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/altSplice/axtCountBeds/axtCountBeds.c src/hg/altSplice/axtCountBeds/axtCountBeds.c
index 184f778..db084b6 100644
--- src/hg/altSplice/axtCountBeds/axtCountBeds.c
+++ src/hg/altSplice/axtCountBeds/axtCountBeds.c
@@ -1,373 +1,373 @@
 /* axtCountBeds.c - Program to count matching bases in bed and output positional information as well. */
 #include "common.h"
 #include "axt.h"
 #include "bed.h"
 #include "linefile.h"
 #include "hdb.h"
 #include "dnaseq.h"
 #include "dnautil.h"
 #include "chromKeeper.h"
 #include "options.h"
 #include "obscure.h"
 
 void usage()
 {
 errAbort("axtCountBeds.c - Program to count matching bases in bed and output\n"
 	 "positional information as well.\n"
 	 "usage:\n   "
 	 "axtCountBeds bedFile axtFile db outFile chrom\n");
 }
 
 struct axt *axtList = NULL;
 boolean ckInit = FALSE;
 
 struct axt* axtReadAll(char* fileName)
 /* Read all of the axt records from a file. */
 {
 struct axt *axtList = NULL;
 struct axt *rec;
 struct lineFile *lf = lineFileOpen(fileName, TRUE);
 while ((rec = axtRead(lf)) != NULL)
     {
     slAddHead(&axtList, rec);
     }
 lineFileClose(&lf);
 if (axtList == NULL)
     errAbort("no alignments found in %s", fileName);
 slReverse(&axtList);
 return axtList;
 }
 
 void chromKeeperForAxt(char *fileName, char *db)
 {
 struct axt *axt = NULL;
 axtList = axtReadAll(fileName);
 if(!ckInit)
     {
     chromKeeperInit(db);
     ckInit = TRUE;
     }
 for(axt = axtList; axt != NULL; axt = axt->next)
     {
     chromKeeperAdd(axt->tName, axt->tStart, axt->tEnd, axt);
     }
 }
 
 void cleanUpChromKeeper()
 /* Clean stuff out of the chromkeeper. */
 {
 struct axt *axt = NULL, *axtNext = NULL;
 for(axt = axtList; axt != NULL; axt = axtNext)
     {
     axtNext = axt->next;
     chromKeeperRemove(axt->tName, axt->tStart, axt->tEnd, axt);
     }
 axtFreeList(&axtList);
 }
 
 void printIntArray(int *array, int count)
 {
 int i;
 for(i = 0; i < count; i++)
     {
     fprintf(stderr, "%d,", array[i]);
     }
 fprintf(stderr, "\n");
 fflush(stderr);
 }
 
 boolean isDna(char c)
 {
 return (strchr("atgcATGC", c)) != NULL;
 }
 
 void scoreMatches(struct axt *axt, int *matches, char *dna, int matchCount, int chromStart, int chromEnd)
 /* Look through the axt record and score mathes in matches. */
 {
 int start = chromStart - axt->tStart;
 int end = min(chromEnd - axt->tStart, axt->tEnd - axt->tStart);
 int i =0;
 int position = 0;
 tolowers(axt->qSym);
 tolowers(axt->tSym);
 while(position < end && axt->qSym[i] != '\0')
     {
     if(axt->tSym[i] == '-')
 	{
 	i++;
 	continue;
 	}
     else if(position >= start && position < end)
 	{
 	dna[position + axt->tStart - chromStart] = axt->tSym[i];
 	if(axt->qSym[i] == axt->tSym[i])
 	    matches[position + axt->tStart - chromStart] = 1;
 	else if((axt->qSym[i] != axt->tSym[i]) && isDna(axt->tSym[i])
 		&& isDna(axt->qSym[i]))
 	    matches[position + axt->tStart - chromStart] = 0;
 	else if(axt->qSym[i] == '-' || axt->tSym[i] == '-' ||
 		axt->qSym[i] == 'n' || axt->tSym[i] == 'n')
 	    matches[position + axt->tStart - chromStart] = -1;
 	else 
 	    errAbort("axtCountBeds::scoreMatches() - Got %c and %c for qSym and tSym. "
 		     "ChromStart %d, chromEnd %d, offSet %d",
 		     axt->qSym[i], axt->tSym[i], chromStart, chromEnd, i);
 	
