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/hgLoadBed/hgLoadBed.c src/hg/makeDb/hgLoadBed/hgLoadBed.c index 709061d..ff438f8 100644 --- src/hg/makeDb/hgLoadBed/hgLoadBed.c +++ src/hg/makeDb/hgLoadBed/hgLoadBed.c @@ -438,37 +438,49 @@ writeFailed(fileName); if (i == wordCount-1) { if (fputc('\n', f) == EOF) writeFailed(fileName); } else if (fputc('\t', f) == EOF) writeFailed(fileName); } } fclose(f); } -static void maybeBedGraph(int col, struct dyString *dy, char *colDefinition) +static void maybeBedGraph(int col, struct dyString *dy, char *format, ...) +#ifdef __GNUC__ +__attribute__((format(printf, 3, 4))) +#endif +; + +static void maybeBedGraph(int col, struct dyString *dy, char *format, ...) /* output definition "default" for column "col" when not bedGraph */ { if (col == bedGraph) - dyStringAppend(dy, " dataValue float not null,\n"); + sqlDyStringPrintf(dy, " dataValue float not null,\n"); else - dyStringAppend(dy, colDefinition); + { + // use format varargs + va_list args; + va_start(args, format); + vaSqlDyStringPrintf(dy, format, args); + va_end(args); + } } static boolean colAlreadyThere(struct sqlConnection *conn, char *tableName, char *col) /* Check to see if there's a field in the table already */ { char existsSql[128]; sqlSafef(existsSql, sizeof(existsSql), "desc %s %s", tableName, col); return sqlExists(conn, existsSql); } static void addBinToEmptyTable(struct sqlConnection *conn, char *tableName) /* Add bin field and corresponding index. */ { if (!colAlreadyThere(conn, tableName, "bin")) { @@ -510,31 +522,31 @@ && (oneName != NULL); i++, oneName = oneName->next) { char query[256]; sqlSafef(query, sizeof(query), "alter table %s drop column %s", tableName, oneName->name); sqlUpdate(conn, query); } } slFreeList(&fieldNames); } static void loadDatabase(char *database, char *track, int bedSize, struct bedStub *bedList) /* Load database from bedList. */ { struct sqlConnection *conn; -struct dyString *dy = newDyString(1024); +struct dyString *dy = dyStringNew(1024); char *tab = (char *)NULL; int loadOptions = (optionExists("onServer") ? SQL_TAB_FILE_ON_SERVER : 0); if ( ! noLoad ) conn = sqlConnect(database); if ((char *)NULL != tmpDir) tab = cloneString(rTempName(tmpDir,"loadBed",".tab")); else tab = cloneString("bed.tab"); if (bedDetail && sqlTable == NULL && !customTrackLoader) errAbort("bedDetail format requires sqlTable option"); if (bedDetail && !strictTab) errAbort("bedDetail format must be tab separated"); @@ -552,102 +564,102 @@ if (s != NULL) *s = 0; if ( !noLoad ) { if (renameSqlTable) { char *pos = stringIn("CREATE TABLE ", sql); if (pos == NULL) errAbort("Can't find CREATE TABLE in %s\n", sqlTable); char *oldSql = cloneString(sql); nextWord(&pos); nextWord(&pos); char *tableName = nextWord(&pos); sql = replaceChars(oldSql, tableName, track); } verbose(1, "Creating table definition for %s from sql: %s\n", track, sqlTable); - // add NOSQLINJ tag - sqlDyStringPrintf(dy, "%-s", sql); + // from trusted .sql disk source. + sqlDyStringPrintf(dy, sql, NULL); sqlRemakeTable(conn, track, dy->string); if (!noBin) addBinToEmptyTable(conn, track); adjustSqlTableColumns(conn, track, bedSize); } freez(&sql); } else if (!oldTable) { int minLength; if (noLoad) minLength=6; else if (maxChromNameLength) minLength = maxChromNameLength; else minLength = hGetMinIndexLength(database); verbose(2, "INDEX chrom length: %d\n", minLength); /* Create definition statement. */ verbose(1, "Creating table definition for %s, bedSize: %d\n", track, bedSize); sqlDyStringPrintf(dy, "CREATE TABLE %s (\n", track); if (!noBin) - dyStringAppend(dy, " bin smallint unsigned not null,\n"); - dyStringAppend(dy, " chrom varchar(255) not null,\n"); - dyStringAppend(dy, " chromStart int unsigned not null,\n"); - dyStringAppend(dy, " chromEnd int unsigned not null,\n"); + sqlDyStringPrintf(dy, " bin smallint unsigned not null,\n"); + sqlDyStringPrintf(dy, " chrom varchar(255) not null,\n"); + sqlDyStringPrintf(dy, " chromStart int unsigned not null,\n"); + sqlDyStringPrintf(dy, " chromEnd int unsigned not null,\n"); if (bedSize >= 4) maybeBedGraph(4, dy, " name varchar(255) not null,\n"); if (bedSize >= 5) { if (allowNegativeScores) maybeBedGraph(5, dy, " score int not null,\n"); else maybeBedGraph(5, dy, " score int unsigned not null,\n"); } if (bedSize >= 6) maybeBedGraph(6, dy, " strand char(1) not null,\n"); if (bedSize >= 7) maybeBedGraph(7, dy, " thickStart int unsigned not null,\n"); if (bedSize >= 8) maybeBedGraph(8, dy, " thickEnd int unsigned not null,\n"); /* As of 2004-11-22 the reserved field is used as itemRgb in code */ if (bedSize >= 9) maybeBedGraph(9, dy, " reserved int unsigned not null,\n"); if (bedSize >= 10) maybeBedGraph(10, dy, " blockCount int unsigned not null,\n"); if (bedSize >= 11) maybeBedGraph(11, dy, " blockSizes longblob not null,\n"); if (bedSize >= 12) maybeBedGraph(12, dy, " chromStarts longblob not null,\n"); if (bedSize >= 13) maybeBedGraph(13, dy, " expCount int unsigned not null,\n"); if (bedSize >= 14) maybeBedGraph(14, dy, " expIds longblob not null,\n"); if (bedSize >= 15) maybeBedGraph(15, dy, " expScores longblob not null,\n"); - dyStringAppend(dy, "#Indices\n"); + sqlDyStringPrintf(dy, "#Indices\n"); if (nameIx && (bedSize >= 4) && (0 == bedGraph)) - dyStringAppend(dy, " INDEX(name(16)),\n"); + sqlDyStringPrintf(dy, " INDEX(name(16)),\n"); if (noBin) { - dyStringPrintf(dy, " INDEX(chrom(%d),chromStart)\n", minLength); + sqlDyStringPrintf(dy, " INDEX(chrom(%d),chromStart)\n", minLength); } else { - dyStringPrintf(dy, " INDEX(chrom(%d),bin)\n", minLength); + sqlDyStringPrintf(dy, " INDEX(chrom(%d),bin)\n", minLength); } - dyStringAppend(dy, ")\n"); + sqlDyStringPrintf(dy, ")\n"); if (noLoad) verbose(2,"%s", dy->string); else sqlRemakeTable(conn, track, dy->string); } verbose(1, "Saving %s\n", tab); writeBedTab(tab, bedList); if ( ! noLoad ) { verbose(1, "Loading %s\n", database); if (customTrackLoader) sqlLoadTabFile(conn, tab, track, loadOptions|SQL_TAB_FILE_WARN_ON_WARN); else