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/hgNibSeq/hgNibSeq.c src/hg/makeDb/hgNibSeq/hgNibSeq.c
index af263fc..3f82da7 100644
--- src/hg/makeDb/hgNibSeq/hgNibSeq.c
+++ src/hg/makeDb/hgNibSeq/hgNibSeq.c
@@ -1,123 +1,123 @@
 /* hgNibSeq - convert DNA to nibble-a-base and store location in 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 "dystring.h"
 #include "fa.h"
 #include "nib.h"
 #include "jksql.h"
 #include "options.h"
 
 
 boolean preMadeNib = FALSE;
 char *tableName = "chromInfo";
 char *chromPrefix = "";
 boolean appendTbl = FALSE;
 char *tableIndex = "PRIMARY KEY(chrom(16))";
 
 void usage()
 /* Explain usage and exit. */
 {
 errAbort(
   "hgNibSeq - convert DNA to nibble-a-base and store location in database\n"
   "usage:\n"
   "   hgNibSeq database nibDir file(s).fa\n"
   "This will create .nib versions of all the input .fa files in nibDir\n"
   "and store pointers to them in the database. Use full path name for nibDir.\n"
   "options:\n"
   "   -preMadeNib  don't bother generating nib files, they exist already\n"
   "   -table=tableName - Use this table name rather than %s\n"
   "   -chromPrefix=str - prefix chrom names with this string\n"
   "   -append - append to existing table, don't delete\n"
   "   -index=str - use str as SQL table index instead of default %s\n"
   , tableName, tableIndex);
 }
 
 char *createSql = 
 "CREATE TABLE %s (\n"
     "chrom varchar(255) not null,	# Chromosome name\n"
     "size int unsigned not null,	# Chromosome size\n"
     "fileName varchar(255) not null,	# Chromosome file (raw one byte per base)\n"
               "#Indices\n"
     "%s\n"
     ")\n";
 
 void createTable(struct sqlConnection *conn)
 /* Make table. */
 {
-struct dyString *dy = newDyString(512);
+struct dyString *dy = dyStringNew(512);
 sqlDyStringPrintf(dy, createSql, tableName, tableIndex);
 sqlRemakeTable(conn, tableName, dy->string);
 dyStringFree(&dy);
 }
 
 void hgNibSeq(char *database, char *destDir, int faCount, char *faNames[])
 /* hgNibSeq - convert DNA to nibble-a-base and store location in database. */
 {
 char dir[256], name[128], chromName[128], ext[64];
 char nibName[512];
 struct sqlConnection *conn = sqlConnect(database);
 char query[512];
 int i;
 char *faName;
 struct dnaSeq *seq = NULL;
 unsigned long total = 0;
 int size;
 
 if (!strchr(destDir, '/'))
    errAbort("Use full path name for nib file dir\n");
 
 makeDir(destDir);
 if ((!appendTbl) || !sqlTableExists(conn, tableName))
     createTable(conn);
 for (i=0; i<faCount; ++i)
     {
     faName = faNames[i];
     splitPath(faName, dir, name, ext);
     sprintf(nibName, "%s/%s.nib", destDir, name);
     printf("Processing %s to %s\n", faName, nibName);
     if (preMadeNib)
         {
 	FILE *nibFile;
 	nibOpenVerify(nibName, &nibFile, &size);
 	carefulClose(&nibFile);
 	}
     else
 	{
 	seq = faReadDna(faName);
 	if (seq != NULL)
 	    {
 	    size = seq->size;
 	    uglyf("Read DNA\n");
 	    nibWrite(seq, nibName);
 	    uglyf("Wrote nib\n");
 	    freeDnaSeq(&seq);
 	    }
 	}
     strcpy(chromName, chromPrefix);
     strcat(chromName, name);
     sqlSafef(query, sizeof query, "INSERT into %s VALUES('%s', %d, '%s')",
         tableName, chromName, size, nibName);
     sqlUpdate(conn,query);
     total += size;
     }
 sqlDisconnect(&conn);
 printf("%lu total bases\n", total);
 }
 
 int main(int argc, char *argv[])
 /* Process command line. */
 {
 optionHash(&argc, argv);
 if (argc < 3)
     usage();
 preMadeNib = optionExists("preMadeNib");
 tableName = optionVal("table", tableName);
 chromPrefix = optionVal("chromPrefix", chromPrefix);
 appendTbl = optionExists("append");
 tableIndex = optionVal("index", tableIndex);
 hgNibSeq(argv[1], argv[2], argc-3, argv+3);
 return 0;
 }