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/cgilib/geneSimilarities.c src/hg/cgilib/geneSimilarities.c index a8b06ba..47e6e99 100644 --- src/hg/cgilib/geneSimilarities.c +++ src/hg/cgilib/geneSimilarities.c @@ -1,213 +1,213 @@ /* Objects to find genePreds given similarity in genome bases annotated. This * is used to relate genes between two gene sets. */ /* Copyright (C) 2014 The Regents of the University of California * See kent/LICENSE or http://genome.ucsc.edu/license/ for licensing information. */ #include "common.h" #include "geneSimilarities.h" #include "genePred.h" #include "genePredReader.h" #include "jksql.h" static struct geneSim *geneSimNew(struct genePred *gene, float sim) /* construct a new geneSim */ { struct geneSim *gs; AllocVar(gs); gs->gene = gene; gs->sim = sim; return gs; } static void geneSimFreeList(struct geneSim **gss) /* free list of geneSims and associated genePreds */ { struct geneSim *gs; while ((gs = slPopHead(gss)) != NULL) { genePredFree(&gs->gene); freeMem(gs); } } struct geneSimilarities *geneSimilaritiesNew(struct genePred *query, boolean cdsSim) /* construct a new geneSimilarities object. Ownership of query is passed. */ { struct geneSimilarities *gss; AllocVar(gss); gss->query = query; gss->cdsSim = cdsSim; return gss; } void geneSimilaritiesFree(struct geneSimilarities **gssPtr) /* free a geneSimilarities object and all contained genePreds */ { struct geneSimilarities *gss = *gssPtr; if (gss != NULL) { geneSimFreeList(&gss->genes); genePredFree(&gss->query); freez(gssPtr); } } void geneSimilaritiesFreeList(struct geneSimilarities **gssList) /* free a list of geneSimilarities objects and all contained genePreds */ { struct geneSimilarities *gss; while ((gss = slPopHead(gssList)) != NULL) geneSimilaritiesFree(&gss); } static int cntOverlapCdsBases(struct genePred *ga, struct genePred *gb) /* determine the number of CDS bases overlaping */ { int overBases = 0, ia, ib; int cdsStartA, cdsEndA, cdsStartB, cdsEndB; for (ia = 0; ia < ga->exonCount; ia++) { if (genePredCdsExon(ga, ia, &cdsStartA, &cdsEndA)) { for (ib = 0; ib < gb->exonCount; ib++) { if (genePredCdsExon(gb, ib, &cdsStartB, &cdsEndB)) { int o = min(cdsEndA, cdsEndB) - max(cdsStartA, cdsStartB); if (o > 0) overBases += o; } } } } return overBases; } static float geneCdsSimilarity(struct genePred *ga, struct genePred *gb) /* computer a CDS similary score for two genes, which is a fraction */ { int gaBases = genePredCodingBases(ga); int gbBases = genePredCodingBases(gb); return ((float)(2*cntOverlapCdsBases(ga, gb)))/(float)(gaBases+gbBases); } static int cntOverlapExonBases(struct genePred *ga, struct genePred *gb) /* determine the number of exon bases overlaping */ { int overBases = 0, ia, ib; for (ia = 0; ia < ga->exonCount; ia++) { for (ib = 0; ib < gb->exonCount; ib++) { int o = min(ga->exonEnds[ia], gb->exonEnds[ib]) - max(ga->exonStarts[ia], gb->exonStarts[ib]); if (o > 0) overBases += o; } } return overBases; } static float geneExonSimilarity(struct genePred *ga, struct genePred *gb) /* computer an exon similary score for two genes, which is a fraction */ { int gaBases = genePredBases(ga); int gbBases = genePredBases(gb); return ((float)(2*cntOverlapExonBases(ga, gb)))/(float)(gaBases+gbBases); } int geneSimCmp(const void *va, const void *vb) /* compare geneSim objects by descending similarity score. */ { struct geneSim *ga = *((struct geneSim **)va); struct geneSim *gb = *((struct geneSim **)vb); if (ga->sim > gb->sim) return -1; else if (ga->sim < gb->sim) return -1; else return 0; } static void findSimilarities(struct geneSimilarities *gss, struct sqlConnection *conn, char *targetGeneTbl) /* find genes similar to the query in gss and add them. */ { char where[64]; -sqlSafefFrag(where, sizeof(where), "strand = \"%s\"", gss->query->strand); +sqlSafef(where, sizeof(where), "strand = \"%s\"", gss->query->strand); int start = gss->cdsSim ? gss->query->cdsStart :gss->query->txStart; int end = gss->cdsSim ? gss->query->cdsEnd :gss->query->txEnd; struct genePred *targetGenes = genePredReaderLoadRangeQuery(conn, targetGeneTbl, gss->query->chrom, start, end, where); struct genePred *gp; while ((gp = slPopHead(&targetGenes)) != NULL) { float sim = gss->cdsSim ? geneCdsSimilarity(gp, gss->query) : geneExonSimilarity(gp, gss->query); slSafeAddHead(&gss->genes, geneSimNew(gp, sim)); } } struct geneSimilarities *geneSimilaritiesBuild(struct sqlConnection *conn, boolean cdsSim, struct genePred *query, char *targetGeneTbl) /* Construct a geneSimilarities object by finding all similar genes in * the specified table. Ownership of query is passed. */ { struct geneSimilarities *gss = geneSimilaritiesNew(query, cdsSim); findSimilarities(gss, conn, targetGeneTbl); slSort(&gss->genes, geneSimCmp); return gss; } struct geneSimilarities *geneSimilaritiesBuildAt(struct sqlConnection *conn, boolean cdsSim, char *queryName, char *queryChrom, int queryStart, char *queryGeneTbl, char *targetGeneTbl) /* Construct a geneSimilarities object by finding the genePred named * queryName with txStart of queryStart in queryGeneTbl and * find similar genes in targetGeneTbl. */ { char where[256]; -sqlSafefFrag(where, sizeof(where), "(chrom = \"%s\") and (txStart = %d)", queryChrom, queryStart); +sqlSafef(where, sizeof(where), "(chrom = \"%s\") and (txStart = %d)", queryChrom, queryStart); struct genePred *query = genePredReaderLoadQuery(conn, queryGeneTbl, where); if (query == NULL) errAbort("gene %s starting at %s:%d not found in %s", queryName, queryChrom, queryStart, queryGeneTbl); // only use the first if by some wierd reason multiple are found genePredFreeList(&query->next); return geneSimilaritiesBuild(conn, cdsSim, query, targetGeneTbl); } struct geneSimilarities *geneSimilaritiesBuildAll(struct sqlConnection *conn, boolean cdsSim, char *queryName, char *queryGeneTbl, char *targetGeneTbl) /* Construct a list of geneSimilarities objects by finding all entries * of queryName in queryGeneTbl and build a geneSimilarities object for each * one from targetGeneTbl. */ { struct geneSimilarities *gssList = NULL; char where[64]; -sqlSafefFrag(where, sizeof(where), "name = \"%s\"", queryName); +sqlSafef(where, sizeof(where), "name = \"%s\"", queryName); struct genePred *queries = genePredReaderLoadQuery(conn, queryGeneTbl, where); struct genePred *query; while ((query = slPopHead(&queries)) != NULL) slSafeAddHead(&gssList, geneSimilaritiesBuild(conn, cdsSim, query, targetGeneTbl)); return gssList; }