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/hgCollection/hgCollection.c src/hg/hgCollection/hgCollection.c
index 27c4fa9..b9c882d 100644
--- src/hg/hgCollection/hgCollection.c
+++ src/hg/hgCollection/hgCollection.c
@@ -418,32 +418,32 @@
 struct hash *groupHash = newHash(10);
 int count = 0;
 
 for(curGroup = groupList; curGroup;  curGroup = curGroup->next)
     {
     if (curGroup->priority == 0)
         curGroup->priority = count--;
     hashAdd(groupHash, curGroup->name, curGroup);
     }
 
 curGroup = NULL;
 if (hubName != NULL)
     curGroup = hashFindVal(groupHash, hubName);
 
 jsInlineF("var collectionData = []; ");
-struct dyString *dyNames = newDyString(1024);
-struct dyString *dyLabels = newDyString(1024);
+struct dyString *dyNames = dyStringNew(1024);
+struct dyString *dyLabels = dyStringNew(1024);
 jsInlineF("var collectionNames = [];");
 jsInlineF("var collectionLabels = [];");
 if (curGroup != NULL)
     {
     // print out all the tracks in all the collections
     struct trackDb *tdb;
     jsInlineF("collectionData['#'] = [");
     boolean first = TRUE;
     for(tdb = trackList; tdb;  tdb = tdb->next)
         {
         if (sameString(tdb->grp, hubName))
             {
             if (!first)
                 {
                 jsInlineF(",");
@@ -459,31 +459,31 @@
         {
         if ( sameString(tdb->grp, curGroup->name))
             {
             subTracksToClient("collectionData", tdb, TRUE);
             addSubtrackNames(dyNames, tdb);
             }
         }
     }
 else
     jsInlineF("collectionData['#'] = [];");
 
 jsInlineF("%s", dyNames->string);
 jsInlineF("%s", dyLabels->string);
 
 jsInlineF("var trackData = []; ");
-struct dyString *rootChildren = newDyString(512);
+struct dyString *rootChildren = dyStringNew(512);
 addVisibleTracks(groupHash, rootChildren, cart, trackList);
 for(curGroup = groupList; curGroup;  curGroup = curGroup->next)
     {
     if ((hubName != NULL) && sameString(curGroup->name, hubName))
         continue;
     if (!isEmpty(rootChildren->string))
         dyStringPrintf(rootChildren, ",");
     dyStringPrintf(rootChildren, "{icon:'../images/folderC.png',id:'%s', text:'%s', parent:'#', children:true,li_attr:{title:'%s'}}", curGroup->name, escapeLabel(curGroup->label), FOLDER_TITLE);
     struct trackDb *tdb;
     jsInlineF("trackData['%s'] = [", curGroup->name);
     boolean first = TRUE;
     for(tdb = trackList; tdb;  tdb = tdb->next)
         {
         if ( sameString(tdb->grp, curGroup->name))
             {
@@ -559,34 +559,33 @@
 puts("<link rel='stylesheet' href='https://code.jquery.com/ui/1.10.3/themes/smoothness/jquery-ui.css'>");
 puts("<link rel='stylesheet' href='https://cdnjs.cloudflare.com/ajax/libs/jstree/3.2.1/themes/default/style.min.css' />");
 puts("<script src='https://cdnjs.cloudflare.com/ajax/libs/jquery/1.12.1/jquery.min.js'></script>");
 puts("<script src=\"//code.jquery.com/ui/1.10.3/jquery-ui.min.js\"></script>");
 puts("<script src=\"https://cdnjs.cloudflare.com/ajax/libs/jstree/3.3.7/jstree.min.js\"></script>\n");
 jsIncludeFile("utils.js", NULL);
 jsIncludeFile("ajax.js", NULL);
 jsIncludeFile("spectrum.min.js", NULL);
 jsIncludeFile("hgCollection.js", NULL);
 webEndGb();
 }
 
 static char *getSqlBigWig(struct sqlConnection *conn, char *db, struct trackDb *tdb)
 // figure out the bigWig for native tables
 {
-char buffer[4096];
-
-safef(buffer, sizeof buffer, "NOSQLINJ select fileName from %s", tdb->table);
-return sqlQuickString(conn, buffer);
+char query[1024];
+sqlSafef(query, sizeof query, "select fileName from %s", tdb->table);
+return sqlQuickString(conn, query);
 }
 
 void dumpTdbAndParents(struct dyString *dy, struct trackDb *tdb, struct hash *existHash, struct hash *wantHash)
 /* Put a trackDb entry into a dyString, stepping up the tree for some variables. */
 {
 struct hashCookie cookie = hashFirst(tdb->settingsHash);
 struct hashEl *hel;
 while ((hel = hashNext(&cookie)) != NULL)
     {
     if (!hashLookup(existHash, hel->name) && ((wantHash == NULL) || hashLookup(wantHash, hel->name)))
         {
         dyStringPrintf(dy, "%s %s\n", hel->name, (char *)hel->val);
         hashStore(existHash, hel->name);
         }
     }
@@ -598,31 +597,31 @@
     dumpTdbAndParents(dy, tdb->parent, existHash, newWantHash);
     }
 }
 
 struct dyString *trackDbString(struct trackDb *tdb)
 /* Convert a trackDb entry into a dyString. */
 {
 struct dyString *dy;
 struct hash *existHash = newHash(5);
 struct hashEl *hel;
 
 hel = hashLookup(tdb->settingsHash, "track");
 if (hel == NULL)
     errAbort("can't find track variable in tdb");
 
-dy = newDyString(200);
+dy = dyStringNew(200);
 dyStringPrintf(dy, "track %s\n", trackHubSkipHubName((char *)hel->val));
 hashStore(existHash, "track");
 
 dumpTdbAndParents(dy, tdb, existHash, NULL);
 
 return dy;
 }
 
 
 static void printTdbToHub(char *db, struct sqlConnection *conn,  FILE *f,   struct trackDb *tdb, int numTabs, int priority)
 // out the trackDb for one track
 {
 char *dataUrl = NULL;
 char *bigDataUrl = trackDbSetting(tdb, "bigDataUrl");