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/oneShot/clusterBox/clusterBox.c src/oneShot/clusterBox/clusterBox.c
index c9a4d4f..55d0c74 100644
--- src/oneShot/clusterBox/clusterBox.c
+++ src/oneShot/clusterBox/clusterBox.c
@@ -1,138 +1,138 @@
 /* clusterBox - Cluster together overlapping boxes,  or technically,
  * overlapping axt's. */
 
 #include "common.h"
 #include "linefile.h"
 #include "hash.h"
 #include "dystring.h"
 #include "dlist.h"
 #include "portable.h"
 #include "options.h"
 #include "localmem.h"
 #include "dlist.h"
 #include "fuzzyFind.h"
 #include "axt.h"
 #include "boxClump.h"
 
 void usage()
 /* Explain usage and exit. */
 {
 errAbort(
   "clusterBox - Cluster together overlaping boxes, or, technically,\n"
   "overlapping axt format alignments\n"
   "usage:\n"
   "   clusterBox input.axt output\n"
   "options:\n"
   "   -xxx=XXX\n"
   );
 }
 
 void printClumps(struct boxClump *clumpList, FILE *f)
 /* Print out all clumps. */
 {
 struct boxClump *clump;
 for (clump = clumpList; clump != NULL; clump = clump->next)
     {
     struct boxIn *box;
     int diag = clump->tStart - clump->qStart;
     fprintf(f, "Cluster of %d %d,%d %d,%d\n", clump->boxCount,
 	clump->qStart, clump->qEnd, clump->tStart, clump->tEnd);
     for (box = clump->boxList; box != NULL; box = box->next)
         fprintf(f, "  (%d) %d,%d %d,%d\n", diag - (box->tStart - box->qStart),
 		box->qStart, box->qEnd, box->tStart, box->tEnd);
     }
 }
 
 struct seqPair
 /* Pair of sequences. */
     {
     struct seqPair *next;
     char *name;	/* Allocated in hash */
     struct axt *axtList; /* List of alignments. */
     };
 
 void clusterPair(struct seqPair *sp, FILE *f)
 /* Make chains for all alignments in sp. */
 {
 struct boxIn *boxList = NULL, *box;
 struct boxClump *clumpList, *clump;
 struct axt *axt;
 
 /* Make initial list containing all axt's. */
 fprintf(f, "Pairing %s - %d axt's initially\n", sp->name, slCount(sp->axtList));
 
 /* Make a box for each axt. */
 for (axt = sp->axtList; axt != NULL; axt = axt->next)
     {
     AllocVar(box);
     box->qStart = axt->qStart;
     box->qEnd = axt->qEnd;
     box->tStart = axt->tStart;
     box->tEnd = axt->tEnd;
     box->data = axt;
     slAddHead(&boxList, box);
     }
 
 /* Cluster and print. */
 clumpList = boxFindClumps(&boxList);
 slSort(&clumpList, boxClumpCmpCount);
 printClumps(clumpList, f);
 fprintf(f, "\n");
 }
 
 
 void clusterAxt(char *axtFile, char *output)
 /* clusterAxt - Cluster together overlapping boxes,  or technically,
  * overlapping axt's. */
 {
 struct hash *pairHash = newHash(0);  /* Hash keyed by qSeq<strand>tSeq */
-struct dyString *dy = newDyString(512);
+struct dyString *dy = dyStringNew(512);
 struct lineFile *lf = lineFileOpen(axtFile, TRUE);
 struct axt *axt;
 struct seqPair *spList = NULL, *sp;
 FILE *f = mustOpen(output, "w");
 int axtCount = 0;
 long t1,t2,t3;
 
 /* Read input file and divide alignments into various parts. */
 t1 = clock1000();
 while ((axt = axtRead(lf)) != NULL)
     {
     if (axt->score < 500)
         {
 	axtFree(&axt);
 	continue;
 	}
     dyStringClear(dy);
     dyStringPrintf(dy, "%s%c%s", axt->qName, axt->qStrand, axt->tName);
     sp = hashFindVal(pairHash, dy->string);
     if (sp == NULL)
         {
 	AllocVar(sp);
 	slAddHead(&spList, sp);
 	hashAddSaveName(pairHash, dy->string, sp, &sp->name);
 	}
     slAddHead(&sp->axtList, axt);
     ++axtCount;
     }
 uglyf("%d axt's\n", axtCount);
 t2 = clock1000();
 for (sp = spList; sp != NULL; sp = sp->next)
     {
     slReverse(&sp->axtList);
     clusterPair(sp, f);
     }
 t3 = clock1000();
 dyStringFree(&dy);
 uglyf("axtRead %fs, clusterPair %fs\n", 0.001 * (t2-t1), 0.001 * (t3-t2) );
 }
 
 int main(int argc, char *argv[])
 /* Process command line. */
 {
 optionHash(&argc, argv);
 if (argc != 3)
     usage();
 clusterAxt(argv[1], argv[2]);
 return 0;
 }