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/mouseStuff/chainStitch/chainStitch.c src/hg/mouseStuff/chainStitch/chainStitch.c
index 88525d7..b7e2e65 100644
--- src/hg/mouseStuff/chainStitch/chainStitch.c
+++ src/hg/mouseStuff/chainStitch/chainStitch.c
@@ -1,590 +1,590 @@
 /* chainStitch - Stitch psls into chains. */
 
 /* 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 "linefile.h"
 #include "hash.h"
 #include "options.h"
 #include "psl.h"
 #include "chain.h"
 #include "dystring.h"
 
 int maxGap=250000;
  
 void usage()
 /* Explain usage and exit. */
 {
 errAbort(
   "chainStitch - Stitch psls into chains\n"
   "usage:\n"
   "   chainStitch psls chains outChains outFound outNotFound\n"
   "options:\n"
   "   -maxGap=N    defines max gap possible (default 250,000)\n"
   );
 }
 
 static struct optionSpec options[] = {
    {"maxGap", OPTION_INT},
    {NULL, 0},
 };
 
 struct cseqPair
 /* Pair of sequences. */
     {
     struct cseqPair *next;
     char *name;	                /* Allocated in hash */
     char *qName;		/* Name of query sequence. */
     char *tName;		/* Name of target sequence. */
     char qStrand;		/* Strand of query sequence. */
     struct chain *chain;
     };
 struct seqPair
 /* Pair of sequences. */
     {
     struct seqPair *next;
     char *name;	                /* Allocated in hash */
     char *qName;		/* Name of query sequence. */
     char *tName;		/* Name of target sequence. */
     char qStrand;		/* Strand of query sequence. */
     struct psl *psl;
     };
 
 
 void addPslBlocks(struct cBlock **pList, struct psl *psl)
 /* Add blocks (gapless subalignments) from psl to block list. */
 {
 int i;
 for (i=0; i<psl->blockCount; ++i)
     {
     struct cBlock *b;
     int size;
     AllocVar(b);
     size = psl->blockSizes[i];
     b->qStart = b->qEnd = psl->qStarts[i];
     b->qEnd += size;
     b->tStart = b->tEnd = psl->tStarts[i];
     b->tEnd += size;
     slAddHead(pList, b);
     }
 slReverse(pList);
 }
 
 int boxInCmpBoth(const void *va, const void *vb)
 /* Compare to sort based on query, then target. */
 {
 const struct cBlock *a = *((struct cBlock **)va);
 const struct cBlock *b = *((struct cBlock **)vb);
 int dif;
 dif = a->tStart - b->tStart;
 if (dif == 0)
     dif = a->qStart - b->qStart;
 return dif;
 }
 
 int seqPairCmp(const void *va, const void *vb)
 /* Compare to sort based on tName,qName. */
 {
 const struct seqPair *a = *((struct seqPair **)va);
 const struct seqPair *b = *((struct seqPair **)vb);
 int dif;
 dif = strcmp(a->tName, b->tName);
 if (dif == 0)
     dif = strcmp(a->qName, b->qName);
 if (dif == 0)
     dif = (int)a->qStrand - (int)b->qStrand;
 return dif;
 }
 
 boolean checkChainRange(struct chain *chain, int qs, int qe, int ts, int te)
 {
 struct cBlock *chainBlock , *nextChainBlock = NULL, *prevChainBlock = NULL;
 
 prevChainBlock = NULL;
 //if ((te < chain->tStart) && (qe < chain->qStart))
     //return FALSE;
 for(chainBlock = chain->blockList; chainBlock; prevChainBlock = chainBlock, chainBlock = nextChainBlock)
     {
     nextChainBlock = chainBlock->next;
     if (((ts < chainBlock->tEnd) && (te > chainBlock->tStart)) ||
 	 (qs < chainBlock->qEnd) && (qe > chainBlock->qStart))
 	return TRUE;
     }
     return FALSE;
 }
 
 boolean deleteChainRange(struct chain *chain, int qs, int qe, int ts, int te, int *deletedBases)
 {
 struct cBlock *chainBlock , *nextChainBlock = NULL, *prevChainBlock = NULL;
 
