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/snp/snpLoad/snpSNP.c src/hg/snp/snpLoad/snpSNP.c index afefcd2..5227518 100644 --- src/hg/snp/snpLoad/snpSNP.c +++ src/hg/snp/snpLoad/snpSNP.c @@ -1,222 +1,222 @@ /* snpSNP - ninth step in dbSNP processing. * Read the chrN_snpTmp tables into memory. * Do lookups into SNP for validation status and heterozygosity. * Could combine this with earlier step snpClassAndObserved, which also uses the SNP table. * Report if missing. * Use UCSC chromInfo. */ /* 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 "hash.h" #include "hdb.h" struct snpData { int validation_status; char *avHet; char *avHetSE; }; static char *snpDb = NULL; FILE *errorFileHandle = NULL; static struct hash *snpDataHash = NULL; void usage() /* Explain usage and exit. */ { errAbort( "snpSNP - lookup validation status and heterozygosity in SNP\n" "recreate chrN_snpTmp\n" "usage:\n" " snpSNP snpDb \n"); } void readSNP() /* get validation status and heterozygosity from SNP table */ /* store in global snpDataHash */ { char query[512]; struct sqlConnection *conn = hAllocConn(); struct sqlResult *sr; char **row; int validInt = 0; struct snpData *sel; /* could increase the default size */ snpDataHash = newHash(16); sqlSafef(query, sizeof(query), "select snp_id, validation_status, avg_heterozygosity, het_se from SNP"); sr = sqlGetResult(conn, query); while ((row = sqlNextRow(sr)) != NULL) { validInt = sqlUnsigned(row[1]); if (validInt > 31) { fprintf(errorFileHandle, "unexpected validation_status %d for snp_id %s\n", validInt, row[0]); validInt = 0; } AllocVar(sel); sel->validation_status = validInt; sel->avHet = cloneString(row[2]); sel->avHetSE = cloneString(row[3]); hashAdd(snpDataHash, cloneString(row[0]), sel); } sqlFreeResult(&sr); hFreeConn(&conn); } void processSnps(char *chromName) /* read through chrN_snpTmp tables */ /* lookup into snpDataHash */ /* write to output file */ { char query[512]; struct sqlConnection *conn = hAllocConn(); struct sqlResult *sr; char **row; char tableName[64]; char fileName[64]; FILE *f; struct snpData *sel = NULL; safef(tableName, ArraySize(tableName), "%s_snpTmp", chromName); safef(fileName, ArraySize(fileName), "%s_snpTmp.tab", chromName); f = mustOpen(fileName, "w"); sqlSafef(query, sizeof(query), "select snp_id, chromStart, chromEnd, loc_type, class, orientation, fxn_class, " "allele, refUCSC, refUCSCReverseComp, observed, weight from %s ", tableName); sr = sqlGetResult(conn, query); while ((row = sqlNextRow(sr)) != NULL) { sel = hashFindVal(snpDataHash, row[0]); if (sel == NULL) { fprintf(f, "%s\t%s\t%s\t%s\t", row[0], row[1], row[2], row[3]); fprintf(f, "%s\t%s\t%s\t", row[4], row[5], row[6]); fprintf(f, "0\t0.0\t0.0\t"); fprintf(f, "%s\t%s\t%s\t%s\t%s\n", row[7], row[8], row[9], row[10], row[11]); fprintf(errorFileHandle, "no match for snp_id %s\n", row[0]); continue; } /* check here for avHet < 0 */ /* check here for class = "single" and isBiallelic(observed) and avHet <= .5 */ /* check here for class = "single" and isTriallelic(observed) and avHet <= .3333 */ /* check here for class = "single" and isQuadallelic(observed) and avHet <= .25 */ fprintf(f, "%s\t%s\t%s\t%s\t", row[0], row[1], row[2], row[3]); fprintf(f, "%s\t%s\t%s\t", row[4], row[5], row[6]); fprintf(f, "%d\t%s\t%s\t", sel->validation_status, sel->avHet, sel->avHetSE); fprintf(f, "%s\t%s\t%s\t%s\t%s\n", row[7], row[8], row[9], row[10], row[11]); } sqlFreeResult(&sr); hFreeConn(&conn); carefulClose(&f); } void recreateDatabaseTable(char *chromName) /* create a new chrN_snpTmp table with new definition */ { struct sqlConnection *conn = hAllocConn(); char tableName[64]; char *createString = "CREATE TABLE %s (\n" " snp_id int(11) not null,\n" " chromStart int(11) not null,\n" " chromEnd int(11) not null,\n" " loc_type tinyint(4) not null,\n" " class varchar(255) not null,\n" " orientation tinyint(4) not null,\n" " fxn_class varchar(255) not null,\n" " validation_status tinyint(4) not null,\n" " avHet float not null, \n" " avHetSE float not null, \n" " allele blob,\n" " refUCSC blob,\n" " refUCSCReverseComp blob,\n" " observed blob,\n" " weight int\n" ");\n"; -struct dyString *dy = newDyString(1024); +struct dyString *dy = dyStringNew(1024); safef(tableName, ArraySize(tableName), "%s_snpTmp", chromName); sqlDyStringPrintf(dy, createString, tableName); sqlRemakeTable(conn, tableName, dy->string); dyStringFree(&dy); hFreeConn(&conn); } void loadDatabase(char *chromName) /* load one table into database */ { FILE *f; struct sqlConnection *conn = hAllocConn(); char tableName[64], fileName[64]; safef(tableName, ArraySize(tableName), "%s_snpTmp", chromName); safef(fileName, ArraySize(fileName), "%s_snpTmp.tab", chromName); f = mustOpen(fileName, "r"); /* hgLoadTabFile closes the file handle */ hgLoadTabFile(conn, ".", tableName, &f); hFreeConn(&conn); } int main(int argc, char *argv[]) /* read chrN_snpTmp, lookup in snpFasta, rewrite to individual chrom tables */ { struct slName *chromList, *chromPtr; char tableName[64]; if (argc != 2) usage(); snpDb = argv[1]; hSetDb(snpDb); chromList = hAllChromNamesDb(snpDb); if (chromList == NULL) { verbose(1, "couldn't get chrom info\n"); return 1; } errorFileHandle = mustOpen("snpSNP.errors", "w"); /* read into global hash */ verbose(1, "reading SNP table into hash...\n"); readSNP(); for (chromPtr = chromList; chromPtr != NULL; chromPtr = chromPtr->next) { safef(tableName, ArraySize(tableName), "%s_snpTmp", chromPtr->name); if (!hTableExists(tableName)) continue; verbose(1, "processing chrom = %s\n", chromPtr->name); processSnps(chromPtr->name); } carefulClose(&errorFileHandle); for (chromPtr = chromList; chromPtr != NULL; chromPtr = chromPtr->next) { safef(tableName, ArraySize(tableName), "%s_snpTmp", chromPtr->name); if (!hTableExists(tableName)) continue; recreateDatabaseTable(chromPtr->name); verbose(1, "loading chrom = %s\n", chromPtr->name); loadDatabase(chromPtr->name); } return 0; }