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/getFeatDna/getFeatDna.c src/hg/getFeatDna/getFeatDna.c index 93da665..bcf84ab 100644 --- src/hg/getFeatDna/getFeatDna.c +++ src/hg/getFeatDna/getFeatDna.c @@ -1,320 +1,329 @@ /* getFeatDna - Get dna for a type of feature. */ /* 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 "linefile.h" #include "hash.h" #include "cheapcgi.h" #include "genePred.h" #include "dnaseq.h" #include "fa.h" #include "dystring.h" #include "jksql.h" #include "hdb.h" #include "psl.h" #include "nib.h" /* Variables set explicitly or optionally from command line. */ char *database = NULL; /* Which database? */ int chromStart = 0; /* Start of range to select from. */ int chromEnd = BIGNUM; /* End of range. */ char *where = NULL; /* Extra selection info. */ boolean breakUp = FALSE; /* Break up things? */ int merge = -1; /* Merge close blocks? */ char *outputType = "fasta"; /* Type of output. */ void usage() /* Explain usage and exit. */ { errAbort( "getFeatDna - Get dna for a type of feature\n" "usage:\n" " getFeatDna database table chrom output.fa\n" "where:\n" " database is the name of a browser database, like 'hg6'\n" " table is the name of a table in this database, like 'exoFish'\n" " chrom is a chromosome name, like 'chr8' or 'chr7_random'. 'all'\n" " can be used here to denote all chromosomes\n" " output.fa is where to put the output in Fasta format\n" "options:\n" " -chromStart=NNN restrict to features that start after NNN\n" " -chromEnd=NNN restrict to features that end before NNN\n" " '-where=some sql pattern' restrict to features matching some sql pattern\n" " -breakUp=how break up alignments into pieces. How is one of\n" " exons - parts that align\n" " introns - parts between alignments\n" " cdsExons - coding exons (only for gene predictions)\n" " -merge=N merge blocks separated by N or less\n" " -output=format format of output. One of:\n" " fasta - fasta sequence (default)\n" " pos - position list\n" " -addStart=NNN How much to add to feature start coordinate\n" " -addEnd=NNN How much to add to feature end coordinate\n" " -addTo=how How to add to feature coordinates. One of:\n" " whole - the whole thing (default)\n" " start - addStart/padEnd relative to feature start\n" " end - addStart/padEnd relative to feature end\n" ); } static int blockIx = 0; /* Index of block written. */ char *makeFaStartLine(char *chrom, char *table, int start, int size) /* Create fa start line. */ { char faName[128]; static char faStartLine[512]; ++blockIx; if (startsWith("chr", table)) sprintf(faName, "%s_%d", table, blockIx); else sprintf(faName, "%s_%s_%d", chrom, table, blockIx); sprintf(faStartLine, "%s %s %s %d %d", faName, database, chrom, start, start+size); return faStartLine; } void writeOut(FILE *f, char *chrom, int start, int size, char strand, DNA *dna, char *faHeader) /* Write output to file */ { if (sameWord(outputType, "pos")) fprintf(f, "%s\t%d\t%d\t%c\n", chrom, start, start+size, strand); else if (sameWord(outputType, "fasta")) faWriteNext(f, faHeader, dna, size); else errAbort("Unknown output type %s\n", outputType); } void outputDna(FILE *f, char *chrom, char *table, int start, int size, char *dna, char *nibFileName, FILE *nibFile, int nibSize, char strand, char *faName) /* Output DNA either directly from nib or by upper-casing DNA. */ { if (merge >= 0) toUpperN(dna + start, size); else { struct dnaSeq *seq = nibLdPart(nibFileName, nibFile, nibSize, start, size); if (strand == '-') reverseComplement(seq->dna, size); if (faName == NULL) faName = makeFaStartLine(chrom, table, start, size); writeOut(f, chrom, start, size, strand, seq->dna, faName); freeDnaSeq(&seq); } } void chromFeatDna(char *table, char *chrom, FILE *f) /* chromFeatDna - Get dna for a type of feature on one chromosome. */ { /* Get chromosome in lower case case. If merging set bits that * are part of feature of interest to upper case, and then scan * for blocks of lower upper case and output them. If not merging * then just output dna for features directly. */ -struct dyString *query = newDyString(512); +struct dyString *query = dyStringNew(512); struct sqlConnection *conn = hAllocConn(database); struct sqlResult *sr; char **row; char chromField[32], startField[32], endField[32]; struct dnaSeq *seq = NULL; DNA *dna = NULL; int s=0,e,sz,i,size=0; boolean lastIsUpper = FALSE, isUpper = FALSE; char nibFileName[512]; FILE *nibFile = NULL; int nibSize; if (!hFindChromStartEndFields(database, table, chromField, startField, endField)) errAbort("Couldn't find chrom/start/end fields in table %s", table); if (merge >= 0) { seq = hLoadChrom(database, chrom); dna = seq->dna; size = seq->size; } else { hNibForChrom(database, chrom, nibFileName); nibOpenVerify(nibFileName, &nibFile, &nibSize); } if (breakUp) { if (sameString(startField, "tStart")) { sqlDyStringPrintf(query, "select * from %s where tStart >= %d and tEnd < %d", table, chromStart, chromEnd); - dyStringPrintf(query, " and %s = '%s'", chromField, chrom); + sqlDyStringPrintf(query, " and %s = '%s'", chromField, chrom); if (where != NULL) - dyStringPrintf(query, " and %s", where); + sqlDyStringPrintf(query, " and %-s", where); sr = sqlGetResult(conn, query->string); while ((row = sqlNextRow(sr)) != NULL) { struct psl *psl = pslLoad(row); if (psl->strand[1] == '-') /* Minus strand on target */ { int tSize = psl->tSize; for (i=0; i<psl->blockCount; ++i) { sz = psl->blockSizes[i]; s = tSize - (psl->tStarts[i] + sz); outputDna(f, chrom, table, s, sz, dna, nibFileName, nibFile, nibSize, '-', NULL); } } else { for (i=0; i<psl->blockCount; ++i) outputDna(f, chrom, table, psl->tStarts[i], psl->blockSizes[i], dna, nibFileName, nibFile, nibSize, '+', NULL); } pslFree(&psl); } } else if (sameString(startField, "txStart")) { sqlDyStringPrintf(query, "select * from %s where txStart >= %d and txEnd < %d", table, chromStart, chromEnd); - dyStringPrintf(query, " and %s = '%s'", chromField, chrom); + sqlDyStringPrintf(query, " and %s = '%s'", chromField, chrom); if (where != NULL) - dyStringPrintf(query, " and %s", where); + sqlDyStringPrintf(query, " and %-s", where); sr = sqlGetResult(conn, query->string); while ((row = sqlNextRow(sr)) != NULL) { struct genePred *gp = genePredLoad(row); for (i=0; i<gp->exonCount; ++i) { s = gp->exonStarts[i]; sz = gp->exonEnds[i] - s; outputDna(f, chrom, table, s, sz, dna, nibFileName, nibFile, nibSize, gp->strand[0], gp->name); } genePredFree(&gp); } } else { errAbort("Can only use breakUp parameter with psl or genePred formatted tables"); } } else { sqlDyStringPrintf(query, "select %s,%s from %s where %s >= %d and %s < %d", startField, endField, table, startField, chromStart, endField, chromEnd); - dyStringPrintf(query, " and %s = '%s'", chromField, chrom); + sqlDyStringPrintf(query, " and %s = '%s'", chromField, chrom); if (where != NULL) - dyStringPrintf(query, " and %s", where); + sqlDyStringPrintf(query, " and %-s", where); sr = sqlGetResult(conn, query->string); while ((row = sqlNextRow(sr)) != NULL) { s = sqlUnsigned(row[0]); e = sqlUnsigned(row[1]); sz = e - s; if (seq != NULL && (sz < 0 || e >= size)) errAbort("Coordinates out of range %d %d (%s size is %d)", s, e, chrom, size); outputDna(f, chrom, table, s, sz, dna, nibFileName, nibFile, nibSize, '+', NULL); } } /* Merge nearby upper case blocks. */ if (merge > 0) { e = -merge-10; /* Don't merge initial block. */ for (i=0; i<=size; ++i) { isUpper = isupper(dna[i]); if (isUpper && !lastIsUpper) { s = i; if (s - e <= merge) { toUpperN(dna+e, s-e); } } else if (!isUpper && lastIsUpper) { e = i; } lastIsUpper = isUpper; } } if (merge >= 0) { for (i=0; i<=size; ++i) { isUpper = isupper(dna[i]); if (isUpper && !lastIsUpper) s = i; else if (!isUpper && lastIsUpper) { e = i; sz = e - s; writeOut(f, chrom, s, sz, '+', dna+s, makeFaStartLine(chrom, table, s, sz)); } lastIsUpper = isUpper; } } hFreeConn(&conn); freeDnaSeq(&seq); carefulClose(&nibFile); } void getFeatDna(char *table, char *chrom, char *outName) /* getFeatDna - Get dna for a type of feature an all relevant chromosomes. */ { char chrTableBuf[256]; struct slName *chromList = NULL, *chromEl; boolean chromSpecificTable = !hTableExists(database, table); char *chrTable = (chromSpecificTable ? chrTableBuf : table); FILE *f = mustOpen(outName, "w"); boolean toStdout = (sameString(outName, "stdout")); if (sameWord(chrom, "all")) chromList = hAllChromNames(database); else chromList = newSlName(chrom); for (chromEl = chromList; chromEl != NULL; chromEl = chromEl->next) { chrom = chromEl->name; if (chromSpecificTable) { sprintf(chrTable, "%s_%s", chrom, table); if (!hTableExists(database, table)) errAbort("table %s (and %s) don't exist in %s", table, chrTable, database); } if (!toStdout) printf("Processing %s %s\n", chrTable, chrom); chromFeatDna(chrTable, chrom, f); } carefulClose(&f); if (!toStdout) printf("%d features extracted to %s\n", blockIx, outName); } int main(int argc, char *argv[]) /* Process command line. */ { cgiSpoof(&argc, argv); if (argc != 5) usage(); chromStart = cgiUsualInt("chromStart", chromStart); chromEnd = cgiUsualInt("chromEnd", chromEnd); + where = cgiOptionalString("where"); +if (where) + { + char whereSafe[4096]; + // TRUST command-line SQL where clause + sqlSafef(whereSafe, sizeof whereSafe, where, NULL); + where = whereSafe; + } + breakUp = cgiBoolean("breakUp"); merge = cgiUsualInt("merge", merge); database = argv[1]; getFeatDna(argv[2], argv[3], argv[4]); return 0; }