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/rnaStructure/utrFa/utrFa.c src/hg/rnaStructure/utrFa/utrFa.c
index 85263fb..ffae992 100644
--- src/hg/rnaStructure/utrFa/utrFa.c
+++ src/hg/rnaStructure/utrFa/utrFa.c
@@ -1,192 +1,192 @@
 /* utrFa - Get UTRs as fasta files. */
 
 /* Copyright (C) 2011 The Regents of the University of California 
  * See kent/LICENSE or http://genome.ucsc.edu/license/ for licensing information. */
 #include "common.h"
 #include "linefile.h"
 #include "hash.h"
 #include "options.h"
 #include "dnaseq.h"
 #include "fa.h"
 #include "jksql.h"
 #include "nib.h"
 #include "genePred.h"
 #include "hdb.h"
 
 
 int minSize = 16;
 char *nibPath = NULL;
 
 void usage()
 /* Explain usage and exit. */
 {
 errAbort(
   "utrFa - Get UTRs as fasta files\n"
   "usage:\n"
   "   utrFa database geneTrack which output.fa\n"
   "The 'which' parameter is either 'utr3' or 'utr5'\n"
   "options:\n"
   "   -nibPath=path - Indicate a nib file directory.\n"
   "   -minSize=N  - Minimum size to output, default %d\n"
   , minSize);
 }
 
 static struct optionSpec options[] = {
    {"chrom", OPTION_STRING},
    {"nibPath", OPTION_STRING},
    {NULL, 0},
 };
 
 struct dnaSeq *genePredUtrSeq(struct genePred *gp, 
 	struct dnaSeq *chromSeq, char *which)
 /* Load 3' or 5' UTR sequence. */
 {
 boolean isUtr3 = FALSE;
 boolean fromEnd;
 int i, s, e;
 struct dyString *dy;
 struct dnaSeq *seq;
 
 /* Figure out if it's a sequence without CDS or without UTR. */
 if (gp->txStart == gp->cdsStart && gp->txEnd == gp->cdsEnd)
     return NULL;
 if (gp->cdsStart >= gp->cdsEnd)
     return NULL;
-dy = newDyString(4*1024);
+dy = dyStringNew(4*1024);
 
 /* Figure out which end we want. */
 if (sameWord(which, "utr3"))
      isUtr3 = TRUE;
 else if (sameWord(which, "utr5"))
      isUtr3 = FALSE;
 else
      errAbort("Unknown 'which' %s", which);
 fromEnd = isUtr3;
 if (gp->strand[0] == '-')
     fromEnd = !fromEnd;
 
 /* Load sequence an exon at a time into dyString */
 for (i=0; i<gp->exonCount; ++i)
     {
     s = gp->exonStarts[i];
     e = gp->exonEnds[i];
     if (fromEnd)
         {
 	if (s < gp->cdsEnd) s = gp->cdsEnd;
 	}
     else
         {
 	if (e > gp->cdsStart) e = gp->cdsStart;
 	}
     if (s < e)
 	dyStringAppendN(dy, chromSeq->dna + s, e-s);
     }
 
 /* Copy sequence into seq structure. */
 AllocVar(seq);
 seq->name = cloneString(gp->name);
 seq->size = dy->stringSize;
 seq->dna = cloneString(dy->string);
 dyStringFree(&dy);
 if (gp->strand[0] == '-')
     reverseComplement(seq->dna, seq->size);
 return seq;
 }
 
 
 void oneChrom(char *database, char *chrom, struct sqlConnection *conn, 
 	char *track, char *which, struct hash *hash)
 /* Process one chromosome into hash. */
 {
 struct sqlResult *sr;
 char **row;
 struct genePred *gp;
 int rowOffset;
 struct dnaSeq *oldSeq, *seq;
 struct hashEl *oldHel;
 struct dnaSeq *chromSeq;
 if (nibPath == NULL) 
     {
     chromSeq = hChromSeq(database, chrom, 0, hChromSize(database, chrom));
     }
 else
     {
     chromSeq = hChromSeqFromPath(nibPath, database, chrom, 0, hChromSize(database, chrom));
     }
 sr = hChromQuery(conn, track, chrom, NULL, &rowOffset);
 while ((row = sqlNextRow(sr)) != NULL)
     {
     gp = genePredLoad(row+rowOffset);
     oldHel = hashLookup(hash, gp->name);
     seq = genePredUtrSeq(gp, chromSeq, which);
     if (seq != NULL)
 	{
 	if (oldHel != NULL)
 	    {
 	    oldSeq = oldHel->val;
 	    if (oldSeq->size > seq->size)
 		freeDnaSeq(&seq);
 	    else
 		{
 		freeDnaSeq(&oldSeq);
 		oldHel->val = seq;
 		}
 	    }
 	else
 	    {
 	    hashAdd(hash, gp->name, seq);
 	    }
 	}
     genePredFree(&gp);
     }
 sqlFreeResult(&sr);
 freeDnaSeq(&chromSeq);
 }
 
 void utrFa(char *database, char *geneTrack, char *which, char *output)
 /* utrFa - Get UTRs as fasta files. */
 {
 struct slName *chromList = NULL, *chrom;
 struct sqlConnection *conn;
 struct hash *hash = newHash(19);	/* DnaSeq valued hash */
 FILE *f = NULL;
 struct hashEl *helList, *hel;
 
 conn = hAllocConn(database);
 if (optionExists("chrom"))
     chromList = slNameNew(optionVal("chrom", NULL));
 else
     chromList = hAllChromNames(database);
 for (chrom = chromList; chrom != NULL; chrom = chrom->next)
     {
     warn("%s", chrom->name);
     oneChrom(database, chrom->name, conn, geneTrack, which, hash);
     }
 hFreeConn(&conn);
 f = mustOpen(output, "w");
 helList = hashElListHash(hash);
 slSort(&helList, hashElCmp);
 for (hel = helList; hel != NULL; hel = hel->next)
     {
     struct dnaSeq *seq = hel->val;
     if (seq->size >= minSize)
 	{
 	char line[512];
 	safef(line, sizeof(line), "%s %s", seq->name, which);
 	faWriteNext(f, line, seq->dna, seq->size);
 	}
     }
 carefulClose(&f);
 }
 
 int main(int argc, char *argv[])
 /* Process command line. */
 {
 optionInit(&argc, argv, options);
 if (argc != 5)
     usage();
 minSize = optionInt("minSize", minSize);
 nibPath = cloneString(optionVal("nibPath", nibPath));
 utrFa(argv[1], argv[2], argv[3], argv[4]);
 return 0;
 }