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/utils/vulgarToPsl/vulgarToPsl.c src/utils/vulgarToPsl/vulgarToPsl.c
index 15e6c4d..71f7cd5 100644
--- src/utils/vulgarToPsl/vulgarToPsl.c
+++ src/utils/vulgarToPsl/vulgarToPsl.c
@@ -1,222 +1,222 @@
 /* vulgarToPsl - Convert the vulgar exonerate format to PSL. */
 
 /* Copyright (C) 2005 The Regents of the University of California 
  * See kent/LICENSE or http://genome.ucsc.edu/license/ for licensing information. */
 
 #include "common.h"
 #include "hash.h"
 #include "psl.h"
 #include "twoBit.h"
 #include "linefile.h"
 #include "dystring.h"
 #include "dnaLoad.h"
 
 void usage() 
 {
 errAbort("vulgarToPsl - Convert the vulgar exonerate format to PSL.\n"
 	 "usage:\n"
 	 "   vulgarToPsl input.vul proteinQ.fa dnaT.fa output.psl");
 }
 
 struct hash *seqHash(bioSeq *seqs)
 /* Hash up all the sequences. */
 {
 bioSeq *seq;
 struct hash *ret = NULL;
 int numSeqs = slCount(seqs);
 ret = newHash(logBase2(numSeqs)+1);
 for (seq = seqs; seq != NULL; seq = seq->next)
     hashAdd(ret, seq->name, seq);
 return ret;
 }
 
 struct psl *vulgarToPsl(struct lineFile *vulg, struct hash *queryHash, struct hash *targetHash)
 /* Convert it. */
 {
 struct psl *list = NULL;
 char *words[32768];
 int numWords;
 while (numWords = lineFileChop(vulg, words))
     {
     struct psl *aln;
-    struct dyString *cDNA = newDyString(2048);
+    struct dyString *cDNA = dyStringNew(2048);
     struct dnaSeq *dna;
     aaSeq *prot;
     char *translated = NULL;
     boolean revComp = FALSE;
     int i, wordIx, dnaIx, blockIx, protIx;
     int startWord = (startsWith("vulgar", words[0])) ? 1 : 0;
     char strand;
 
     /* Do a check, then load the data, error on not finding it. */
     if (numWords == 32768)
 	{
 	warn("Line %d of %s actually had 32768 words on that line.  Skipping this one.\n", vulg->lineIx, vulg->fileName);
 	continue;
 	}
     dna = (struct dnaSeq *)hashMustFindVal(targetHash, words[startWord+4]);
     prot = (aaSeq *)hashMustFindVal(queryHash, words[startWord]);
 
     /* Everything's cool, so initialize data */
     AllocVar(aln);
     aln->match = 0;
     aln->misMatch = 0;
     aln->repMatch = 0;
     aln->nCount = 0;
     aln->qNumInsert = 0;
     aln->qBaseInsert = 0;
     aln->tNumInsert = 0;
     aln->tBaseInsert = 0;
     strand = words[startWord + 7][0];
     aln->strand[0] = '+';
     aln->strand[1] = (strand == '+') ? '+' : '-';
     aln->qName = cloneString(words[startWord]);
     aln->qStart = atoi(words[startWord + 1]);
     aln->qEnd = atoi(words[startWord + 2]);
     aln->qSize = prot->size;
     aln->tName = cloneString(words[startWord + 4]);
     dnaIx = atoi(words[startWord + 5]);
     if (strand == '-')
 	revComp = TRUE;
     if (revComp)
 	{
 	aln->tStart = atoi(words[startWord + 6]);
 	aln->tEnd = dnaIx;
 	dnaIx--;
 	}
     else
 	{
 	aln->tStart = dnaIx;
 	aln->tEnd = atoi(words[startWord + 6]);
 	}
     aln->tSize = dna->size;
     aln->blockCount = 0;
 
