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/lib/xap.c src/lib/xap.c
index 3201aa2..c16df64 100644
--- src/lib/xap.c
+++ src/lib/xap.c
@@ -1,182 +1,182 @@
 /* xap - XML Automatic Parser - together with autoXml this helps automatically
  * read in automatically generated data structures.  Calls lower level routine
  * in xp module, which originally was just a thin shell around expat. 
  *
  * This file is copyright 2002 Jim Kent, but license is hereby
  * granted for all use - public, private or commercial. */
 
 #include "common.h"
 #include "xap.h"
 #include "errAbort.h"
 #include "xp.h"
 
 
 void xapError(struct xap *xap, char *format, ...)
 /* Issue an error message and abort*/
 {
 va_list args;
 va_start(args, format);
 vaWarn(format, args);
 errAbort("line %d of %s", xpLineIx(xap->xp), xap->fileName);
 va_end(args);
 }
 
 static void xapStartTag(void *userData, char *name, char **atts)
 /* Handle beginning of a tag. */
 {
 struct xap *xap = userData;
 struct xapStack *stack;
 
 stack = --xap->stack;
 if (stack < xap->stackBuf)
     xapError(xap, "xap stack overflow");
 ++xap->stackDepth;
 if (stack->text == NULL)
-    stack->text = newDyString(256);
+    stack->text = dyStringNew(256);
 stack->elName = (char*)name;
 if (xap->skipDepth == 0)
     stack->object = xap->startHandler(xap, (char*)name, (char**)atts);
 if (xap->stackDepth == 1)
     {
     freeMem(xap->topType);
     xap->topType = cloneString(stack->elName);
     xap->topObject = stack->object;
     }
 }
 
 static void xapEndTag(void *userData, char *name, char *text)
 /* Handle end of tag. */
 {
 struct xap *xap = userData;
 struct xapStack *stack;
 
 dyStringAppend(xap->stack->text, text);
 if (xap->skipDepth == 0 || xap->skipDepth <= xap->stackDepth)
     {
     xap->skipDepth = 0;
     if (xap->endHandler)
 	xap->endHandler(xap, (char*)name);
     }
 stack = xap->stack++;
 if (xap->stack > xap->endStack)
     xapError(xap, "xap stack underflow");
 --xap->stackDepth;
 dyStringClear(stack->text);
 }
 
 #ifdef EXPAT
 static void xapText(void *userData, char *s, int len)
 /* Handle some text. */
 {
 struct xap *xap = userData;
 if (xap->skipDepth == 0)
     dyStringAppendN(xap->stack->text, (char *)s, len);
 }
 #endif /* EXPAT */
 
 static int xapRead(void *userData, char *buf, int bufSize)
 /* Read some text. */
 {
 struct xap *xap = userData;
 return fread(buf, 1, bufSize, xap->f);
 }
 
 struct xap *xapNew(void *(*startHandler)(struct xap *xap, char *name, char **atts),
 	void (*endHandler)(struct xap *xap, char *name) , char *fileName)
 /* Create a new parse stack. */
 {
 struct xap *xap;
 AllocVar(xap);
 xap->endStack = xap->stack = xap->stackBuf + ArraySize(xap->stackBuf) - 1;
 xap->startHandler = startHandler;
 xap->endHandler = endHandler;
 xap->xp = xpNew(xap, xapStartTag, xapEndTag, xapRead, fileName);
 xap->fileName = cloneString(fileName);
 return xap;
 }
 
 void xapFree(struct xap **pXp)
 /* Free up a parse stack. */
 {
 struct xap *xap = *pXp;
 if (xap != NULL)
     {
     struct xapStack *stack;
     for (stack = xap->stackBuf; stack < xap->endStack; ++stack)
         {
 	if (stack->text != NULL)
-	   freeDyString(&stack->text);
+	   dyStringFree(&stack->text);
 	}
     xpFree(&xap->xp);
     freeMem(xap->fileName);
     freeMem(xap->topType);
     freez(pXp);
     }
 }
 
 void xapParseFile(struct xap *xap, char *fileName)
 /* Open up file and parse it all. */
 {
 xap->f = mustOpen(fileName, "r");
 xpParse(xap->xp);
 carefulClose(&xap->f);
 }
 
 void xapIndent(int count, FILE *f)
 /* Write out some spaces. */
 {
 int i;
 for (i=0; i<count; ++i)
     {
     fputc(' ', f);
     }
 }
 
 void xapSkip(struct xap *xap)
 /* Skip current tag and any children.  Called from startHandler. */
 {
 xap->skipDepth = xap->stackDepth;
 }
 
 void xapParseAny(char *fileName, char *type, 
 	void *(*startHandler)(struct xap *xap, char *name, char **atts),
 	void (*endHandler)(struct xap *xap, char *name),
 	char **retType, void *retObj)
 /* Parse any object out of an XML file. 
  * If type parameter is non-NULL, force type.
  * example:
  *     xapParseAny("file.xml", "das", dasStartHandler, dasEndHandler, &type, &obj); */
 {
 struct xap *xap = xapNew(startHandler, endHandler, fileName);
 void **pObj = retObj;
 xapParseFile(xap, fileName);
 if (type != NULL && !sameString(xap->topType, type))
     xapError(xap, "Got %s, expected %s\n", xap->topType, type);
 if (retType != NULL)
     *retType = cloneString(xap->topType);
 *pObj = xap->topObject;
 xapFree(&xap);
 }
 
 struct xap *xapOpen(char *fileName, 
 	void *(*startHandler)(struct xap *xap, char *name, char **atts),
 	void (*endHandler)(struct xap *xap, char *name))
 /* Open up an xml file, but don't start parsing it yet.
  * Instead call xapNext to get the elements you want out of
  * the file.  When all done call xapFree. */
 {
 struct xap *xap = xapNew(startHandler, endHandler, fileName);
 xap->f =  mustOpen(fileName, "r");
 return xap;
 }
 
 void *xapNext(struct xap *xap, char *tag)
 /* Return next item matching tag (and all of it's children). */
 {
 if (!xpParseNext(xap->xp, tag))
     return NULL;
 if (!sameString(xap->topType, tag))
     errAbort("Expecting %s tag, got %s tag", tag, xap->topType);
 return xap->topObject;
 }