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/mouseStuff/netClass/netClass.c src/hg/mouseStuff/netClass/netClass.c
index 3b7197b..07d216b 100644
--- src/hg/mouseStuff/netClass/netClass.c
+++ src/hg/mouseStuff/netClass/netClass.c
@@ -134,31 +134,33 @@
 }
 
 void getSeqGapsUnsplit(struct sqlConnection *conn, struct hash *chromHash)
 /* Return a tree of ranges for sequence gaps in all chromosomes, 
  * assuming an unsplit gap table -- when the table is unsplit, it's 
  * probably for a scaffold assembly where we *really* don't want 
  * to do one query per scaffold! */
 {
 struct rbTreeNode **stack = lmAlloc(qLm, 256 * sizeof(stack[0]));
 struct rbTree *tree = rbTreeNewDetailed(simpleRangeCmp, qLm, stack);
 int rowOffset = hOffsetPastBin(sqlGetDatabase(conn), NULL, "gap");
 struct sqlResult *sr;
 char **row;
 char *prevChrom = NULL;
 
-sr = sqlGetResult(conn, NOSQLINJ "select * from gap order by chrom");
+char query[1024];
+sqlSafef(query, sizeof query, "select * from gap order by chrom");
+sr = sqlGetResult(conn, query);
 while ((row = sqlNextRow(sr)) != NULL)
     {
     struct agpGap gap;
     struct simpleRange *range;
     agpGapStaticLoad(row+rowOffset, &gap);
     if (prevChrom == NULL)
 	prevChrom = cloneString(gap.chrom);
     else if (! sameString(prevChrom, gap.chrom))
 	{
 	setNGap(prevChrom, chromHash, tree);
 	freeMem(prevChrom);
 	stack = lmAlloc(qLm, 256 * sizeof(stack[0]));
 	tree = rbTreeNewDetailed(simpleRangeCmp, qLm, stack);
 	prevChrom = cloneString(gap.chrom);
 	}
@@ -206,32 +208,35 @@
 	     "looks like they weren't for %s", chr);
 chrom->trf = tree;
 }
 
 void getTrfUnsplit(struct sqlConnection *conn, struct hash *chromHash)
 /* Return a tree of ranges for simple repeats in all chromosomes, 
  * from a single query on the whole (unsplit) simpleRepeat table. */
 {
 struct rbTreeNode **stack = lmAlloc(qLm, 256 * sizeof(stack[0]));
 struct rbTree *tree = rbTreeNewDetailed(simpleRangeCmp, qLm, stack);
 struct simpleRange *range, *prevRange = NULL;
 struct sqlResult *sr;
 char **row;
 char *prevChrom = NULL;
 
-sr = sqlGetResult(conn, NOSQLINJ "select chrom,chromStart,chromEnd from simpleRepeat"
+char query[1024];
+sqlSafef(query, sizeof query, 
+"select chrom,chromStart,chromEnd from simpleRepeat"
 		  " order by chrom,chromStart");
+sr = sqlGetResult(conn, query);
 while ((row = sqlNextRow(sr)) != NULL)
     {
     if (prevChrom == NULL)
 	prevChrom = cloneString(row[0]);
     else if (! sameString(prevChrom, row[0]))
 	{
 	rbTreeAdd(tree, prevRange);
 	setTrf(prevChrom, chromHash, tree);
 	prevRange = NULL;
 	freeMem(prevChrom);
 	stack = lmAlloc(qLm, 256 * sizeof(stack[0]));
 	tree = rbTreeNewDetailed(simpleRangeCmp, qLm, stack);
 	prevChrom = cloneString(row[0]);
 	}
     lmAllocVar(tree->lm, range);
@@ -318,33 +323,35 @@
 	struct hash *chromHash, struct hash *arHash)
 /* Return a tree of ranges for sequence gaps all chromosomes, 
  * assuming an unsplit table -- when the table is unsplit, it's 
  * probably for a scaffold assembly where we *really* don't want 
  * to do one query per scaffold! */
 {
 struct sqlResult *sr;
 char **row;
 struct rbTreeNode **stack = lmAlloc(qLm, 256 * sizeof(stack[0]));
 struct rbTree *allTree = rbTreeNewDetailed(simpleRangeCmp, qLm, stack);
 struct rbTreeNode **newstack = lmAlloc(qLm, 256 * sizeof(newstack[0]));
 struct rbTree *newTree = rbTreeNewDetailed(simpleRangeCmp, qLm, newstack);
 char *prevChrom = NULL;
 struct simpleRange *prevRange = NULL, *prevNewRange = NULL;
 
