure that stsMapMouseNew has an entry for this identNo */ if (identNo != NULL) { - sqlSafefFrag(cond_str, sizeof(cond_str), "identNo=%s", identNo); + sqlSafef(cond_str, sizeof(cond_str), "identNo=%s", identNo); identNo = sqlGetField(database, "stsMapMouseNew", "identNo", cond_str); } } return(identNo); } int main(int argc, char *argv[]) { struct sqlConnection *conn2, *conn3; char query2[256], query3[256]; struct sqlResult *sr2, *sr3; char **row2, **row3; FILE *outF; char *database; char *mgiID, *name, *description, *flank1, *flank2, *peak; char *peakChrom, *peakChromStart, *peakChromEnd; char *identNo; char *flanks[2]; char *qtlChrom, *qtlChromStart, *qtlChromEnd, *qtlName, *qtlScore, *qtlStrand; char *qtlThickStart, *qtlThickEnd, *qtlMarker, *qtlMgiID, *qtlDescription, *qtlCMScore; char *flankChrom, *flankChromStart, *flankChromEnd; char na[10] = {""}; char zero[10] = {"0"}; int qtlValid; int pos; int iFlank; int regionStart, regionEnd; if (argc != 2) usage(); database = argv[1]; /* the following fields are not available yet */ qtlScore = strdup("0"); qtlCMScore = strdup("0"); qtlStrand = strdup("."); outF = fopen("jaxQTL3.tab", "w"); conn2= hAllocConn(database); conn3= hAllocConn(database); sqlSafef(query2, sizeof query2, "select * from %s.jaxQtlRaw", database); sr2 = sqlMustGetResult(conn2, query2); row2 = sqlNextRow(sr2); while (row2 != NULL) { mgiID = row2[0]; name = row2[1]; description = row2[2]; flank1 = row2[4]; flank2 = row2[5]; peak = row2[6]; flanks[0] = flank1; flanks[1] = flank2; qtlValid = 0; /* this record is not valid until we found something to put out */ qtlMgiID = mgiID; qtlName = name; qtlDescription = description; /* set default values */ qtlChrom = strdup(na); qtlChromStart = zero; qtlChromEnd = zero; qtlThickStart = zero; qtlThickEnd = zero; qtlMarker = na; regionStart = 0; regionEnd = 0; peakChrom = strdup(na); /* process peak marker */ if (!sameWord(peak, "")) { identNo = getStsId(conn3, database, peak); /* if getStsId result is not NULL, there exist an entry in stsMapMouseNew */ if (identNo != NULL) { qtlValid = 1; sqlSafef(query3, sizeof query3, "select * from %s.stsMapMouseNew where identNo=%s", database, identNo); sr3 = sqlMustGetResult(conn3, query3); row3 = sqlNextRow(sr3); /* only a few markers have mulitple answers, so just grab the first one */ peakChrom = strdup(row3[0]); peakChromStart = strdup(row3[1]); peakChromEnd = strdup(row3[2]); qtlChrom = peakChrom; qtlChromStart = peakChromStart; qtlChromEnd = peakChromEnd; qtlThickStart = peakChromStart; qtlThickEnd = peakChromEnd; qtlMarker = peak; qtlValid = 1; sqlFreeResult(&sr3); } } else { /* printf("%s has no peak marker.\n", name);fflush(stdout); */ } /* process flanking markers to get regionStart and regionEnd if both flanking markers exist */ if (!sameWord(flank1, "") && !sameWord(flank2,"")) { for (iFlank=0; iFlank<2; iFlank++) { if (flanks[iFlank] != NULL) { qtlValid = 1; identNo = getStsId(conn3, database, flanks[iFlank]); if (identNo != NULL) { sqlSafef(query3, sizeof query3, "select * from %s.stsMapMouseNew where identNo=%s",database,identNo); sr3 = sqlMustGetResult(conn3, query3); row3 = sqlNextRow(sr3); /* only a few has mulitple answers, so just grab the first one */ flankChrom = row3[0]; flankChromStart = row3[1]; flankChromEnd = row3[2]; /* if this QTL does not have a peak, use flanking marker's chrom */ if (sameWord(qtlChrom,na)) qtlChrom = strdup(flankChrom); pos = sqlUnsigned(flankChromStart); /* initialize regionStart if not initialized */ if (regionStart == 0) regionStart = pos; if (pos < regionStart) regionStart = pos; if (pos > regionEnd) regionEnd = pos; pos = sqlUnsigned(flankChromEnd); if (pos < regionStart) regionStart = pos; if (pos > regionEnd) regionEnd = pos; sqlFreeResult(&sr3); } } } } /* set regionStart/End for those entries that does not have flanking markers */ if ((regionStart == 0) && !sameWord(qtlChromStart, zero)) { regionStart = atoi(qtlChromStart); } if ((regionEnd == 0) && !sameWord(qtlChromEnd, zero)) { regionEnd = atoi(qtlChromEnd); } /* fix problematic cases that thickStart/thickEnd are outside regionStart/regionEnd */ pos = atoi(qtlThickStart); if (! ((pos >= regionStart) && (pos <= regionEnd))) { qtlThickStart = strdup(zero); } pos = atoi(qtlThickEnd); if (! ((pos >= regionStart) && (pos <= regionEnd))) { qtlThickEnd = strdup(zero); } /* the following logic was used to check raw data vs processed data */ /* sprintf(chrCheck, "chr%s", chrom); if (!sameWord(chrCheck, qtlChrom))printf("=== "); if (!sameWord(peak, "") && !sameWord(peakPos, "0")) printf("%s\t%s\txx%dxx\t%s\t%s\n", name, peak, -(atoi(peakChromStart)-atoi(peakPos)), peakPos, peakChromStart);fflush(stdout); */ /* only put out valid entries */ if (qtlValid && !sameWord(qtlChrom, na)) fprintf(outF, "%s\t%d\t%d\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\n", qtlChrom, regionStart, regionEnd, qtlName, qtlScore, qtlStrand, qtlThickStart, qtlThickEnd, qtlMarker, qtlMgiID, qtlDescription, qtlCMScore, flank1, flank2); else { /* printf("%s\t%s\t%s\t%s\n", flank1, peak, flank2, qtlName);fflush(stdout); */ } row2 = sqlNextRow(sr2); } sqlFreeResult(&sr2); hFreeConn(&conn2); hFreeConn(&conn3); fclose(outF); return(0); }