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/hgGoldGapGl/hgLoadGap.c src/hg/makeDb/hgGoldGapGl/hgLoadGap.c index 9f6d626..b53ea91 100644 --- src/hg/makeDb/hgGoldGapGl/hgLoadGap.c +++ src/hg/makeDb/hgGoldGapGl/hgLoadGap.c @@ -1,225 +1,225 @@ /* hgGoldGapGl - Put chromosome .agp and .gl files into browser database.. */ /* 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 "linefile.h" #include "dystring.h" #include "hash.h" #include "options.h" #include "agpFrag.h" #include "agpGap.h" #include "jksql.h" #include "ntContig.h" #include "glDbRep.h" #include "hdb.h" /* Command line switches. */ char *chrom = NULL; boolean unsplit = FALSE; boolean noLoad = FALSE; /* command line option specifications */ static struct optionSpec optionSpecs[] = { {"chrom", OPTION_STRING}, {"unsplit", OPTION_BOOLEAN}, {"noLoad", OPTION_BOOLEAN}, {NULL, 0} }; void usage() /* Explain usage and exit. */ { errAbort( "hgLoadGap - Load gap table from AGP-style file containing only gaps\n" "usage:\n" " hgLoadGap database dir\n" "options:\n" " -chrom=chrN - just do a single chromosome. Don't delete old tables.\n" " -unsplit - Instead of making chr*_gap tables from .gap files found \n" " in dir, expect dir to be a .gap file and make an \n" " unsplit gap table from its contents.\n" " -noLoad - Don't load the database table (for testing).\n" "example:\n" " hgLoadGap fr1 /cluster/data/fr1\n" " Gap file must be named with .gap extension \n" " This is only needed if gap table needs to be rebuilt,\n" " without changing the gold table.\n" ); } static int maxChromNameSize = 0; char *createGapSplit = "CREATE TABLE %s (\n" " bin smallint not null," " chrom varchar(255) not null, # which chromosome\n" " chromStart int unsigned not null, # start position in chromosome\n" " chromEnd int unsigned not null, # end position in chromosome\n" " ix int not null, # ix of this fragment (useless)\n" " n char(1) not null, # always 'N'\n" " size int unsigned not null, # size of gap\n" " type varchar(255) not null, # contig, clone, fragment, etc.\n" " bridge varchar(255) not null, # yes, no, mrna, bacEndPair, etc.\n" " #Indices\n" " INDEX(bin),\n" " UNIQUE(chromStart)\n" ")\n"; char *createGapUnsplit = "CREATE TABLE %s (\n" " bin smallint not null," " chrom varchar(255) not null, # which chromosome\n" " chromStart int unsigned not null, # start position in chromosome\n" " chromEnd int unsigned not null, # end position in chromosome\n" " ix int not null, # ix of this fragment (useless)\n" " n char(1) not null, # always 'N'\n" " size int unsigned not null, # size of gap\n" " type varchar(255) not null, # contig, clone, fragment, etc.\n" " bridge varchar(255) not null, # yes, no, mrna, bacEndPair, etc.\n" " #Indices\n" " INDEX(chrom(%d), bin),\n" " UNIQUE(chrom(%d), chromStart)\n" ")\n"; void gapFileToTable(struct sqlConnection *conn, char *gapFileName, char *gapTableName) /* Build a single gap table from a single gap file. */ { struct lineFile *lf = lineFileOpen(gapFileName, TRUE); char tabFileName[256]; FILE *tabFile = NULL; char *words[16]; int wordCount; safef(tabFileName, sizeof(tabFileName), "%s.tab", gapTableName); tabFile = mustOpen(tabFileName, "w"); while ((wordCount = lineFileChop(lf, words)) > 0) { if (wordCount < 5) errAbort("Short line %d of %s", lf->lineIx, lf->fileName); if (words[4][0] == 'N' || words[4][0] == 'U') { int len = strlen(words[0]); if (len > maxChromNameSize) { maxChromNameSize = len; if (maxChromNameSize > 254) errAbort("ERROR: chrom name size is over 254(%d) characters: " "'%s'", maxChromNameSize, words[0]); } struct agpGap gap; agpGapStaticLoad(words, &gap); gap.chromStart -= 1; fprintf(tabFile, "%u\t", hFindBin(gap.chromStart, gap.chromEnd)); agpGapTabOut(&gap, tabFile); } } lineFileClose(&lf); fclose(tabFile); if (! noLoad) { - struct dyString *ds = newDyString(2048); + struct dyString *ds = dyStringNew(2048); if (unsplit) sqlDyStringPrintf(ds, createGapUnsplit, gapTableName, maxChromNameSize, maxChromNameSize); else sqlDyStringPrintf(ds, createGapSplit, gapTableName); char query[1024]; sqlRemakeTable(conn, gapTableName, ds->string); sqlSafef(query, sizeof(query), "LOAD data local infile '%s' into table %s", tabFileName, gapTableName); sqlUpdate(conn, query); remove(tabFileName); - freeDyString(&ds); + dyStringFree(&ds); } } void makeGap(struct sqlConnection *conn, char *chromDir) /* Read in .gap files in chromDir and use them to create the * gap table for the corresponding chromosome(s). */ { struct fileInfo *fiList, *fi; fiList = listDirX(chromDir, "*.gap", TRUE); for (fi = fiList; fi != NULL; fi = fi->next) { char dir[256], chrom[128], ext[64]; char *ptr; char gapName[128]; char *gapFileName = fi->name; verbose(1, "Processing %s\n", gapFileName); /* Get full path name of .gap file and process it * into table names. */ splitPath(gapFileName, dir, chrom, ext); while ((ptr = strchr(chrom, '.')) != NULL) *ptr = '_'; safef(gapName, sizeof(gapName), "%s_gap", chrom); gapFileToTable(conn, gapFileName, gapName); } } void hgLoadGap(char *database, char *ooDir, char *oneChrom) /* hgLoadGap - Put chromosome .gap files into browser database.. */ { struct sqlConnection *conn = sqlConnect(database); /* target prefix is used in zoo browser */ if (oneChrom != NULL) { if (startsWith("chr", oneChrom)) oneChrom += 3; else if (startsWith("target", oneChrom)) oneChrom += 6; } if (unsplit) gapFileToTable(conn, ooDir, "gap"); else { struct fileInfo *chrFiList, *chrFi; char pathName[512]; boolean gotAny = FALSE; chrFiList = listDirX(ooDir, "*", FALSE); for (chrFi = chrFiList; chrFi != NULL; chrFi = chrFi->next) { if (chrFi->isDir && ((strlen(chrFi->name) <= 2) || startsWith("NA_", chrFi->name))) { if (oneChrom == NULL || sameWord(chrFi->name, oneChrom)) { safef(pathName, sizeof(pathName), "%s/%s", ooDir, chrFi->name); makeGap(conn, pathName); gotAny = TRUE; verbose(2, "done %s\n", chrFi->name); } } } slFreeList(&chrFiList); if (!gotAny) errAbort("No .gap files found"); } sqlDisconnect(&conn); } int main(int argc, char *argv[]) /* Process command line. */ { optionInit(&argc, argv, optionSpecs); if (argc != 3) usage(); chrom = optionVal("chrom", chrom); unsplit = optionExists("unsplit"); noLoad = optionExists("noLoad"); hgLoadGap(argv[1], argv[2], chrom); return 0; }