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/bedItemOverlapCount/bedItemOverlapCount.c src/hg/bedItemOverlapCount/bedItemOverlapCount.c index e2ca1f7..2aa4a1f 100644 --- src/hg/bedItemOverlapCount/bedItemOverlapCount.c +++ src/hg/bedItemOverlapCount/bedItemOverlapCount.c @@ -1,327 +1,329 @@ /* bedItemOverlapCount - count how many times a base is overlapped in a bed file */ /* 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 "options.h" #include "linefile.h" #include "obscure.h" #include "hash.h" #include "cheapcgi.h" #include "jksql.h" #include "dystring.h" #include "chromInfo.h" #include "wiggle.h" #include "hdb.h" /* define unitSize to be a larger storage class if your counts * are overflowing. */ typedef unsigned int unitSize; #define MAXCOUNT (unitSize)~0 #define MAXMESSAGE "Overflow of overlap counts. Max is %lu. Recompile with bigger unitSize or use -max option" #define INCWOVERFLOW(countArray,x) if(countArray[x] == MAXCOUNT) {if(!doMax) errAbort(MAXMESSAGE,(unsigned long)MAXCOUNT);} else countArray[x]++ /* Command line switches. */ static struct hash *chromHash = NULL; static char *host = NULL; static char *user = NULL; static char *password = NULL; char *chromSizes = NULL; /* read chrom sizes from file instead of database . */ boolean doMax; /* if overlap count will overflow, just keep max */ boolean doZero; /* add blocks with 0 counts */ boolean doBed12; /* expect bed12 and process block by block */ boolean doOutBounds; /* output min/max to stderr */ unitSize overMin = ~1; unitSize overMax = 0; /* command line option specifications */ static struct optionSpec optionSpecs[] = { {"chromSize", OPTION_STRING}, {"host", OPTION_STRING}, {"user", OPTION_STRING}, {"password", OPTION_STRING}, {"max", OPTION_BOOLEAN}, {"zero", OPTION_BOOLEAN}, {"bed12", OPTION_BOOLEAN}, {"outBounds", OPTION_BOOLEAN}, {NULL, 0} }; void usage() /* Explain usage and exit. */ { errAbort( "bedItemOverlapCount - count number of times a base is overlapped by the\n" "\titems in a bed file. Output is bedGraph 4 to stdout.\n" "usage:\n" " sort bedFile.bed | bedItemOverlapCount [options] <database> stdin\n" "To create a bigWig file from this data to use in a custom track:\n" " sort -k1,1 bedFile.bed | bedItemOverlapCount [options] <database> stdin \\\n" " > bedFile.bedGraph\n" " bedGraphToBigWig bedFile.bedGraph chrom.sizes bedFile.bw\n" " where the chrom.sizes is obtained with the script: fetchChromSizes\n" " See also:\n" " http://genome-test.gi.ucsc.edu/~kent/src/unzipped/utils/userApps/fetchChromSizes\n" "options:\n" " -zero add blocks with zero count, normally these are ommitted\n" " -bed12 expect bed12 and count based on blocks\n" " Without this option, only the first three fields are used.\n" " -max if counts per base overflows set to max (%lu) instead of exiting\n" " -outBounds output min/max to stderr\n" " -chromSize=sizefile\tRead chrom sizes from file instead of database\n" " sizefile contains two white space separated fields per line:\n" " chrom name and size\n" " -host=hostname\tmysql host used to get chrom sizes\n" " -user=username\tmysql user\n" " -password=password\tmysql password\n\n" "Notes:\n" " * You may want to separate your + and - strand\n" " items before sending into this program as it only looks at\n" " the chrom, start and end columns of the bed file.\n" " * Program requires a <database> connection to lookup chrom sizes for a sanity\n" " check of the incoming data. Even when the -chromSize argument is used\n" " the <database> must be present, but it will not be used.\n\n" " * The bed file *must* be sorted by chrom\n" " * Maximum count per base is %lu. Recompile with new unitSize to increase this",(unsigned long)MAXCOUNT, (unsigned long)MAXCOUNT ); } static struct hash *loadAllChromInfo(char *database, unsigned *largest) /* Load up all chromosome infos, return largest one if asked to do so. */ { struct chromInfo *el; struct sqlConnection *conn = NULL; struct sqlResult *sr = NULL; struct hash *ret; char **row; unsigned max = 0; if(host) { conn = sqlConnectRemote(host, user, password, database); } else { conn = sqlConnect(database); } ret = newHash(0); -sr = sqlGetResult(conn, NOSQLINJ "select * from chromInfo"); +char query[1024]; +sqlSafef(query, sizeof query, "select * from chromInfo"); +sr = sqlGetResult(conn, query); while ((row = sqlNextRow(sr)) != NULL) { el = chromInfoLoad(row); if (el->size > max) max = el->size; verbose(4, "Add hash %s value %u (%#lx)\n", el->chrom, el->size, (unsigned long)&el->size); hashAdd(ret, el->chrom, (void *)(& el->size)); } sqlFreeResult(&sr); sqlDisconnect(&conn); if (largest) *largest = max; return ret; } static unsigned chromosomeSize(char *chromosome) /* Return full extents of chromosome. Warn and fill