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/hgGcPercent/hgGcPercent.c src/hg/makeDb/hgGcPercent/hgGcPercent.c index 0e76a0d..f35a627 100644 --- src/hg/makeDb/hgGcPercent/hgGcPercent.c +++ src/hg/makeDb/hgGcPercent/hgGcPercent.c @@ -1,449 +1,450 @@ /* hgGcPercent - Calculate GC Percentage in 20kb windows. */ /* 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 "portable.h" #include "dnautil.h" #include "dnaseq.h" #include "nib.h" #include "jksql.h" #include "hdb.h" #include "cheapcgi.h" #include "options.h" #include "twoBit.h" #include "bed.h" /* Command line switches. */ int winSize = 20000; /* window size */ boolean noLoad = FALSE; /* Suppress loading mysql table . */ char *file = (char *)NULL; /* file name for output */ char *chr = (char *)NULL; /* process only chromosome listed */ boolean noRandom = FALSE; /* process only non-random chromosomes */ boolean noDots = FALSE; /* TRUE == do not display ... progress */ boolean doGaps = FALSE; /* TRUE == process gaps correctly */ boolean wigOut = FALSE; /* TRUE == output wiggle ascii data */ int overlap = 0; /* overlap size */ char *bedRegionInName = NULL; /* file of regions for calculating gc content */ char *bedRegionOutName = NULL; /* output file of regions for gc content */ FILE *bedRegionOutFile = NULL; /* command line option specifications */ static struct optionSpec optionSpecs[] = { {"win", OPTION_INT}, {"noLoad", OPTION_BOOLEAN}, {"file", OPTION_STRING}, {"chr", OPTION_STRING}, {"noRandom", OPTION_BOOLEAN}, {"noDots", OPTION_BOOLEAN}, {"doGaps", OPTION_BOOLEAN}, {"overlap", OPTION_INT}, {"wigOut", OPTION_BOOLEAN}, {"bedRegionIn", OPTION_STRING}, {"bedRegionOut", OPTION_STRING}, {NULL, 0} }; static char * previousChrom = (char *) NULL; void usage() /* Explain usage and exit. */ { errAbort( "hgGcPercent - Calculate GC Percentage in 20kb windows\n" "usage:\n" " hgGcPercent [options] database nibDir\n" " nibDir can be a .2bit file, a directory that contains a\n" " database.2bit file, or a directory that contains *.nib files.\n" " Loads gcPercent table with counts from sequence.\n" "options:\n" " -win=<size> - change windows size (default %d)\n" " -noLoad - do not load mysql table - create bed file\n" " -file=<filename> - output to <filename> (stdout OK) (implies -noLoad)\n" " -chr=<chrN> - process only chrN from the nibDir\n" " -noRandom - ignore randome chromosomes from the nibDir\n" " -noDots - do not display ... progress during processing\n" " -doGaps - process gaps correctly (default: gaps are not counted as GC)\n" " -wigOut - output wiggle ascii data ready to pipe to wigEncode\n" " -overlap=N - overlap windows by N bases (default 0)\n" " -verbose=N - display details to stderr during processing\n" " -bedRegionIn=input.bed Read in a bed file for GC content in specific regions and write to bedRegionsOut\n" " -bedRegionOut=output.bed Write a bed file of GC content in specific regions from bedRegionIn\n\n" "example:\n" " calculate GC percent in 5 base windows using a 2bit assembly (dp2):\n" " hgGcPercent -wigOut -doGaps -win=5 -file=stdout -verbose=0 \\\n" " dp2 /cluster/data/dp2 \\\n" " | wigEncode stdin gc5Base.wig