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/utils/liftUpBedFromTable/liftUpBedFromTable.c src/hg/utils/liftUpBedFromTable/liftUpBedFromTable.c
index 6affe81..2089dea 100644
--- src/hg/utils/liftUpBedFromTable/liftUpBedFromTable.c
+++ src/hg/utils/liftUpBedFromTable/liftUpBedFromTable.c
@@ -1,304 +1,304 @@
 /* liftUpBedFromTable - Convert coordinate systems using a positional table in the database.. */
 
 /* Copyright (C) 2007 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 "hdb.h"
 
 void usage()
 /* Explain usage and exit. */
 {
 errAbort(
   "liftUpBedFromTable - Convert coordinate systems using a positional table in the database.\n"
   "usage:\n"
   "   liftUpBedFromTable db table in.bed out.bed\n"
   "options:\n"
   "   -plus=N   File has first N fields which are bed, plus more after that.\n"
   "   -cds      Lift off positional table's CDS start (or end if using -end).\n"
   "   -end      Lift off the end of the position instead of the beginning.\n"
   "WARNING: This utility isn't yet mature.  in.bed should be BED 6 or less, and\n"
   "the output could be off so double-check stuff.\n"
   );
 }
 
 static struct optionSpec options[] = {
    {"plus", OPTION_INT},
    {"cds", OPTION_BOOLEAN},
    {"end", OPTION_BOOLEAN},
    {NULL, 0},
 };
 
 /* Option-related globals. */
 
 static int numBedFields = 0;
 static boolean usingCds = FALSE;
 static boolean usingEnd = FALSE;
 
 struct bedPlus 
 /* Store bed plus the rest of the line. */
     {
     struct bedPlus *next;
     struct bed *bed;
     char *rest;
     }; 
 
 void bedPlusFree(struct bedPlus **pBp)
 /* freedom. */
 {
 struct bedPlus *bp;
 if ((bp = *pBp) == NULL)
     return;
 bedFree((struct bed **)&(bp->bed));
 freeMem((char *)bp->rest);
 freez(pBp);
 }
 
 void bedPlusFreeList(struct bedPlus **pList)
 /* typical freeList function. */
 {
 struct bedPlus *el, *next;
 for (el = *pList; el != NULL; el = next)
     {
     next = el->next;
     bedPlusFree(&el);
     }
 *pList = NULL;
 }
 
 struct bedPlus *bedPlusNLoad(char *row[], int wordCount, int bedWordCount)
 /* Load a single row array like bedLoadN would... but handle extra info. */
 {
 struct bedPlus *newBp;
 AllocVar(newBp);
 if (bedWordCount > 0)
     {
-    struct dyString *ds = newDyString(0);
+    struct dyString *ds = dyStringNew(0);
     int i;
     newBp->bed = bedLoadN(row, bedWordCount);
     for (i = bedWordCount; i < wordCount; i++)
 	{
 	dyStringAppend(ds, row[i]);
 	if (i < (wordCount-1))
 	    dyStringAppendC(ds, '\t');
 	}
     newBp->rest = dyStringCannibalize(&ds);
     }
 else
     {
     newBp->bed = bedLoadN(row, wordCount);
     }
 return newBp;
 }
 
 struct bedPlus *bedPlusFileLoad(char *fileName)
 /* Load all the beds from a file using either the */
 /* N number of fields, or whatever we find. */
 {
 struct bedPlus *list = NULL;
 struct lineFile *lf = lineFileOpen(fileName, TRUE);
 char *words[128];
 int wordCount;
 int bedWordCount = optionInt("plus", 0);
 numBedFields = bedWordCount;
 while ((wordCount = lineFileChopTab(lf, words)) > 0)
     {
     struct bedPlus *newBp;
     if (numBedFields == 0)
 	numBedFields = wordCount;
     if (numBedFields < 4)
 	errAbort("Too few bed fields.");
     newBp = bedPlusNLoad(words, wordCount, bedWordCount);
     slAddHead(&list, newBp);
     }
 slReverse(&list);
 lineFileClose(&lf);
 return list;
 }
 
 void bedPlusTabOut(FILE *f, struct bedPlus *bp)
 /* Output and handle plus info. */
 {
 if (bp->rest == NULL)
     bedOutputN(bp->bed, numBedFields, f, '\t', '\n');
 else
     {
     bedOutputN(bp->bed, numBedFields, f, '\t', '\t');
     fprintf(f, "%s\n", bp->rest);
     }
 }
 
 struct hash *hashUpPositions(struct bed **pBedList)
 /* Add beds to a hash of lists. */
 {
 struct bed *popped;
 struct hash *theHash = hashNew(22);
 while ((popped = slPopHead(pBedList)) != NULL)
     {
     struct slRef *ref = slRefNew(popped);
     struct slRef *list = (struct slRef *)hashFindVal(theHash, popped->name);
     ref->next = list;
     hashReplace(theHash, popped->name, ref);
     }
 return theHash;
 }
 
 void slRefAndBedFree(struct slRef **pRef)
 /* designed to be called by slRefListAndBedFree. */
 {
 struct slRef *ref;
 if ((ref = *pRef) == NULL) 
     return;
 bedFree((struct bed **)&(ref->val));
 freez(pRef);
 }
 
