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/utils/motifFinder/motifFinder.c src/hg/utils/motifFinder/motifFinder.c index 907242f..7834058 100644 --- src/hg/utils/motifFinder/motifFinder.c +++ src/hg/utils/motifFinder/motifFinder.c @@ -1,264 +1,264 @@ /* motifFinder - find largest scoring motif in bed items. */ /* 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 "bed6FloatScore.h" #include "linefile.h" #include "hash.h" #include "options.h" #include "dnaseq.h" #include "dnaMotif.h" #include "dnaMotifSql.h" #include "dnaMarkov.h" #include "jksql.h" #include "hdb.h" #include "chromInfo.h" static float minScoreCutoff; static char *motifTable = "transRegCodeMotifPseudoCounts"; static char *markovTable; static boolean originalCoordinates = FALSE; static boolean topOnly = FALSE; static boolean uniformBackground = FALSE; struct chromInfo *chromInfo; static float prior = 0.5; // our prior belief that there is at least one binding site in a peak static float priorBackoff = 0.01; // our prior belief that there are > 1 binding sites in a given peak = PRIOR * priorBackoff^n) void usage() /* Explain usage and exit. */ { errAbort( "motifFinder - find largest scoring motif in bed items\n" "factorName is loaded from table '%s'.\n" "usage:\n" " motifFinder assembly factorName file(s)\n" "options:\n" " -markovTable\t\tUse given 2nd-markov model for background\n" " -originalCoordinates\tPrint original coordinates, rather than just the coordinates of the highest scoring motif\n", motifTable ); } static struct optionSpec options[] = { {"markovTable", OPTION_STRING}, {"minScoreCutoff", OPTION_FLOAT}, {"originalCoordinates", OPTION_BOOLEAN}, {"prior", OPTION_FLOAT}, {"priorBackoff", OPTION_FLOAT}, {"topOnly", OPTION_BOOLEAN}, {"uniformBackground", OPTION_BOOLEAN}, {NULL, 0}, }; static unsigned getChromSize(struct chromInfo *ci, char *chrom) { // XXXX use hash to speedup? for(; ci != NULL; ci = ci->next) { if(sameString(ci->chrom, chrom)) return ci->size; } errAbort("couldn't find getChromSize for chrom '%s'", chrom); return 0; } static int bed6FloatCmpDesc(const void *va, const void *vb) /* Compare two floats (remember that we have to return an int) */ { const struct bed6FloatScore *a = *((struct bed6FloatScore **)va); const struct bed6FloatScore *b = *((struct bed6FloatScore **)vb); return (int) (1000 * (b->score - a->score)); } void motifFinder(char *database, char *name, int fileCount, char *files[]) /* motifFinder - find largest scoring motif in bed items. */ { struct sqlConnection *conn = sqlConnect(database); int fileNum; char where[256]; struct chromInfo *ci = createChromInfoList(NULL, database); -sqlSafefFrag(where, sizeof(where), "name = '%s'", name); +sqlSafef(where, sizeof(where), "name = '%s'", name); struct dnaMotif *motif = dnaMotifLoadWhere(conn, motifTable, where); if(markovTable != NULL) dnaMotifMakeLog2(motif); if(motif == NULL) errAbort("couldn't find motif '%s'", name); for (fileNum = 0; fileNum < fileCount; fileNum++) { char *words[64], *line; char **row; struct lineFile *lf = lineFileOpen(files[fileNum], TRUE); while (lineFileNextReal(lf, &line)) { int dnaLength, i, j, rowOffset, length, wordCount = chopTabs(line, words); unsigned chromSize; boolean markovFound = FALSE; double mark0[5]; double mark2[5][5][5]; struct dnaSeq *seq = NULL; char *dupe = NULL; if (0 == wordCount) continue; lineFileExpectAtLeast(lf, 3, wordCount); dupe = cloneString(line); char *chrom = words[0]; int chromStart = lineFileNeedNum(lf, words, 1); if(markovTable != NULL) chromStart = max(2, chromStart); unsigned chromEnd = lineFileNeedNum(lf, words, 2); if (chromEnd < 1) errAbort("ERROR: line %d:'%s'\nchromEnd is less than 1\n", lf->lineIx, dupe); if (chromStart > chromEnd) errAbort("ERROR: line %d:'%s'\nchromStart after chromEnd (%d > %d)\n", lf->lineIx, dupe, chromStart, chromEnd); length = chromEnd - chromStart; chromSize = getChromSize(ci, chrom); if(markovTable == NULL) { dnaLength = length; seq = hDnaFromSeq(database, chrom, chromStart, chromEnd, dnaUpper); if(uniformBackground) { int