     /* First pass: count the number of blocks in the alignment and various things that only need one pass. */
     for (wordIx = startWord + 9; wordIx < numWords; wordIx += 3)
         {
 	char type = words[wordIx][0];
 	int first = atoi(words[wordIx+1]);
 	int second = atoi(words[wordIx+2]);
 	if (type == 'M')
 	    aln->blockCount++;
 	else if (type == 'G')
 	    {
 	    if (first > 0)
 		{
 		aln->qNumInsert++;
 		aln->qBaseInsert += first;
 		}
 	    else 
 		{
 		aln->tNumInsert++;
 		aln->qBaseInsert += second;		
 		}
 	    }
 	else if ((type == 'I') || (type == '5') || (type == '3') || (type == 'F'))
 	    {
 	    if ((type == 'I') || (type == 'F'))
 		aln->tNumInsert++;
 	    aln->tBaseInsert += second;
 	    }	
 	}
     aln->blockSizes = needMem(sizeof(unsigned) * aln->blockCount);
     aln->qStarts = needMem(sizeof(unsigned) * aln->blockCount);
     aln->tStarts = needMem(sizeof(unsigned) * aln->blockCount);
 
     /* Second pass: go through the vulgar blocks and build a protein out of the cDNA. */
     blockIx = 0;
     protIx = 0;
     for (wordIx = startWord + 9; wordIx < numWords; wordIx += 3)
         {
 	char type = words[wordIx][0];
 	int first = atoi(words[wordIx+1]);
 	int second = atoi(words[wordIx+2]);
 
 	if (type == 'M')
 	    {
 	    aln->blockSizes[blockIx] = first;
 	    aln->qStarts[blockIx] = protIx;
 	    aln->tStarts[blockIx] = (revComp) ? dna->size - dnaIx - 1 : dnaIx;
 	    blockIx++;
 	    }	
 	protIx += first;
 	for (i = 0; i < second; i++)
 	    {
 	    char base = 0;
 	    if (revComp) 
 		{
 		base = ntCompTable[dna->dna[dnaIx]];
 		dnaIx--;
 		}
 	    else 
 		{
 		base = dna->dna[dnaIx];
 		dnaIx++;
 		}
 	    if ((type == 'M') || (type == 'S'))
 		dyStringAppendC(cDNA, base);
 	    }
 	}
 
     /* Translate the cDNA and count matches, etc. */
     translated = needMem(sizeof(char) * (aln->qSize + 1));
     dnaTranslateSome(cDNA->string, translated, aln->qSize+1);
     protIx = 0;
     for (i = aln->qStart; i < aln->qEnd; i++)
 	{
 	boolean repAA = FALSE;
 	if (protIx >= strlen(translated))
 	    break;
 	/* count the repeats/N's at this amino acid (in the codon). */
 	for (dnaIx = protIx*3; dnaIx < (protIx*3) + 3; dnaIx++)
 	    if ((cDNA->string[dnaIx] == 'N') || (cDNA->string[dnaIx] == 'X'))
 		aln->nCount++;
 	    else if ((!repAA) && (islower(cDNA->string[dnaIx])))
 		repAA = TRUE;
 	if (translated[protIx++] == prot->dna[i])
 	    {
 	    if (repAA)
 		aln->repMatch++;
 	    else
 		aln->match++;
 	    }
 	else
 	    aln->misMatch++;
 	}
     freeMem(translated);
-    freeDyString(&cDNA);
+    dyStringFree(&cDNA);
     slAddHead(&list, aln);
     }
 slReverse(&list);
 return list;
 }
 
 int main(int argc, char *argv[])
 /* The program */
 {
 struct psl *pslList = NULL, *psl;
 struct hash *queryHash, *targetHash;
 struct lineFile *vulg;
 aaSeq *querySeqs;
 struct dnaSeq *targetSeqs;
 if (argc != 5)
     usage();
 /* Load up everything at beginning */
 vulg = lineFileOpen(argv[1], TRUE);
 querySeqs = dnaLoadAll(argv[2]);
 targetSeqs = dnaLoadAll(argv[3]);
 queryHash = seqHash(querySeqs);
 targetHash = seqHash(targetSeqs);
 /* Main business */
 pslList = vulgarToPsl(vulg, queryHash, targetHash);
 pslWriteAll(pslList, argv[4], FALSE);
 /* Free up everything */
 freeDnaSeqList(&querySeqs);
 freeDnaSeqList(&targetSeqs);
 freeHash(&targetHash);
 freeHash(&queryHash);
 pslFreeList(&pslList);
 lineFileClose(&vulg);
 return 0;
 }