 void slRefListAndBedFree(void **pList)
 /* designed to be called by bedFreeWithVals. */
 {
 struct slRef *el, *next;
 for (el = *pList; el != NULL; el = next)
     {
     next = el->next;
     slRefAndBedFree(&el);
     }
 *pList = NULL;
 }
 
 struct hash *positionHash(char *db, char *table)
 /* Load up table from database and return a hash from it. */
 {
 struct bed *list = hGetFullBedDb(db, table);
 struct hash *theHash = hashUpPositions(&list);
 return theHash;
 }
 
 void liftAndOutput(struct hash *posHash, struct bedPlus *bpList, char *outfile)
 /* Combine the two sources of data, do the coordinate math, and output. */
 {
 FILE *f = mustOpen(outfile, "w");
 struct bedPlus *bp;
 for (bp = bpList; bp != NULL; bp = bp->next)
     {
     struct slRef *refList = hashFindVal(posHash, bp->bed->chrom);
     /* Skips lifting ones that don't have chroms with names among those in */
     /* the table. */
     if (refList)
 	{
 	struct slRef *ref;
 	for (ref = refList; ref != NULL; ref = ref->next)
 	    {
 	    struct bedPlus *liftedBp;
 	    struct bed *liftedBed;
 	    struct bed *pos = ref->val;
 	    char newName[64];
 	    int size = bp->bed->chromEnd - bp->bed->chromStart;
 	    boolean minusStrand = FALSE;
 	    if (((pos->strand[0] == '+') && (bp->bed->strand[0] == '-')) || 
 		((pos->strand[0] == '-') && (bp->bed->strand[0] == '+')))
 		minusStrand = TRUE;
 	    safef(newName, sizeof(newName), "%s.%s", pos->name, bp->bed->name);	   
 	    AllocVar(liftedBp);
 	    AllocVar(liftedBed);
 	    liftedBed->name = cloneString(newName);
 	    liftedBed->chrom = cloneString(pos->chrom);
 	    liftedBed->score = bp->bed->score;
 	    liftedBed->strand[0] = (minusStrand) ? '-' : '+';
 	    liftedBed->strand[1] = '\0';
 	    /* coordinate hell... obnoxious. */
 	    if (usingEnd)
 		{
 		if (usingCds)
 		    {
 		    if (minusStrand)
 			{
 			liftedBed->chromEnd = pos->thickStart - bp->bed->chromStart - 1;
 			liftedBed->chromStart = liftedBed->chromEnd - size;
 			}
 		    else 
 			{
 			liftedBed->chromStart = pos->thickEnd + bp->bed->chromStart;
 			liftedBed->chromEnd = liftedBed->chromStart + size;
 			}
 		    }		
 		else
 		    {
 		    if (minusStrand)
 			{
 			liftedBed->chromEnd = pos->chromStart - bp->bed->chromStart - 1;
 			liftedBed->chromStart = liftedBed->chromEnd - size;
 			}
 		    else 
 			{
 			liftedBed->chromStart = pos->chromEnd + bp->bed->chromStart;
 			liftedBed->chromEnd = liftedBed->chromStart + size;
 			}
 		    }
 		}
 	    else
 		{
 		if (usingCds)
 		    {
 		    if (minusStrand)
 			{
 			liftedBed->chromEnd = pos->thickEnd - bp->bed->chromStart - 1;
 			liftedBed->chromStart = liftedBed->chromEnd - size;
 			}
 		    else 
 			{
 			liftedBed->chromStart = pos->thickStart + bp->bed->chromStart;
 			liftedBed->chromEnd = liftedBed->chromStart + size;
 			}
 		    }
 		else
 		    {
 		    if (minusStrand)
 			{
 			liftedBed->chromEnd = pos->chromEnd - bp->bed->chromStart - 1;
 			liftedBed->chromStart = liftedBed->chromEnd - size;
 			}
 		    else 
 			{
 			liftedBed->chromStart = pos->chromStart + bp->bed->chromStart;
 			liftedBed->chromEnd = liftedBed->chromStart + size;
 			}
 		    }
 		}
 	    liftedBp->bed = liftedBed;
 	    liftedBp->rest = cloneString(bp->rest);
 	    /* Output! */
 	    bedPlusTabOut(f, liftedBp);
 	    bedPlusFree(&liftedBp);
 	    }
 	}
     else
 	fprintf(stderr, "warning: %s not found in table\n", bp->bed->chrom);
     }
 carefulClose(&f);
 }
 
 void liftUpBedFromTable(char *db, char *table, char *inFile, char *outFile)
 /* liftUpBedFromTable - Convert coordinate systems using a positional table in the database.. */
 {
 struct hash *posHash = positionHash(db, table);
 struct bedPlus *bpList = bedPlusFileLoad(inFile);
 if (optionExists("cds"))
     usingCds = TRUE;
 if (optionExists("end"))
     usingEnd = TRUE;
 liftAndOutput(posHash, bpList, outFile);
 bedPlusFreeList(&bpList);
 hashFreeWithVals(&posHash, slRefListAndBedFree);
 }
 
 int main(int argc, char *argv[])
 /* Process command line. */
 {
 optionInit(&argc, argv, options);
 if (argc != 5)
     usage();
 liftUpBedFromTable(argv[1], argv[2], argv[3], argv[4]);
 return 0;
 }