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/snpClassAndObserved.c src/hg/snp/snpLoad/snpClassAndObserved.c index 1bd3b4e..d2bd230 100644 --- src/hg/snp/snpLoad/snpClassAndObserved.c +++ src/hg/snp/snpLoad/snpClassAndObserved.c @@ -1,325 +1,325 @@ /* Copyright (C) 2013 The Regents of the University of California * See kent/LICENSE or http://genome.ucsc.edu/license/ for licensing information. */ /* snpClassAndObserved -- new seventh step * Hash the UniVariation table, storing subsnp_class and var_str. * subsnp_class is a number from 0-8. * Log and skip rows where subsnp_class = 0 or subsnp_class > 8. * Should only be a few of these. * Hash the SNP table, storing univar_id as string. * Again, log and skip rows where univar_id = 0. * There are likely order(10K) of these. * Serially read the chrN_snpTmp tables. * Do lookups into snpHash and univarHash. * Use UCSC chromInfo. */ /* Could drop refUCSCReverseComp here. */ /* Dropping ctg_id at this point. */ #include "common.h" #include "hash.h" #include "hdb.h" struct snpData { int classInt; char *observed; }; static struct hash *univarHash = NULL; static struct hash *snpHash = NULL; static char *snpDb = NULL; FILE *errorFileHandle = NULL; /* we will promote in-del to insertion if loc_type == 3 */ /* we will promote in-del to deletion if loc_type == 1 or loc_type == 2 */ /* we are hoping for no no-var and hardly any het */ char *classStrings[] = { "single", "in-del", "het", "microsatellite", "named", "no-var", "mixed", "mnp" }; int classCount = sizeof(classStrings); void usage() /* Explain usage and exit. */ { errAbort( "snpClassAndObserved - lookup class and observed in SNP and UniVariation tables\n" "check for errors in observed\n" "recreate chrN_snpTmp\n" "usage:\n" " snpClassAndObserved snpDb \n"); } struct hash *getUnivarHash() /* read var_str and subsnp_class of UniVar into hash indexed by univar_id. */ { struct snpData *el; char query[512]; struct sqlConnection *conn = hAllocConn(); struct sqlResult *sr; char **row; struct hash *ret = NULL; int classInt = 0; int rowCount = 0; int skipCount = 0; verbose(1, "create univarHash...\n"); ret = newHash(0); sqlSafef(query, sizeof(query), "select univar_id, var_str, subsnp_class from UniVariation"); sr = sqlGetResult(conn, query); while ((row = sqlNextRow(sr)) != NULL) { rowCount++; classInt = sqlUnsigned(row[2]); if (classInt == 0) { fprintf(errorFileHandle, "subsnp_class = 0 (zero) for univar_id %s (skipping)\n", row[0]); skipCount++; continue; } if (classInt > classCount) { fprintf(errorFileHandle, "unexpected subsnp_class = %d for univar_id %s (skipping)\n", classInt, row[0]); skipCount++; continue; } AllocVar(el); el->observed = cloneString(row[1]); el->classInt = classInt; hashAdd(ret, cloneString(row[0]), el); } sqlFreeResult(&sr); hFreeConn(&conn); verbose(1, "read %d rows in UniVariation\n", rowCount); verbose(1, "skipped %d rows \n", skipCount); return ret; } struct hash *getSNPHash() /* Store univar_id from SNP into hash indexed by snp_id. */ { char query[512]; struct sqlConnection *conn = hAllocConn(); struct sqlResult *sr; char **row; struct hash *ret = NULL; int id = 0; int rowCount = 0; int skipCount = 0; struct hashEl *univarElement = NULL; struct snpData *snpElementNew = NULL; struct snpData *snpElementOld = NULL; verbose(1, "creating snpHash...\n"); ret = newHash(16); sqlSafef(query, sizeof(query), "select snp_id, univar_id from SNP"); sr = sqlGetResult(conn, query); while ((row = sqlNextRow(sr)) != NULL) { rowCount++; id = sqlUnsigned(row[1]); if (id == 0) { fprintf(errorFileHandle, "univar_id = 0 (zero) for %s (skipping)\n", row[0]); skipCount++; continue; } /* check that this univar_id is in univarHash */ univarElement = hashLookup(univarHash, row[1]); if (univarElement == NULL) { fprintf(errorFileHandle, "univar_id = %s for %s missing from UniVariation table (leaving out of snpHash)\n", row[1], row[0]); skipCount++; continue; } /* clone */ snpElementOld = (struct snpData *)univarElement->val; AllocVar(snpElementNew); snpElementNew->observed = cloneString(snpElementOld->observed); snpElementNew->classInt = snpElementOld->classInt; hashAdd(ret, cloneString(row[0]), snpElementNew); } sqlFreeResult(&sr); hFreeConn(&conn); verbose(1, "read %d rows in SNP\n", rowCount); verbose(1, "skipped %d rows \n", skipCount); return ret; } void processSnps(char *chromName) /* read through all rows in snpTmp */ /* look up class and observed */ /* 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 hashEl *univarElement = NULL; struct snpData *dataElement = NULL; int classInt = 0; char *classString = NULL; int loc_type = 0; int skipCount = 0; 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, orientation, allele, refUCSC, refUCSCReverseComp, weight from %s ", tableName); sr = sqlGetResult(conn, query); while ((row = sqlNextRow(sr)) != NULL) { loc_type = sqlUnsigned(row[3]); /* get univarElement from snpHash */ univarElement = hashLookup(snpHash, row[0]); if (univarElement == NULL) { { fprintf(errorFileHandle, "no data for %s (dropping)\n", row[0]); skipCount++; continue; } } dataElement = (struct snpData *)univarElement->val; classInt = dataElement->classInt; // verbose(1, "classInt = %d\n", classInt); assert(classInt >= 1 && classInt <= classCount); /* lookup classString */ classString = classStrings[classInt-1]; /* special handling for class = in-del; split into classes of our own construction */ if (sameString(classString, "in-del")) { if (loc_type == 3) classString = cloneString("insertion"); if (loc_type == 1 || loc_type == 2) classString = cloneString("deletion"); } fprintf(f, "%s\t%s\t%s\t%d\t%s\t", row[0], row[1], row[2], loc_type, classString); fprintf(f, "%s\t%s\t%s\t%s\t%s\t%s\n", row[4], row[5], row[6], row[7], dataElement->observed, row[8]); } sqlFreeResult(&sr); hFreeConn(&conn); carefulClose(&f); if (skipCount > 0) verbose(1, "%d rows dropped\n", skipCount); } 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" " 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[]) /* hash subsnp_class and var_str from UniVariation */ /* read SNP for univar_id, lookup into univarHash */ /* store univarHash elements in snpHash */ /* read through chrN_snpTmp, rewrite with extensions to individual chrom tables */ { struct slName *chromList, *chromPtr; char tableName[64]; if (argc != 2) usage(); snpDb = argv[1]; hSetDb(snpDb); /* check for necessary tables */ if(!hTableExistsDb(snpDb, "SNP")) errAbort("missing SNP table"); if(!hTableExistsDb(snpDb, "UniVariation")) errAbort("missing UniVariation table"); chromList = hAllChromNamesDb(snpDb); errorFileHandle = mustOpen("snpClassAndObserved.errors", "w"); univarHash = getUnivarHash(); snpHash = getSNPHash(); for (chromPtr = chromList; chromPtr != NULL; chromPtr = chromPtr->next) { safef(tableName, ArraySize(tableName), "%s_snpTmp", chromPtr->name); if (!hTableExists(tableName)) continue; verbose(1, "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; }