in if none. */ { struct hashEl *el = hashLookup(chromHash,chromosome); if (el == NULL) errAbort("Couldn't find size of chromosome %s", chromosome); return *(unsigned *)el->val; } static void outputCounts(unitSize *counts, char *chrom, unsigned size) { if (size == 0) errAbort("got 0 for size of chrom %s\n", chrom); if (doOutBounds) { if (counts[0] < overMin) overMin = counts[0]; if (counts[0] > overMax) overMax = counts[0]; } int ii; int prevValue = counts[0]; int startPoint = 0; for(ii=1; ii < size; ii++) { if (doOutBounds) { if (counts[ii] < overMin) overMin = counts[ii]; if (counts[ii] > overMax) overMax = counts[ii]; } if (counts[ii] != prevValue) { if (doZero || (prevValue != 0)) printf("%s\t%u\t%u\t%u\n", chrom, startPoint, ii, prevValue); startPoint = ii; prevValue = counts[ii]; } } if (doZero || (prevValue != 0)) printf("%s\t%u\t%u\t%u\n", chrom, startPoint, ii, prevValue); } static void bedItemOverlapCount(char *database, int fileCount, char *fileList[]) { unsigned maxChromSize = 0; int i; unitSize *counts = (unitSize *)NULL; if (chromSizes != NULL) { chromHash = newHash(0); struct lineFile *lf = lineFileOpen(chromSizes, TRUE); char *row[2]; while (lineFileRow(lf, row)) { unsigned *ptr; AllocVar(ptr); *ptr = sqlUnsigned(row[1]); maxChromSize = max(*ptr, maxChromSize); hashAdd(chromHash, row[0], ptr); } lineFileClose(&lf); } else { chromHash = loadAllChromInfo(database, &maxChromSize); } verbose(2,"#\tmaxChromSize: %u\n", maxChromSize); if (maxChromSize < 1) errAbort("maxChromSize is zero ?"); /* Allocate just once for the largest chrom and reuse this array */ counts = needHugeMem(sizeof(unitSize) * maxChromSize); /* Reset the array to be zero to be reused */ memset((void *)counts, 0, sizeof(unitSize)*(size_t)maxChromSize); unsigned chromSize = 0; char *prevChrom = (char *)NULL; boolean outputToDo = FALSE; struct hash *seenHash = newHash(5); for (i=0; i<fileCount; ++i) { struct lineFile *bf = lineFileOpen(fileList[i] , TRUE); struct bed *bed = (struct bed *)NULL; char *row[12]; int numFields = doBed12 ? 12 : 3; while (lineFileNextRow(bf,row, numFields)) { int i; bed = bedLoadN(row, numFields); verbose(3,"#\t%s\t%d\t%d\n",bed->chrom,bed->chromStart, bed->chromEnd); if (prevChrom && differentWord(bed->chrom,prevChrom)) // End a chr { verbose(2,"#\tchrom %s done, size %d\n", prevChrom, chromSize); if (outputToDo) outputCounts(counts, prevChrom, chromSize); outputToDo = FALSE; memset((void *)counts, 0, sizeof(unitSize)*(size_t)maxChromSize); /* zero counts */ freez(&prevChrom); // prevChrom is now NULL so it will be caught by next if! } if ((char *)NULL == prevChrom) // begin a chr { if (hashLookup(seenHash, bed->chrom)) errAbort("ERROR:input file not sorted. %s seen before on line %d\n", bed->chrom, bf->lineIx); hashAdd(seenHash, bed->chrom, NULL); prevChrom = cloneString(bed->chrom); chromSize = chromosomeSize(prevChrom); verbose(2,"#\tchrom %s starting, size %d\n", prevChrom,chromSize); } if (bed->chromEnd > chromSize) { // check for circular chrM if (doBed12 || bed->chromStart>=chromSize || !isMito(bed->chrom)) { warn("ERROR: %s\t%d\t%d", bed->chrom, bed->chromStart, bed->chromEnd); errAbort("chromEnd > chromSize ? %d > %d", bed->chromEnd,chromSize); } for (i = bed->chromStart; i < chromSize; ++i) INCWOVERFLOW(counts,i); for (i = 0; i < (bed->chromEnd - chromSize); ++i) INCWOVERFLOW(counts,i); } else if (doBed12) { int *starts = bed->chromStarts; int *sizes = bed->blockSizes; int *endStarts = &bed->chromStarts[bed->blockCount]; for(; starts < endStarts; starts++, sizes++) { unsigned int end = *starts + *sizes + bed->chromStart; for (i = *starts + bed->chromStart; i < end; ++i) INCWOVERFLOW(counts,i); } } else { for (i = bed->chromStart; i < bed->chromEnd; ++i) INCWOVERFLOW(counts, i); } outputToDo = TRUE; bedFree(&bed); // plug the memory leak } lineFileClose(&bf); // Note, next file could be on same chr! } if (outputToDo) outputCounts(counts, prevChrom, chromSize); if (doOutBounds) fprintf(stderr, "min %lu max %lu\n", (unsigned long)overMin, (unsigned long)overMax); verbose(2,"#\tchrom %s done, size %d\n", prevChrom, chromSize); freeMem(counts); freez(&prevChrom); // hashFreeWithVals(&chromHash, freez); freeHash(&seenHash); } int main(int argc, char *argv[]) /* Process command line. */ { optionInit(&argc, argv, optionSpecs); if (argc < 3) usage(); host = optionVal("host", NULL); user = optionVal("user", NULL); password = optionVal("password", NULL); chromSizes = optionVal("chromSize", NULL); doMax = optionExists("max"); doBed12 = optionExists("bed12"); doZero = optionExists("zero"); doOutBounds = optionExists("outBounds"); verbose(2, "#\tworking on database: %s\n", argv[1]); bedItemOverlapCount(argv[1], argc-2, argv+2); optionFree(); return 0; }