 prevChainBlock = NULL;
 for(chainBlock = chain->blockList; chainBlock; prevChainBlock = chainBlock, chainBlock = nextChainBlock)
     {
     nextChainBlock = chainBlock->next;
     if (((ts <= chainBlock->tEnd) && (te > chainBlock->tStart)) &&
 	 (qs <= chainBlock->qEnd) && (qe > chainBlock->qStart))
 	{
 	while(chainBlock && ((chainBlock->tStart < te) || (chainBlock->qStart < qe)))
 	    {
 	    nextChainBlock = chainBlock->next;
 	    *deletedBases += chainBlock->tEnd - chainBlock->tStart;
 	    if (prevChainBlock == NULL)
 		chain->blockList = nextChainBlock;
 	    else
 		prevChainBlock->next = nextChainBlock;
 	    freez(&chainBlock);
 	    chainBlock = nextChainBlock;
 	    }
 
 	return TRUE;
 	}
     }
     return FALSE;
 }
 
 boolean addPslToChain(struct chain *chain, struct psl *psl, int *addedBases)
 {
 struct cBlock *bList;
 struct cBlock *chainBlock , *nextChainBlock = NULL, *prevChainBlock = NULL;
 int qStart = psl->qStarts[0];
 int qEnd = psl->qStarts[psl->blockCount - 1] + psl->blockSizes[psl->blockCount - 1];
 int tStart = psl->tStarts[0];
 int tEnd = psl->tStarts[psl->blockCount - 1] + psl->blockSizes[psl->blockCount - 1];
 
 prevChainBlock = NULL;
 for(chainBlock = chain->blockList; chainBlock; prevChainBlock = chainBlock, chainBlock = nextChainBlock)
     {
     nextChainBlock = chainBlock->next;
     if ((chainBlock->tEnd > tStart) || (chainBlock->qEnd > qStart))
 	{
 	if  (prevChainBlock && !((prevChainBlock->tEnd < tStart) && (prevChainBlock->qEnd < qStart)))
 	    return FALSE;
 	if  (chainBlock && !((chainBlock->tStart > tEnd) && (chainBlock->qStart > qEnd)))
 	    return FALSE;
 
 	break;
 	}
     }
 
     bList = NULL;
     addPslBlocks(&bList, psl);
 
     if (prevChainBlock == NULL)
 	{
 	chain->blockList = bList;
 	chain->tStart = bList->tStart;
 	chain->qStart = bList->qStart;
 	}
     else
 	{
 	if (chainBlock == NULL)
 	    {
 	    chain->tEnd = tEnd;
 	    chain->qEnd = qEnd;
 	    }
 	prevChainBlock->next = bList;
 	}
 
     for(;bList->next; bList = bList->next)
 	*addedBases += bList->tEnd - bList->tStart;
     *addedBases += bList->tEnd - bList->tStart;
     bList->next = chainBlock;
 
     //slSort(&chain->blockList,  boxInCmpBoth);
     return TRUE;
 }
 
 void checkInChains(struct psl **pslList, struct chain **chainList, FILE *outFound, int *addedBases)
 {
 struct chain *nextChain, *prevChain;
 struct chain *chain;
 struct psl *psl;
 struct psl *prevPsl, *nextPsl;
 
 prevPsl = NULL;
 for(psl = *pslList; psl ;  psl = nextPsl)
     {
     nextPsl = psl->next;
     int qStart = psl->qStarts[0];
     int qEnd = psl->qStarts[psl->blockCount - 1] + psl->blockSizes[psl->blockCount - 1];
     int tStart = psl->tStarts[0];
     int tEnd = psl->tStarts[psl->blockCount - 1] + psl->blockSizes[psl->blockCount - 1];
 
     assert(tEnd > tStart);
     assert(qEnd > qStart);
     prevChain = 0;
     for(chain = *chainList; chain ; prevChain = chain , chain = nextChain)
 	{
 	nextChain = chain->next;
 	if (((tStart < chain->tEnd) && (tEnd > chain->tStart)) &&
 	     (qStart < chain->qEnd) && (qEnd > chain->qStart))
 	    {
 	    if ( addPslToChain(chain, psl, addedBases))
 		{
 		pslTabOut(psl, outFound);
 		}
 
 	    if (prevPsl != NULL)
 		prevPsl->next = nextPsl;
 	    else
 		*pslList = nextPsl;
 		
 	    freez(&psl);
 	    break;
 	    }
 	}
     if (chain == NULL)
 	prevPsl = psl;
     