 	}
     i++;
     position++;
     }
 }
 
 void initMatches(int *matches, int count, int val)
 {
 int i;
 for(i=0; i<count; i++)
     matches[i] = val;
 }
 
 void outputHeader(FILE *out)
 {
 fprintf(out,"%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\n",
 	"chrom", "chromStart", "chromEnd", "name", "score", "strand", 
 	"match", "mismatch", "notAlign", "percentId", "dna", "matchesSize", "matches");
 }
 
 void writeAxt(FILE *out, struct bed *bed, struct binElement *beList, boolean qrnaStyle)
 {
-struct dyString *outSeq = newDyString(bed->chromEnd - bed->chromStart+100);
-struct dyString *outSeqOrtho = newDyString(bed->chromEnd - bed->chromStart+100);
+struct dyString *outSeq = dyStringNew(bed->chromEnd - bed->chromStart+100);
+struct dyString *outSeqOrtho = dyStringNew(bed->chromEnd - bed->chromStart+100);
 int currentStart = bed->chromStart;
 int currentEnd = bed->chromEnd;
 struct binElement *be = NULL;
 fprintf(out, ">%s.%d.%s.%s:%d-%d\n", 
 	bed->name, bed->score, bed->strand, 
 	bed->chrom, bed->chromStart,bed->chromEnd);
 for(be = beList; be != NULL; be = be->next)
     {
     struct axt *axt = be->val;
     int start = currentStart - axt->tStart;
     int end = 0;//max(currentEnd - axt->tStart, axt->tEnd - currentStart);
     int pos = 0;
     int i = 0;
     struct dnaSeq *seq = NULL;
     end = min(axt->tEnd - axt->tStart, currentEnd - axt->tStart);
     if(bed->chromEnd >= axt->tStart && bed->chromStart <= axt->tEnd)
 	{
 	/* If axt doesn't cover, pad things with genomic dna. */
 	if(start < 0)
 	    {
 	    seq = hChromSeq(bed->chrom, currentStart, axt->tStart);
 	    for(i = 0; i < abs(start); i++)
 		{
 		dyStringPrintf(outSeq, "%c", seq->dna[i]);
 		dyStringPrintf(outSeqOrtho, "-");
 		}
 	    dnaSeqFree(&seq);
 	    currentStart = axt->tStart;
 	    start = 0;
 	    }
 	i = 0;
 	/* Loop through incrementing position when non-indel characters
 	   are found in target sequence. */
 	while(pos < end && axt->qSym[i] != '\0') 
 	    {
 	    if(pos >= start && pos < end)
 		{
 		dyStringPrintf(outSeq, "%c", axt->tSym[i]);
 		dyStringPrintf(outSeqOrtho, "%c", axt->qSym[i]);
 		if(axt->tSym[i] != '-')
 		    currentStart++;
 		}
 	    if(axt->tSym[i] != '-')
 		{
 		pos++;
 		}
 	    i++;
 	    }
 	}
     }
 /* Pad out the end with sequence. */
 if(currentStart < bed->chromEnd)
     {
     struct dnaSeq *seq = NULL;
     int i = 0;
     seq = hChromSeq(bed->chrom, currentStart, bed->chromEnd);
     for(i = 0; i < bed->chromEnd - currentStart; i++)
 	{
 	dyStringPrintf(outSeq, "%c", seq->dna[i]);
 	dyStringPrintf(outSeqOrtho, "-");
 	}
     dnaSeqFree(&seq);
     }
 if(bed->strand[0] == '-')
     {
     reverseComplement(outSeq->string, outSeq->stringSize);
     reverseComplement(outSeqOrtho->string, outSeqOrtho->stringSize);
     }
 
 if(qrnaStyle)
     {
     writeSeqWithBreaks(out, outSeq->string, outSeq->stringSize, 50);
     fprintf(out, ">%s.%d.%s.%s:%d-%d-Ortho\n", 
 	    bed->name, bed->score, bed->strand, 
 	    bed->chrom, bed->chromStart,bed->chromEnd);
     writeSeqWithBreaks(out, outSeqOrtho->string, outSeqOrtho->stringSize, 50);
     }
 else
     {
     fprintf(out, "%s\n", outSeq->string);
     fprintf(out, "%s\n", outSeqOrtho->string);
     }
 dyStringFree(&outSeq);
 dyStringFree(&outSeqOrtho);
 }
 
 void countMatches(struct bed *bed, FILE *out, FILE *axtOut, FILE *qrnaOut)
 /* Count up the matches for a particular bed. */
 {
 struct axt *axtList = NULL, *axt;
 struct binElement *beList = NULL, *be = NULL;
 int *matches = NULL;
 int matchSize = 0, i = 0;
 int match = 0, misMatch=0, notAlign=0;
 
 struct slRef *refList = NULL, *ref = NULL;
 char *dna = NULL;
 struct dnaSeq *seq = NULL;
 matchSize = bed->chromEnd - bed->chromStart;
 AllocArray(matches, matchSize);
 AllocArray(dna, matchSize+1);
 initMatches(matches, matchSize, -1);
 beList = chromKeeperFind(bed->chrom, bed->chromStart, bed->chromEnd);
 for(be = beList; be != NULL; be = be->next)
     {
     axt = be->val;
     scoreMatches(axt, matches, dna, matchSize, bed->chromStart, bed->chromEnd);
     } 
 
 if(axtOut != NULL && slCount(beList) != 0 )
     writeAxt(axtOut, bed, beList, FALSE);
 
 if(qrnaOut != NULL && slCount(beList) != 0)
     writeAxt(qrnaOut, bed, beList, TRUE);
 
 else
     {
     warn("Nothing for %s %s:%d-%d", bed->name, bed->chrom, bed->chromStart, bed->chromEnd);
     }
 
