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/bedExtendRanges/bedExtendRanges.c src/hg/utils/bedExtendRanges/bedExtendRanges.c index 7a3863b..949d5f6 100644 --- src/hg/utils/bedExtendRanges/bedExtendRanges.c +++ src/hg/utils/bedExtendRanges/bedExtendRanges.c @@ -1,208 +1,210 @@ /* bedExtendRanges - extend bed item sizes. */ /* 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 "jksql.h" #include "dystring.h" #include "chromInfo.h" #include "hdb.h" #include "portable.h" static boolean strictTab = FALSE; /* Separate on tabs. */ static struct hash *chromHash = NULL; char *host = NULL; char *user = NULL; char *password = NULL; static struct optionSpec optionSpecs[] = { {"tab", OPTION_BOOLEAN}, {"host", OPTION_STRING}, {"user", OPTION_STRING}, {"password", OPTION_STRING}, {NULL, 0} }; /* Command line switches. */ void usage() /* Explain usage and exit. */ { errAbort( "bedExtendRanges - extend length of entries in bed 6+ data to be at least the given length,\n" "taking strand directionality into account.\n\n" "usage:\n" " bedExtendRanges database length files(s)\n\n" "options:\n" " -host\tmysql host\n" " -user\tmysql user\n" " -password\tmysql password\n" " -tab\t\tSeparate by tabs rather than space\n" " -verbose=N - verbose level for extra information to STDERR\n\n" "example:\n\n" " bedExtendRanges hg18 250 stdin\n\n" " bedExtendRanges -user=genome -host=genome-mysql.soe.ucsc.edu hg18 250 stdin\n\n" "will transform:\n" " chr1 500 525 . 100 +\n" " chr1 1000 1025 . 100 -\n" "to:\n" " chr1 500 750 . 100 +\n" " chr1 775 1025 . 100 -\n" ); } static struct hash *loadAllChromInfo(char *database) /* Load up all chromosome infos. */ { struct chromInfo *el; struct sqlConnection *conn = NULL; struct sqlResult *sr = NULL; struct hash *ret; char **row; boolean localDb = TRUE; if(host) { conn = sqlConnectRemote(host, user, password, database); localDb = FALSE; } else { conn = hAllocConn(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); 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); if(localDb) hFreeConn(&conn); 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 (note: chrom names are case sensitive)", chromosome); return *(unsigned *)el->val; } static void processOneFile(char *fileName, int bedSize, int length) { struct lineFile *lf = lineFileOpen(fileName, TRUE); char *words[64], *line; int wordCount; verbose(1, "Reading %s\n", lf->fileName); while (lineFileNextReal(lf, &line)) { int i; char *dupe = cloneString(line); if (strictTab) wordCount = chopTabs(line, words); else wordCount = chopLine(line, words); /* ignore empty lines */ if (0 == wordCount) continue; lineFileExpectAtLeast(lf, bedSize, wordCount); char *chrom = words[0]; // use signed for chromStart b/c calculations below may (temorarily) yield a negative number. int chromStart = lineFileNeedNum(lf, words, 1); unsigned chromEnd = lineFileNeedNum(lf, words, 2); char *name = words[3]; int score = lineFileNeedNum(lf, words, 4); char *strand = words[5]; 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); int delta = length - (chromEnd - chromStart); if(delta && delta > 0) { if(sameString(strand, "+")) chromEnd += delta; else if (sameString(strand, "-")) chromStart -= delta; else { chromStart -= delta / 2; chromEnd += delta / 2 + delta % 2; } } chromStart = max(0, chromStart); unsigned size = chromosomeSize(chrom); // XXXX special-case chrM? chromEnd = min(chromEnd, size); char sep = strictTab ? '\t' : ' '; printf("%s%c%d%c%d%c%s%c%d%c%s", chrom, sep, chromStart, sep, chromEnd, sep, name, sep, score, sep, strand); // print out remaining (unprocessed) fields. for(i=6;i<wordCount;i++) { printf("%c%s", sep, words[i]); } printf("\n"); freeMem(dupe); } } static void bedExtendRanges(char *database, int length, int count, char *files[]) /* bedExtendRanges - process each file to extend ranges. */ { int i; chromHash = loadAllChromInfo(database); if (verboseLevel() > 2) { struct hashCookie cookie; struct hashEl *el; cookie = hashFirst(chromHash); verbose(3,"chrom\tsize\n"); while ((el = hashNext(&cookie)) != NULL) { unsigned size; size = chromosomeSize(el->name); verbose(3,"%s\t%u\n", el->name, size); } } for (i=0; i<count; ++i) processOneFile(files[i], 6, length); } int main(int argc, char *argv[]) /* Process command line. */ { optionInit(&argc, argv, optionSpecs); if (argc < 3) usage(); strictTab = optionExists("tab"); host = optionVal("host", NULL); user = optionVal("user", NULL); password = optionVal("password", NULL); bedExtendRanges(argv[1], atoi(argv[2]), argc-3, argv+3); return 0; }