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/hgTracks/gencodeTracks.c src/hg/hgTracks/gencodeTracks.c
index 2960563..47fe47e 100644
--- src/hg/hgTracks/gencodeTracks.c
+++ src/hg/hgTracks/gencodeTracks.c
@@ -232,31 +232,31 @@
 /* generate SQL where clause for annotation tag filtering */
 {
 gencodeQueryBeginSubWhere(gencodeQuery);
 filterByTagChoicesQuery(filterBy, gencodeQuery);
 gencodeQuery->joinTag = TRUE;
 gencodeQueryEndSubWhere(gencodeQuery);
 }
 
 static void filterByAttrsQuery(struct track *tg, filterBy_t *filterBy, struct gencodeQuery *gencodeQuery)
 /* handle adding on filterBy clause for attributes table */
 {
 char *clause = filterByClause(filterBy);
 if (clause != NULL)
     {
     gencodeQueryBeginSubWhere(gencodeQuery);
-    dyStringPrintf(gencodeQuery->where, "%s", clause);
+    sqlDyStringPrintf(gencodeQuery->where, "%-s", clause);
     gencodeQuery->joinAttrs = TRUE;
     gencodeQueryEndSubWhere(gencodeQuery);
     freeMem(clause);
     }
 }
 
 static void gencodeFilterByQuery(struct track *tg, filterBy_t *filterBy, struct gencodeQuery *gencodeQuery)
 /* handle adding on filterBy clause for gencode */
 {
 if (sameString(filterBy->column, "transcriptMethod"))
     filterByMethodQuery(tg, filterBy, gencodeQuery);
 else if (sameString(filterBy->column, "supportLevel"))
     filterBySupportLevelQuery(tg, filterBy, gencodeQuery);
 else if (sameString(filterBy->column, "tag"))
     filterByTagQuery(tg, filterBy, gencodeQuery);
@@ -271,70 +271,71 @@
 /* build where sql clauses for filters or highlights. */
 {
 filterBy_t *filterBySet = filterBySetGetFunc(tg->tdb, cart, NULL);
 filterBy_t *filterBy;
 for (filterBy = filterBySet; filterBy != NULL; filterBy = filterBy->next)
     {
     if (!filterByAllChosen(filterBy))
         gencodeFilterByQuery(tg, filterBy, gencodeQuery);
     }
 filterBySetFree(&filterBySet);
 }
 
 static void addQueryTables(struct track *tg, struct gencodeQuery *gencodeQuery)
 /* add required from tables and joins */
 {
-sqlDyStringPrintfFrag(gencodeQuery->from, "%s g", tg->table);
+sqlDyStringPrintf(gencodeQuery->from, "%s g", tg->table);
 if (gencodeQuery->joinAttrs)
     {
     sqlDyStringPrintf(gencodeQuery->from, ", %s attrs", trackDbRequiredSetting(tg->tdb, "wgEncodeGencodeAttrs"));
-    dyStringAppend(gencodeQuery->where, " and (attrs.transcriptId = g.name)");
+    sqlDyStringPrintf(gencodeQuery->where, " and (attrs.transcriptId = g.name)");
     }
 if (gencodeQuery->joinTranscriptSource)
     {
     sqlDyStringPrintf(gencodeQuery->from, ", %s transSrc", trackDbRequiredSetting(tg->tdb, "wgEncodeGencodeTranscriptSource"));
-    dyStringAppend(gencodeQuery->where, " and (transSrc.transcriptId = g.name)");
+    sqlDyStringPrintf(gencodeQuery->where, " and (transSrc.transcriptId = g.name)");
     }
 if (gencodeQuery->joinSupportLevel)
     {
     sqlDyStringPrintf(gencodeQuery->from, ", %s supLevel", trackDbRequiredSetting(tg->tdb, "wgEncodeGencodeTranscriptionSupportLevel"));
-    dyStringAppend(gencodeQuery->where, " and (supLevel.transcriptId = g.name)");
+    sqlDyStringPrintf(gencodeQuery->where, " and (supLevel.transcriptId = g.name)");
     }
 if (gencodeQuery->joinTag)
     {
     sqlDyStringPrintf(gencodeQuery->from, ", %s tag", trackDbRequiredSetting(tg->tdb, "wgEncodeGencodeTag"));
-    dyStringAppend(gencodeQuery->where, " and (tag.transcriptId = g.name)");
+    sqlDyStringPrintf(gencodeQuery->where, " and (tag.transcriptId = g.name)");
     }
 }
 
 static void addQueryCommon(struct track *tg, filterBySetGetFuncType filterBySetGetFunc, struct gencodeQuery *gencodeQuery)
 /* Add tables and joins for both gene and highlight queries */
 {
 // bin range overlap part
 hAddBinToQuery(winStart, winEnd, gencodeQuery->where);
 sqlDyStringPrintf(gencodeQuery->where, "(g.chrom = \"%s\") and (g.txStart < %u) and (g.txEnd > %u)", chromName, winEnd, winStart);
 
 gencodeFilterBySetQuery(tg, filterBySetGetFunc, gencodeQuery);
 addQueryTables(tg, gencodeQuery);
 }
 
 static struct sqlResult *executeQuery(struct sqlConnection *conn, struct gencodeQuery *gencodeQuery)
 /* execute the actual SQL query */
 {
 struct dyString *query = dyStringNew(0);
+sqlCkIl(fieldsSafe,dyStringContents(gencodeQuery->fields))
 sqlDyStringPrintf(query, "select %-s from %-s where %-s", 
-    sqlCkIl(dyStringContents(gencodeQuery->fields)), dyStringContents(gencodeQuery->from), dyStringContents(gencodeQuery->where));
+    fieldsSafe, dyStringContents(gencodeQuery->from), dyStringContents(gencodeQuery->where));
 struct sqlResult *sr = sqlGetResult(conn, dyStringContents(query));
 dyStringFree(&query);
 return sr;
 }
 
 static boolean annotIsGenePredExt(struct track *tg)
 /* determine if a table has genePred extended fields.  two-way consensus
  * pseudo doesn't have them. */
 {
 struct sqlConnection *conn = hAllocConn(database);
 struct slName *fields = sqlFieldNames(conn, tg->table);
 hFreeConn(&conn);
 boolean isGenePredX = slNameInList(fields, "score");
 slFreeList(&fields);
 return isGenePredX;