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/sampleTracks.c src/hg/hgTracks/sampleTracks.c
index 7dd585c..c5aeb34 100644
--- src/hg/hgTracks/sampleTracks.c
+++ src/hg/hgTracks/sampleTracks.c
@@ -475,31 +475,31 @@
 char *where = NULL;
 char query[256];
 
 /*see if we have a summary table*/
 sqlSafef(query, sizeof(query), 
 	"select name from %s where name = '%s' limit 1", 
 	tg->table, tg->shortLabel);
 //errAbort( "%s", query );
 hasDense = sqlQuickQuery(conn, query, query, sizeof(query));
 
 /* If we're in dense mode and have a summary table load it. */
 if(tg->visibility == tvDense)
     {
     if(hasDense != NULL)
 	{
-	sqlSafefFrag(query, sizeof(query), " name = '%s' ", tg->shortLabel);
+	sqlSafef(query, sizeof(query), " name = '%s' ", tg->shortLabel);
 	where = cloneString(query);
 	}
     }
 
 sr = hRangeQuery(conn, tg->table, chromName, winStart, winEnd, where, &rowOffset);
 while ((row = sqlNextRow(sr)) != NULL)
     {
     sample = sampleLoad(row + rowOffset);
     lf = lfFromSample(sample);
     slAddHead(&lfList, lf);
     sampleFree(&sample);
     }
 if(where != NULL)
     freez(&where);
 sqlFreeResult(&sr);
@@ -559,68 +559,65 @@
 }
 
 void loadHumMusL(struct track *tg)
 /* Load humMusL track with 2 zoom levels and one normal level. 
  * Also used for loading the musHumL track (called Human Cons) 
  * on the mouse browser. It decides which of 4 tables to
  * load based on how large of a window the user is looking at*/
 {
 struct sqlConnection *conn = hAllocConn(database);
 struct sqlResult *sr;
 char **row;
 int rowOffset;
 struct sample *sample;
 struct linkedFeatures *lfList = NULL, *lf;
 char *hasDense = NULL;
-char *where = NULL;
 char tableName[256];
 int z;
 
 if(tl.picWidth == 0)
     errAbort("hgTracks.c::loadHumMusL() - can't have pixel width of 0");
 
 /* Determine zoom level. */
  if (!strstr(tg->table,"HMRConservation"))
    z = humMusZoomLevel();
  else z=0;
 
 
 if(z == 1 )
     safef(tableName, sizeof(tableName), "%s_%s", "zoom1",
 	    tg->table);
 else if( z == 2)
     safef(tableName, sizeof(tableName), "%s_%s", "zoom50",
 	    tg->table);
 else if(z == 3)
     safef(tableName, sizeof(tableName), "%s_%s",
 	    "zoom2500", tg->table);
 else
     safef(tableName, sizeof(tableName), "%s", tg->table);
 
 //printf("(%s)", tableName );
 
 sr = hRangeQuery(conn, tableName, chromName, winStart, winEnd,
-    where, &rowOffset);
+    NULL, &rowOffset);
 while ((row = sqlNextRow(sr)) != NULL)
     {
     sample = sampleLoad(row+rowOffset);
     lf = lfFromSample(sample);
     slAddHead(&lfList, lf);
     sampleFree(&sample);
     }
-if(where != NULL)
-    freez(&where);
 sqlFreeResult(&sr);
 hFreeConn(&conn);
 slReverse(&lfList);
 
 /* sort to bring items with common names to the same line
    but only for tracks with a summary table (with name=shortLabel)
    in
    dense mode*/
 if( hasDense != NULL )
     {
     sortGroupList = tg; /* used to put track name at
 	                 * top of sorted list. */
     slSort(&lfList, lfNamePositionCmp);
     sortGroupList = NULL;
     }
@@ -777,31 +774,31 @@
 char query[256];
 char option[64];
 
 zooSpeciesHashInit();
 
 /*see if we have a summary table*/
 sqlSafef(query, sizeof(query), "select name from %s where name = '%s' limit 1", tg->table, tg->shortLabel);
 //errAbort( "%s", query );
 hasDense = sqlQuickQuery(conn, query, query, sizeof(query));
 
 /* If we're in dense mode and have a summary table load it. */
 if(tg->visibility == tvDense)
     {
     if(hasDense != NULL)
 	{
-	sqlSafefFrag(query, sizeof(query), " name = '%s' ", tg->shortLabel);
+	sqlSafef(query, sizeof(query), " name = '%s' ", tg->shortLabel);
 	where = cloneString(query);
 	}
     }
 
 sr = hRangeQuery(conn, tg->table, chromName, winStart, winEnd, where, &rowOffset);
 while ((row = sqlNextRow(sr)) != NULL)
     {
     sample = sampleLoad(row + rowOffset);
     lf = lfFromSample(sample);
     safef( option, sizeof(option), "zooSpecies.%s", sample->name );
     if( cartUsualBoolean(cart, option, TRUE ))
     slAddHead(&lfList, lf);
     sampleFree(&sample);
     }
 if(where != NULL)
@@ -880,31 +877,31 @@
     sqlSafef(query, sizeof(query), "select name from %s where name = '%s' limit 1",  tableName, tg->shortLabel);
 else
     {
     warn("<p>Couldn't find table %s<br><br>", tableName);
     sqlSafef(query, sizeof(query), "select name from %s where name = '%s' limit 1",  tg->table, tg->shortLabel);
     safef(tableName, sizeof(tableName), "%s", tg->table);
     }
 
 hasDense = sqlQuickQuery(conn, query, query, sizeof(query));
 
 /* If we're in dense mode and have a summary table load it. */
 if(tg->visibility == tvDense)
     {
     if(hasDense != NULL)
 	{
-	sqlSafefFrag(query, sizeof(query), " name = '%s' ", tg->shortLabel);
+	sqlSafef(query, sizeof(query), " name = '%s' ", tg->shortLabel);
 	where = cloneString(query);
 	}
     }
 
 sr = hRangeQuery(conn, tableName, chromName, winStart, winEnd, where, &rowOffset);
 while ((row = sqlNextRow(sr)) != NULL)
     {
     sample = sampleLoad(row+rowOffset);
     lf = lfFromSample(sample);
     slAddHead(&lfList, lf);
     sampleFree(&sample);
     }
 if(where != NULL)
     freez(&where);
 sqlFreeResult(&sr);