     }
 }
 
 void checkAfterChains(struct psl **pslList, struct chain **chainList, FILE *outFound, int *addedBases)
 {
 struct cBlock *block;
 struct chain *nextChain, *prevChain;
 struct chain *chain;
 struct psl *psl;
 struct psl *prevPsl, *nextPsl;
 prevPsl = NULL;
 for(psl = *pslList; psl ;  psl = nextPsl)
     {
     nextPsl = psl->next;
     int qStart = psl->qStarts[0];
     int qEnd = psl->qStarts[psl->blockCount - 1] + psl->blockSizes[psl->blockCount - 1];
     int tStart = psl->tStarts[0];
     int tEnd = psl->tStarts[psl->blockCount - 1] + psl->blockSizes[psl->blockCount - 1];
 
     prevChain = 0;
     for(chain = *chainList; chain ; prevChain = chain , chain = nextChain)
 	{
 	nextChain = chain->next;
 	if (((tStart <= chain->tEnd + maxGap) && (tStart > chain->tEnd)) &&
 	     (qStart <= chain->qEnd + maxGap) && (qStart > chain->qEnd))
 	    {
 	    if (!addPslToChain(chain, psl, addedBases))
 		errAbort("after chains");
 
 	    if (prevPsl != NULL)
 		prevPsl->next = nextPsl;
 	    else
 		*pslList = nextPsl;
 		
 	    pslTabOut(psl, outFound);
 	    freez(&psl);
 	    break;
 	    }
 	}
     if (chain == NULL)
 	prevPsl = psl;
     
     }
 }
 
 struct chain *aggregateChains( struct chain *chainIn)
 {
 struct chain *outChain = NULL;
 struct chain *chain1, *chain2, *chain1Next;
 
 //printf("%s%c%s\n",chainIn->qName, chainIn->qStrand, chainIn->tName);
 for(chain1 = chainIn; chain1 ; chain1 = chain1Next)
     {
     chain1Next = chain1->next;
     for(chain2 = chain1Next; chain2 ; chain2 = chain2->next)
 	{
 	    if ((chain1->tStart <= chain2->tStart) && (chain1->tEnd + maxGap > chain2->tStart)
 	       && (chain1->qStart <= chain2->qStart) && (chain1->qEnd + maxGap > chain2->qStart) &&
 		(chain1->qEnd < chain2->qStart) && (chain1->tEnd < chain2->tStart))
 		{
 		assert(chain1->tStart < chain1->tEnd);
 		assert(chain1->qStart < chain1->qEnd);
 		assert(chain2->tStart < chain2->tEnd);
 		assert(chain2->qStart < chain2->qEnd);
 		assert(chain1->qEnd < chain2->qStart);
 		assert(chain1->qEnd < chain2->qStart);
 		chain2->tStart = chain1->tStart;
 		chain2->qStart = chain1->qStart;
 		chain2->tEnd = max(chain1->tEnd, chain2->tEnd);
 		chain2->qEnd = max(chain1->qEnd, chain2->qEnd);
 		chain2->blockList = slCat(chain1->blockList,chain2->blockList);
 	//	slSort(&chain2->blockList,  boxInCmpBoth);
 		freez(&chain1);
 		break;
 		}
 	    else if ((chain1->tStart >= chain2->tEnd) && (chain1->tStart - maxGap < chain2->tEnd)
 		&& (chain1->qStart >= chain2->qEnd) && (chain1->qStart - maxGap < chain2->qEnd))
 		{
 		errAbort("shouldn't get here\n");
 		chain2->tEnd = chain1->tEnd;
 		chain2->qEnd = chain1->qEnd;
 		chain2->blockList = slCat(chain2->blockList,chain1->blockList);
 		freez(&chain1);
 		break;
 		}
 	}
 
     if (chain2 == NULL)
 	{
 	slAddHead(&outChain, chain1);
 	}
     }
 return outChain;
 }
 
 void checkBeforeChains(struct psl **pslList, struct chain **chainList, FILE *outFound, int *addedBases)
 {
 struct cBlock *block;
 struct chain *nextChain, *prevChain;
 struct chain *chain;
 struct psl *psl;
 struct psl *prevPsl, *nextPsl;
 prevPsl = NULL;
 for(psl = *pslList; psl ;  psl = nextPsl)
     {
     nextPsl = psl->next;
     int qStart = psl->qStarts[0];
     int qEnd = psl->qStarts[psl->blockCount - 1] + psl->blockSizes[psl->blockCount - 1];
     int tStart = psl->tStarts[0];
     int tEnd = psl->tStarts[psl->blockCount - 1] + psl->blockSizes[psl->blockCount - 1];
 