gc5Base.wib" , winSize); } char *createTable = "#Displays GC percentage in 20Kb blocks for genome\n" "CREATE TABLE gcPercent (\n" "chrom varchar(255) not null, # Human chromosome number\n" "chromStart int unsigned not null, # Start position in genoSeq\n" "chromEnd int unsigned not null, # End position in genoSeq\n" "name varchar(255) not null, # Constant string GCpct\n" "gcPpt int unsigned not null, # GC percentage for 20Kb block\n" "#Indices\n" "UNIQUE(chrom(%d),chromStart)\n" ");\n"; static void wigOutLine(FILE *f, char *chrom, int start, int end, int ppt) { /* only full winSize spans are valid */ if ((end - start) < winSize) return; /* see if we are starting on a new chrom */ if (! (previousChrom && (sameWord(previousChrom, chrom)))) { freeMem(previousChrom); previousChrom = cloneString(chrom); fprintf(f, "variableStep chrom=%s span=%d\n", chrom, winSize-overlap); } fprintf(f, "%d\t%g\n", start+1, ppt/10.0); } void makeGcLineFromSeq(DNA *dna, char *chrom, int start, int end, FILE *f) /* Given a sequence and window within the sequence, print out a line of * BED 5 with the GC parts per thousand (not percent) in the window (or * ascii-wiggle if -wigOut). */ { static int dotMod = 0; int minCount = winSize/4; int i, count, gcCount, val, ppt, gapCount; if ((++dotMod&127) == 0) { if (!noDots) { verbose(1, "."); if ((dotMod & 8191) == 0) verbose(1, "\n"); fflush(stdout); } } gapCount = count = gcCount = 0; for (i = start; i < end; ++i) { if ((val = ntVal[(int)dna[i]]) >= 0) { ++count; if (val == G_BASE_VAL || val == C_BASE_VAL) { ++gcCount; } } else { ++gapCount; } } if (count >= minCount) ppt = round(1000.0*(double)gcCount/(double)count); else ppt = 0; if (!doGaps || gapCount < (end - start)) { if (wigOut) wigOutLine(f, chrom, start, end, ppt); else fprintf(f, "%s\t%d\t%d\t%s\t%d\n", chrom, start, end, "GC", ppt); } } void writeBedLineCountFromSeq(struct dnaSeq *seq, char *chrom, int start, int end, FILE *f) /* Given a window of sequence, print out a line of BED 5 with the GC counts * in the window. (not percents or parts per thousand)*/ { static int dotMod = 0; DNA *dna = seq->dna; int i, count, gcCount, val, gapCount; if ((++dotMod&127) == 0 && !noDots) { verbose(1, "."); if ((dotMod & 8191) == 0) verbose(1, "\n"); fflush(stdout); } gapCount = count = gcCount = 0; for (i=0; i < seq->size; ++i) if ((val = ntVal[(int)dna[i]]) >= 0) { ++count; if (val == G_BASE_VAL || val == C_BASE_VAL) ++gcCount; } else ++gapCount; if (doGaps) { if (gapCount < seq->size) fprintf(f, "%s\t%d\t%d\t%d\t%s\n", chrom, start, end, gcCount, "gcCount"); } else fprintf(f, "%s\t%d\t%d\t%d\t%s\n", chrom, start, end, gcCount, "gcCount"); } void makeGcTabFromNib(char *nibFile, char *chrom, FILE *f, struct bed *bedRegions) /* Scan through nib file and write out GC percentage info. */ { int start = 0, end = 0; int chromSize; FILE *nf = NULL; struct dnaSeq *seq = NULL; struct bed *bed = NULL; nibOpenVerify(nibFile, &nf, &chromSize); seq = nibLdPart(nibFile, nf, chromSize, 0, chromSize); if (f==NULL) errAbort("No output file"); if ((bedRegionInName != NULL)) for (bed=bedRegions; bed!