-sr = sqlGetResult(conn,
-    NOSQLINJ "select genoName,genoStart,genoEnd,repName,repClass,repFamily from rmsk "
+char query[1024];
+sqlSafef(query, sizeof query, 
+    "select genoName,genoStart,genoEnd,repName,repClass,repFamily from rmsk "
     "order by genoName,genoStart");
+sr = sqlGetResult(conn, query);
 while ((row = sqlNextRow(sr)) != NULL)
     {
     struct simpleRange *range;
     char arKey[512];
     if (prevChrom == NULL)
 	prevChrom = cloneString(row[0]);
     else if (! sameString(prevChrom, row[0]))
 	{
 	rbTreeAdd(allTree, prevRange);
 	if (prevNewRange != NULL)
 	    rbTreeAdd(newTree, prevNewRange);
 	setRepeats(prevChrom, chromHash, allTree, newTree);
 	freeMem(prevChrom);
 	prevRange = prevNewRange = NULL;
 	stack = lmAlloc(qLm, 256 * sizeof(stack[0]));
@@ -646,50 +653,54 @@
 /* Get hash of ancient repeats.  This keyed by name.family.class. */
 {
 struct sqlConnection *conn = NULL;
 struct sqlResult *sr;
 char **row;
 char key[512];
 struct hash *hash = newHash(10);
 
 if (sqlTableExists(tConn, "ancientRepeat"))
     conn = tConn;
 else if (sqlTableExists(qConn, "ancientRepeat"))
     conn = qConn;
 else
     errAbort("Can't find ancientRepeat table in %s or %s",
 	     sqlGetDatabase(tConn), sqlGetDatabase(qConn));
-sr = sqlGetResult(conn, NOSQLINJ "select name,family,class from ancientRepeat");
+char query[1024];
+sqlSafef(query, sizeof query, "select name,family,class from ancientRepeat");
+sr = sqlGetResult(conn, query);
 while ((row = sqlNextRow(sr)) != NULL)
     {
     sprintf(key, "%s.%s.%s", row[0], row[1], row[2]);
     hashAdd(hash, key, NULL);
     }
 sqlFreeResult(&sr);
 return hash;
 }
 
 void getChroms(struct sqlConnection *conn, struct hash **retHash,
 	       struct chrom **retList)
 /* Get hash of chromosomes from database. */
 {
 struct sqlResult *sr;
 char **row;
 struct chrom *chromList = NULL, *chrom;
 struct hash *hash = hashNew(8);
 
-sr = sqlGetResult(conn, NOSQLINJ "select chrom,size from chromInfo");
+char query[1024];
+sqlSafef(query, sizeof query, "select chrom,size from chromInfo");
+sr = sqlGetResult(conn, query);
 while ((row = sqlNextRow(sr)) != NULL)
     {
     AllocVar(chrom);
     hashAddSaveName(hash, row[0], chrom, &chrom->name);
     chrom->size = atoi(row[1]);
     slAddHead(&chromList, chrom);
     }
 sqlFreeResult(&sr);
 slReverse(&chromList);
 *retHash = hash;
 *retList = chromList;
 }
 
 int liftStart(char *name, int start, struct hash *liftHash)
 /* Lift start if necessary. */