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/snpFunction.c src/hg/snp/snpLoad/snpFunction.c
index 3419b52..823c0bd 100644
--- src/hg/snp/snpLoad/snpFunction.c
+++ src/hg/snp/snpLoad/snpFunction.c
@@ -1,183 +1,183 @@
 /* snpFunction: eighth step in dbSnp processing.
  * Add fxn_class values (can be more than one) to chrN_snpTmp.
  * Create a hash from ContigLocusIdCondense table. */
 
 /* 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"
 
 
 static char *snpDb = NULL;
 static struct hash *functionHash = NULL;
 
 void usage()
 /* Explain usage and exit. */
 {
 errAbort(
     "snpFunction - add function to chrN_snpTmp tables\n"
     "usage:\n"
     "    snpFunction snpDb \n");
 }
 
 
 
 struct hash *createFunctionHash()
 {
 struct hash *ret;
 char query[512];
 struct sqlConnection *conn = hAllocConn();
 struct sqlResult *sr;
 char **row;
 char *snpString = NULL;
 char *functionString = NULL;
 
 verbose(1, "building function hash...\n");
 ret = newHash(18);
 sqlSafef(query, sizeof(query), "select snp_id, fxn_class from ContigLocusIdCondense");
 sr = sqlGetResult(conn, query);
 while ((row = sqlNextRow(sr)) != NULL)
     {
     snpString = cloneString(row[0]);
     functionString = cloneString(row[1]);
     // hashAdd(ret, snpString, (void *)(&functionString));
     hashAdd(ret, snpString, functionString);
     }
 sqlFreeResult(&sr);
 hFreeConn(&conn);
 return ret;
 }
 
 
 void addFunction(char *chromName)
 /* Look up function for each row */
 {
 char query[512];
 struct sqlConnection *conn = hAllocConn();
 struct sqlResult *sr;
 char **row;
 struct hashEl *el1;
 FILE *f;
 char fileName[64];
 char tableName[64];
 
 safef(tableName, ArraySize(tableName), "%s_snpTmp", chromName);
 if (!hTableExists(tableName)) return;
 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, "
     "allele, refUCSC, refUCSCReverseComp, observed, weight from %s", tableName);
 
 sr = sqlGetResult(conn, query);
 while ((row = sqlNextRow(sr)) != NULL)
     {
     fprintf(f, "%s\t%s\t%s\t%s\t%s\t%s\t", row[0], row[1], row[2], row[3], row[4], row[5]);
     el1 = hashLookup(functionHash,row[0]);
     if (el1 == NULL)
 	fprintf(f, "unknown\t");
     else
         fprintf(f, "%s\t", (char *)el1->val);
     fprintf(f, "%s\t%s\t%s\t%s\t%s\n", row[6], row[7], row[8], row[9], row[10]);
     }
 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"
 "    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(conn, ".", tableName, &f);
 
 hFreeConn(&conn);
 }
 
 
 
 int main(int argc, char *argv[])
 /* Read chromInfo into hash. */
 /* Read ContigLocusIdCondense into hash. */
 /* Recreate chrN_snpTmp, adding fxn_classes. */
 {
 struct slName *chromList, *chromPtr;
 char tableName[64];
 
 if (argc != 2)
     usage();
 
 snpDb = argv[1];
 hSetDb(snpDb);
 chromList = hAllChromNamesDb(snpDb);
 
 /* check for needed tables */
 if(!hTableExistsDb(snpDb, "ContigLocusIdCondense"))
     errAbort("no ContigLocusIdCondense table in %s\n", snpDb);
 if(!hTableExistsDb(snpDb, "chromInfo"))
     errAbort("no chromInfo table in %s\n", snpDb);
 
 functionHash = createFunctionHash();
 
 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);
     addFunction(chromPtr->name);
     }
 
 for (chromPtr = chromList; chromPtr != NULL; chromPtr = chromPtr->next)
     {
     safef(tableName, ArraySize(tableName), "%s_snpTmp", chromPtr->name);
     if (!hTableExists(tableName)) continue;
     verbose(1, "loading chrom = %s\n", chromPtr->name);
     recreateDatabaseTable(chromPtr->name);
     loadDatabase(chromPtr->name);
     }
 
 return 0;
 }