     prevChain = 0;
     for(chain = *chainList; chain ; prevChain = chain , chain = nextChain)
 	{
 	nextChain = chain->next;
 	if (((tStart > chain->tStart - maxGap) && (tEnd < chain->tStart)) &&
 	     (qStart > chain->qStart - maxGap) && (qEnd < chain->qStart))
 	    {
 	    if (!addPslToChain(chain, psl, addedBases))
 		errAbort("before chains");
 
 	    if (prevPsl != NULL)
 		prevPsl->next = nextPsl;
 	    else
 		*pslList = nextPsl;
 		
 	    pslTabOut(psl, outFound);
 	    freez(&psl);
 	    break;
 	    }
 	}
     if (chain == NULL)
 	prevPsl = psl;
     
     }
 }
 
 void chainStitch(char *psls, char *chains, char *outChainName, char *outFoundName, char *outNotFoundName)
 /* chainStitch - Stitch psls into chains. */
 {
 int lastChainId = -1;
 struct psl *prevPsl, *nextPsl;
 struct psl *fakePslList;
 int jj;
 int deletedBases, addedBases;
 FILE *outFound = mustOpen(outFoundName, "w");
 FILE *outNotFound = mustOpen(outNotFoundName, "w");
 FILE *outChains = mustOpen(outChainName, "w");
 struct lineFile *chainsLf = lineFileOpen(chains, TRUE);
 struct cseqPair *cspList = NULL, *csp;
 struct seqPair *spList = NULL, *sp;
 struct lineFile *pslLf = pslFileOpen(psls);
-struct dyString *dy = newDyString(512);
+struct dyString *dy = dyStringNew(512);
 struct psl *psl;
 struct hash *pslHash = newHash(0);  /* Hash keyed by qSeq<strand>tSeq */
 struct hash *chainHash = newHash(0);  /* Hash keyed by qSeq<strand>tSeq */
 struct chain *chain, *chainList = NULL;
 struct cBlock *block , *nextBlock = NULL, *prevBlock = NULL;
 int count;
 
 count = 0;
 while ((psl = pslNext(pslLf)) != NULL)
     {
     assert((psl->strand[1] == 0) || (psl->strand[1] == '+'));
     count++;
     dyStringClear(dy);
     dyStringPrintf(dy, "%s%c%s", psl->qName, psl->strand[0], psl->tName);
     sp = hashFindVal(pslHash, dy->string);
     if (sp == NULL)
         {
 	AllocVar(sp);
 	slAddHead(&spList, sp);
 	hashAddSaveName(pslHash, dy->string, sp, &sp->name);
 	sp->qName = cloneString(psl->qName);
 	sp->tName = cloneString(psl->tName);
 	sp->qStrand = psl->strand[0];
 	}
 
     slAddHead(&sp->psl, psl);
     }
 lineFileClose(&pslLf);
 printf("read in  %d psls\n",count);
 
 for(sp = spList; sp; sp = sp->next)
     slReverse(&sp->psl);
     //slSort(&sp->psl, pslCmpTarget);
 
 count = 0;
 while ((chain = chainRead(chainsLf)) != NULL)
     {
     if (chain->id > lastChainId)
 	lastChainId = chain->id;
     dyStringClear(dy);
     dyStringPrintf(dy, "%s%c%s", chain->qName, chain->qStrand, chain->tName);
     csp = hashFindVal(chainHash, dy->string);
     if (csp == NULL)
         {
 	AllocVar(csp);
 	slAddHead(&cspList, csp);
 	hashAddSaveName(chainHash, dy->string, csp, &csp->name);
 	csp->qName = cloneString(chain->qName);
 	csp->tName = cloneString(chain->tName);
 	csp->qStrand = chain->qStrand;
 	}
     slAddHead(&csp->chain, chain);
     count++;
     }
 lineFileClose(&chainsLf);
 printf("read in %d chains\n",count);
 
 for(csp = cspList; csp; csp = csp->next)
     {
     slSort(&csp->chain, chainCmpTarget);
 //    csp->chain = aggregateChains(csp->chain);
     }
 
 addedBases = deletedBases = 0;
 for(sp = spList; sp; sp = sp->next)
     {
 #ifdef NOTNOW
     /* find the chains associated with this strand */
     if ((csp = hashFindVal(chainHash, sp->name)) != NULL)
 	{
 	/* first check to see if psl blocks are in any chains */
 	checkInChains(&sp->psl, &csp->chain, outFound, &addedBases);
 