i; mark0[0] = 1; for(i = 1; i <= 4; i++) mark0[i] = 0.25; } else { dnaMark0(seq, mark0, NULL); } } else { dnaLength = length + 4; if(chromStart - 2 + dnaLength > chromSize) // can't do analysis for potential peak hanging off the end of the chrom continue; seq = hDnaFromSeq(database, chrom, chromStart - 2, chromEnd + 2, dnaUpper); struct sqlResult *sr = hRangeQuery(conn, markovTable, chrom, chromStart, chromStart + 1, NULL, &rowOffset); if((row = sqlNextRow(sr)) != NULL) { dnaMark2Deserialize(row[rowOffset + 3], mark2); dnaMarkMakeLog2(mark2); markovFound = TRUE; } else errAbort("markov table '%s' is missing; non-markov analysis is current not supported", markovTable); sqlFreeResult(&sr); } struct bed6FloatScore *hits = NULL; for (i = 0; i < 2; i++) { double mark0Copy[5]; char strand = i == 0 ? '+' : '-'; for (j = 0; j <= 4; j++) mark0Copy[j] = mark0[j]; if(strand == '-') { // reverse markov table too! double tmp; reverseComplement(seq->dna, dnaLength); tmp = mark0Copy[1]; mark0Copy[1] = mark0Copy[3]; mark0Copy[3] = tmp; tmp = mark0Copy[2]; mark0Copy[2] = mark0Copy[4]; mark0Copy[4] = tmp; } for (j = 0; j < length - motif->columnCount + 1; j++) // tricky b/c if(markovFound) then seq includes the two bytes on either side of actual sequence. { double score; if(markovFound) score = dnaMotifBitScoreWithMarkovBg(motif, seq->dna + j, mark2); else score = dnaMotifBitScoreWithMark0Bg(motif, seq->dna + j, mark0Copy); if(score >= minScoreCutoff) { int start; if(strand == '-') start = (chromEnd - j) - motif->columnCount; else start = chromStart + j; struct bed6FloatScore *hit = NULL; // Watch out for overlapping hits (on either strand; yes, I've seen that happen); // we report only the highest scoring hit in this case. // O(n^2) where n == number of motifs in a peak, but I expect n to be almost always very small. if(!originalCoordinates) { for (hit = hits; hit != NULL; hit = hit->next) { if(hit->chromEnd > start && hit->chromStart <= (start + motif->columnCount)) { verbose(3, "found overlapping hits: %d-%d overlaps with %d-%d\n", start, start + motif->columnCount, hit->chromStart, hit->chromEnd); break; } } } if(hit == NULL || hit->score < score) { if(hit == NULL) { AllocVar(hit); slAddHead(&hits, hit); hit->chrom = cloneString(chrom); } hit->chromStart = originalCoordinates ? chromStart : start; hit->chromEnd = originalCoordinates ? chromEnd : start + motif->columnCount; hit->score = score; hit->strand[0] = strand; } } verbose(3, "j: %d; score: %.2f\n", j, score); } } slSort(&hits, bed6FloatCmpDesc); int count; float currentPrior = prior; for(count = 1; hits != NULL; count++, hits = hits->next) { if(topOnly && count > topOnly) break; // Use a progressively weaker prior for hits with lower scores verbose(3, "count: %d; score: %.2f; prior: %.2f; log2(prior / (1 - prior)): %.2f\n", count, hits->score, currentPrior, log2(currentPrior / (1 - currentPrior))); if(hits->score >= minScoreCutoff - log2(currentPrior / (1 - currentPrior))) { printf("%s\t%d\t%d\t%s\t%.2f\t%c\n", chrom, originalCoordinates ? chromStart : hits->chromStart, originalCoordinates ? chromEnd : hits->chromStart + motif->columnCount, name, hits->score, hits->strand[0]); currentPrior = count == 1 ? priorBackoff : currentPrior * priorBackoff; if(count > 2) verbose(3, "hit for count: %d at %s:%d-%d\n", count, chrom, hits->chromStart, hits->chromStart + motif->columnCount); } else break; } freeDnaSeq(&seq); freeMem(dupe); } lineFileClose(&lf); } sqlDisconnect(&conn); } int main(int argc, char *argv[]) /* Process command line. */ { optionInit(&argc, argv, options); markovTable = optionVal("markovTable", NULL); originalCoordinates = optionExists("originalCoordinates"); minScoreCutoff = optionFloat("minScoreCutoff", 0); prior = optionFloat("prior", prior); priorBackoff = optionFloat("priorBackoff", priorBackoff); topOnly = optionExists("topOnly"); uniformBackground = optionExists("uniformBackground"); if (argc < 4) usage(); motifFinder(argv[1], argv[2], argc-3, argv+3); return 0; }