 /* Output bed. */
 bedOutputN(bed, 6, out, '\t', '\t');
 /* Gather info for percent id */
 for(i = 0; i < matchSize; i++)
     {
     if(matches[i] == 1)
 	match++;
     else if(matches[i] == 0)
 	misMatch++;
     else if(matches[i] == -1)
 	notAlign++;
     else
 	errAbort("agxCountBeds::countMatches() - matches array at position %d is: %d, not 1, 0, or -1",
 		 i, matches[i]);
     }
 /* Get sequence. */
 seq = hChromSeq(bed->chrom, bed->chromStart, bed->chromEnd);
 if(strlen(dna) == seq->size && differentString(seq->dna, dna) && refList != NULL) 
     warn("axtCountBeds::countMatches() - Different sequences from coordinates and axt file.:\ncoord: %s\naxt:    %s\n",
 	 seq->dna, dna);
 if(sameString(bed->strand, "-"))
     reverseComplement(seq->dna, seq->size);
 fprintf(out, "%d\t%d\t%d\t%f\t",  match, misMatch, notAlign, (float)match/(match+misMatch));
 fprintf(out, "%s\t", seq->dna);
 fprintf(out, "%d\t", matchSize);
 if(sameString(bed->strand, "-"))
     {
     for(i=matchSize-1; i >= 0; i--)
 	fprintf(out, "%d,", matches[i]);
     }
 else
     {
     for(i=0; i<matchSize; i++)
 	fprintf(out, "%d,", matches[i]);
     }
 /* for(i=0; i<matchSize; i++) */
 /*     fprintf(out, "%d,", matches[i]); */
 fprintf(out, "\n");
 freez(&matches);
 freez(&dna);
 dnaSeqFree(&seq);
 slFreeList(&beList);
 }
 
 
 void axtCountBeds(char *bedFile, char *axtFile, char *db, char *outFile, char *chrom)
 {
 struct bed *bedList = NULL, *bed = NULL;
 struct rbTree *axtTree = NULL;
 FILE *out = NULL;
 FILE *axtOut = NULL;
 FILE *qrnaOut = NULL;
 char *axtOutName = optionVal("axtOut", NULL);
 char *qrnaOutName = optionVal("qrnaOut", NULL);
 struct sqlConnection *conn = NULL;
 struct sqlResult *sr = NULL;
 char **row;
 char query[256];
 struct dyString *axtChromFile = NULL;
 
 warn("Loading Beds.");
 bedList = bedLoadAll(bedFile);
 hSetDb(db);
 conn = hAllocConn();
 if(sameString(chrom, "all"))
     sqlSafef(query, sizeof(query), "select chrom from chromInfo where chrom like '%%' order by chrom;");
 else
     sqlSafef(query, sizeof(query), "select chrom from chromInfo where chrom like '%s';", chrom);
 sr = sqlGetResult(conn, query);
 out = mustOpen(outFile, "w");
 outputHeader(out);
-axtChromFile = newDyString(strlen(axtFile)+100);
+axtChromFile = dyStringNew(strlen(axtFile)+100);
 if(axtOutName != NULL)
     axtOut = mustOpen(axtOutName, "w");
 if(qrnaOutName != NULL)
     qrnaOut = mustOpen(qrnaOutName, "w");
 dotForUserInit(1);
 warn("Reading axts.");
 while((row = sqlNextRow(sr)) != NULL)
     {
     dyStringClear(axtChromFile);
     dyStringPrintf(axtChromFile, "%s/%s.axt", axtFile, row[0]);
     /* If the .axt isn't there try to find a gzipped version. */
     if(!fileExists(axtChromFile->string)) 
 	{
 	dyStringClear(axtChromFile);
 	dyStringPrintf(axtChromFile, "%s/%s.axt.gz", axtFile, row[0]);
 	}
     dotForUser();
     chromKeeperForAxt(axtChromFile->string, db);
     for(bed = bedList; bed != NULL; bed = bed->next)
 	{
 	if(sameString(bed->strand,""))
 	    bed->strand[0] = '+';
 	if(differentString(bed->chrom, row[0]))
 	    continue;
 	countMatches(bed, out, axtOut, qrnaOut);
 	}
     cleanUpChromKeeper();
     }
 carefulClose(&out);
 carefulClose(&axtOut);
 warn("\nDone.");
 }
 
 int main(int argc, char *argv[])
 {
 optionInit(&argc, argv, NULL);
 if(argc <= 2)
     usage();
 dnaUtilOpen();
 axtCountBeds(argv[1], argv[2], argv[3], argv[4], argv[5]);
 return 0;
 }