 	/* now extend chains to the right */
 	checkAfterChains(&sp->psl, &csp->chain, outFound, &addedBases);
 
 	/* now extend chains to the left */
 	slReverse(&sp->psl);
 	checkBeforeChains(&sp->psl, &csp->chain, outFound, &addedBases);
 	}
 #endif
 
     /* do we still have psl's */
     if (sp->psl != NULL)
 	{
 	/* make sure we have a chainList */
 	chainList = NULL;
 	if (csp == NULL)
 	    {
 	    AllocVar(csp);
 	    slAddHead(&cspList, csp);
 	    csp->qName = cloneString(sp->psl->qName);
 	    csp->tName = cloneString(sp->psl->tName);
 	    csp->qStrand = sp->psl->strand[0];
 	    dyStringClear(dy);
 	    dyStringPrintf(dy, "%s%c%s", csp->qName, csp->qStrand, csp->tName);
 	    hashAddSaveName(chainHash, dy->string, csp, &csp->name);
 	    }
 	for(psl = sp->psl; psl ;  psl = nextPsl)
 	    {
 	    /* this psl will either fit a chain or make a new one */
 
 	    nextPsl = psl->next;
 	    sp->psl  = nextPsl;
 
 	    psl->next = NULL;
 	    fakePslList = psl;
 	    if (chainList)
 		checkInChains(&fakePslList, &chainList, outFound, &addedBases);
 	    if (fakePslList == NULL)
 		{
 		//freez(&psl);
 		continue;
 		}
 	//    if (chainList)
 	//	checkAfterChains(&fakePslList, &chainList, outFound, &addedBases);
 	    if (fakePslList == NULL)
 		{
 		//freez(&psl);
 		continue;
 		}
 	    if (chainList)
 		checkBeforeChains(&fakePslList, &chainList, outFound, &addedBases);
 	    if (fakePslList == NULL)
 		{
 		//freez(&psl);
 		continue;
 		}
 
 	    AllocVar(chain);
 	    chain->tStart = psl->tStarts[0];
 	    chain->qStart = psl->qStarts[0];
 	    chain->tEnd = psl->tStarts[psl->blockCount - 1] + psl->blockSizes[psl->blockCount - 1];
 	    chain->qEnd = psl->qStarts[psl->blockCount - 1] + psl->blockSizes[psl->blockCount - 1];
 	    chain->tSize = psl->tSize;
 	    chain->qSize = psl->qSize;
 	    chain->qName = cloneString(psl->qName);
 	    chain->tName = cloneString(psl->tName);
 	    chain->qStrand = psl->strand[0];
 	    chain->id = ++lastChainId;
 
 	    if (!addPslToChain(chain, psl, &addedBases))
 		errAbort("new ");
 	    slAddHead(&chainList, chain);
 
 	    pslTabOut(psl, outFound);
 	    freez(&psl);
 	    }
 
 	csp->chain = slCat(csp->chain, chainList);
 	}
 
     slSort(&csp->chain, chainCmpTarget);
     csp->chain = aggregateChains(csp->chain);
     }
 fclose(outFound);
 printf("deleted %d bases\n",deletedBases);
 printf("added %d bases\n",addedBases);
 count = 0;
 for(sp = spList; sp; sp = sp->next)
     for(psl = sp->psl ; psl ; psl = psl->next)
 	{
 	pslTabOut(psl, outNotFound);
 	count++;
 	}
 fclose(outNotFound);
 
 printf("%d psls remain\n",count);
 
 for(csp = cspList; csp; csp = csp->next)
     for(chain = csp->chain ; chain ; chain = chain->next)
 	{
 	//slSort(&chain->blockList, boxInCmpBoth);
 	chain->tStart = chain->blockList->tStart;
 	chain->qStart = chain->blockList->qStart;
 
 	for(block = chain->blockList; block; block = block->next)
 	    {
 	    chain->tEnd = block->tEnd;
 	    chain->qEnd = block->qEnd;
 	    }
 	chainWrite(chain,  outChains);
 	}
 fclose(outChains);
 
 dyStringFree(&dy);
 }
 
 
 int main(int argc, char *argv[])
 /* Process command line. */
 {
 optionInit(&argc, argv, options);
 if (argc != 6)
     usage();
 maxGap = optionInt("maxGap", maxGap);
 chainStitch(argv[1], argv[2], argv[3], argv[4], argv[5]);
 return 0;
 }