=NULL; bed=bed->next) { if(sameString(bed->chrom, chrom)) { struct dnaSeq *subSeq = NULL; DNA *subSeqDNA = NULL; if (bed->chromEnd > chromSize) bed->chromEnd = chromSize; subSeqDNA = cloneStringZ(seq->dna + bed->chromStart, bed->chromEnd - bed->chromStart); subSeq = newDnaSeq(subSeqDNA, bed->chromEnd - bed->chromStart, NULL); writeBedLineCountFromSeq(subSeq, chrom, bed->chromStart, bed->chromEnd, bedRegionOutFile); freeDnaSeq(&subSeq); } } else for (start=0, end=0; start < chromSize && end < chromSize; start = end - overlap) { end = start + winSize; if (end > chromSize) end = chromSize; makeGcLineFromSeq(seq->dna, chrom, start, end, f); } freeDnaSeq(&seq); carefulClose(&nf); if (!noDots) verbose(1, "\n"); } void makeGcTabFromTwoBit(char *twoBitFileName, FILE *f, struct bed *bedRegions) /* Scan through all sequenes in .2bit file and write out GC percentage info. */ { struct slName *twoBitNames = twoBitSeqNames(twoBitFileName); struct slName *el = NULL; struct twoBitFile *tbf = twoBitOpen(twoBitFileName); struct bed *bed = NULL; if ((bedRegionInName != NULL)) for (bed=bedRegions; bed!=NULL; bed=bed->next) { for (el = twoBitNames; el != NULL; el = el->next) { int chromSize = twoBitSeqSize(tbf, el->name); char *chrom = el->name; struct dnaSeq *seq = NULL; if (chr) { verbose(2, "#\tchecking name: %s =? %s\n", chrom, chr); if (! sameString(chrom, chr)) continue; } if (! sameString(chrom, bed->chrom)) continue; verbose(2, "#\tProcessing twoBit sequence %s for bed item %s:%d-%d\n", chrom, bed->chrom, bed->chromStart, bed->chromEnd); if (bed->chromEnd > chromSize) bed->chromEnd = chromSize; seq = twoBitReadSeqFrag(tbf, chrom, bed->chromStart, bed->chromEnd); writeBedLineCountFromSeq(seq, chrom, bed->chromStart, bed->chromEnd, bedRegionOutFile); freeDnaSeq(&seq); } } else { for (el = twoBitNames; el != NULL; el = el->next) { int start = 0, end = 0; int chromSize = twoBitSeqSize(tbf, el->name); char *chrom = el->name; struct dnaSeq *seq = NULL; if (chr) { verbose(2, "#\tchecking name: %s =? %s\n", chrom, chr); if (! sameString(chrom, chr)) continue; } verbose(2, "#\tProcessing twoBit sequence %s\n", chrom); seq = twoBitReadSeqFrag(tbf, chrom, 0, chromSize); for (start=0, end=0; start < chromSize && end < chromSize; start = end - overlap) { end = start + winSize; if (end > chromSize) end = chromSize; makeGcLineFromSeq(seq->dna, chrom, start, end, f); } freeDnaSeq(&seq); } } if (!noDots) verbose(1, "\n"); } void hgGcPercent(char *database, char *nibDir) /* hgGcPercent - Calculate GC Percentage on all chromosomes, load db table. */ { char *tabFileName = file ? file : "gcPercent.bed"; FILE *tabFile = mustOpen(tabFileName, "w"); char twoBitFile[512]; struct bed *bedRegionList = NULL; verbose(1, "#\tCalculating gcPercent with window size %d\n", winSize); verbose(2, "#\tWriting to tab file %s\n", tabFileName); if (bedRegionInName) { struct lineFile *lf = lineFileOpen(bedRegionInName, TRUE); struct bed *bed; char *row[3]; while (lineFileRow(lf, row)) { if (startsWith(row[0],"#")) continue; bed = bedLoad3(row); slAddHead(&bedRegionList, bed); } lineFileClose(&lf); slReverse(&bedRegionList); } if (twoBitIsFile(nibDir)) safef(twoBitFile, sizeof(twoBitFile), "%s", nibDir); else safef(twoBitFile, sizeof(twoBitFile), "%s/%s.2bit", nibDir, database); if (fileExists(twoBitFile)) { verbose(1, "#\tUsing twoBit: %s\n", twoBitFile); makeGcTabFromTwoBit(twoBitFile, tabFile, bedRegionList); } else { struct fileInfo *nibList, *nibEl; boolean gotNib = FALSE; nibList = listDirX(nibDir, "*.nib", TRUE); for (nibEl = nibList; nibEl != NULL; nibEl = nibEl->next) { char dir[256], chrom[128], ext[64]; splitPath(nibEl->name, dir, chrom, ext); if (noRandom && endsWith(chrom,"random")) continue; if (chr) { verbose(2, "#\tchecking name: %s =? %s\n", chrom, chr); if (! sameString(chrom, chr)) continue; } verbose(1, "#\tProcessing %s\n", nibEl->name); makeGcTabFromNib(nibEl->name, chrom, tabFile, bedRegionList); gotNib = TRUE; } slFreeList(&nibList); if (! gotNib) warn("Warning: nibDir argument (%s) did not expand to any sequence " "files.", nibDir); } carefulClose(&tabFile); verbose(1, "#\tFile %s created\n", tabFileName); /* Load that file in database. */ if (!noLoad) { struct sqlConnection *conn = sqlConnect(database); int indexLen = hGetMinIndexLength(database); char query[1024]; sqlSafef(query, sizeof(query), createTable, indexLen); verbose(1, "#\tLoading gcPercent table\n"); sqlRemakeTable(conn, "gcPercent", query); - sqlUpdate(conn, NOSQLINJ "DELETE from gcPercent"); + sqlSafef(query, sizeof(query), "DELETE from gcPercent"); + sqlUpdate(conn, query); sqlSafef(query, sizeof(query), "LOAD data local infile '%s' into table gcPercent", tabFileName); sqlUpdate(conn, query); sqlDisconnect(&conn); } } int main(int argc, char *argv[]) /* Process command line. */ { optionInit(&argc, argv, optionSpecs); if (argc <3) usage(); dnaUtilOpen(); winSize = optionInt("win", 20000); noLoad = optionExists("noLoad"); noDots = optionExists("noDots"); doGaps = optionExists("doGaps"); wigOut = optionExists("wigOut"); overlap = optionInt("overlap", 0); file = optionVal("file", NULL); chr = optionVal("chr", NULL); noRandom = optionExists("noRandom"); file = optionVal("file", NULL); bedRegionInName = optionVal("bedRegionIn", NULL); bedRegionOutName = optionVal("bedRegionOut", NULL); /* sending output to file implies no loading of DB, and also if the * stated file is "stdout" we should not do ... progress reports */ if (file) { noLoad = TRUE; if (sameString(file,"stdout")) noDots = TRUE; } if (bedRegionOutName) bedRegionOutFile = mustOpen(bedRegionOutName, "w"); if ((bedRegionInName && !bedRegionOutName) || (!bedRegionInName && bedRegionOutName)) errAbort("bedRegionIn and bedRegionOut must both be specified"); if (verboseLevel() >= 2) { fprintf(stderr, "#\thgGcPercent -win=%d", winSize); if (file) fprintf(stderr, " -file=%s", file); if (noLoad) fprintf(stderr, " -noLoad"); if (noDots) fprintf(stderr, " -noDots"); if (doGaps) fprintf(stderr, " -doGaps"); if (wigOut) fprintf(stderr, " -wigOut"); if (chr) fprintf(stderr, " -chr=%s", chr); if (bedRegionInName) fprintf(stderr, " -bedRegionInName=%s", bedRegionInName); if (bedRegionOutName) fprintf(stderr, " -bedRegionOutName=%s", bedRegionOutName); fprintf(stderr, "\n"); } hgGcPercent(argv[1], argv[2]); return 0; }