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/xp.c src/lib/xp.c
index 87e67fa..82afacd 100644
--- src/lib/xp.c
+++ src/lib/xp.c
@@ -1,553 +1,553 @@
 /* xp - A minimal non-verifying xml parser.  It's
  * stream oriented much like expas.  It's a bit faster
  * and smaller than expas.  I'm not sure it handles unicode
  * as well.
  *
  * This file is copyright 2002-2005 Jim Kent, but license is hereby
  * granted for all use - public, private or commercial. */
 
 #include "common.h"
 #include "dystring.h"
 #include "errAbort.h"
 #include "hash.h"
 #include "xp.h"
 #include "xmlEscape.h"
 
 
 
 char xpNextBuf(struct xp *xp)
 /* Fetch a new buffer and return first char.  Return 0 at EOF. */
 {
 int size = xp->read(xp->userData, xp->inBuf, sizeof(xp->inBuf));
 if (size <= 0)
     return 0;
 xp->inBufEnd = xp->inBuf + size;
 xp->in = xp->inBuf+1;
 return xp->inBuf[0];
 }
 
 #define xpGetChar(xp) \
     (xp->in < xp->inBufEnd ? *xp->in++ : xpNextBuf(xp))
 /* Macro to quickly fetch next char. */
 
 #define xpUngetChar(xp) \
     (--xp->in)
 /* Oops, don't fetch that after all. */
 
 struct xp *xpNew(void *userData, 
    void (*atStartTag)(void *userData, char *name, char **atts),
    void (*atEndTag)(void *userData, char *name, char *text),
    int (*read)(void *userData, char *buf, int bufSize),
    char *fileName)
 /* Form a new xp parser.  File name may be NULL - just used for
  * error reporting. */
 {
 struct xp *xp;
 AllocVar(xp);
 xp->stack = xp->stackBufEnd = xp->stackBuf + ArraySize(xp->stackBuf);
 xp->userData = userData;
 xp->atStartTag = atStartTag;
 xp->atEndTag = atEndTag;
 xp->read = read;
 xp->lineIx = 1;
-xp->endTag = newDyString(64);
+xp->endTag = dyStringNew(64);
 if (fileName)
     xp->fileName = cloneString(fileName);
 else
     xp->fileName = cloneString("XML");
 xp->inBufEnd = xp->in = xp->inBuf;		
 xp->symHash = xmlEscapeSymHash();
 return xp;
 }
 
 int xpReadFromFile(void *userData, char *buf, int bufSize)
 /* Read some text assuming a file was passed in as user data. */
 {
 FILE *f = userData;
 return fread(buf, 1, bufSize, f);
 }
 
 
 
 void xpFree(struct xp **pXp)
 /* Free up an xp parser. */
 {
 int i;
 struct xp *xp = *pXp;
 if (xp != NULL)
     {
     struct xpStack *stack;
     for (stack = xp->stackBufEnd; --stack >= xp->stackBuf; )
         {
 	if (stack->tag == NULL)
 	    break;
-	freeDyString(&stack->tag);
-	freeDyString(&stack->text);
+	dyStringFree(&stack->tag);
+	dyStringFree(&stack->text);
 	}
     for (i=0; i<ArraySize(xp->attDyBuf); ++i)
         {
 	if (xp->attDyBuf[i] == NULL)
 	    break;
-	freeDyString(&xp->attDyBuf[i]);
+	dyStringFree(&xp->attDyBuf[i]);
 	}
-    freeDyString(&xp->endTag);
+    dyStringFree(&xp->endTag);
     freeMem(xp->fileName);
     hashFree(&xp->symHash);
     freez(pXp);
     }
 }
 
 int xpLineIx(struct xp *xp)
 /* Return current line number. */
 {
 return xp->lineIx;
 }
 
 char *xpFileName(struct xp *xp)
 /* Return current file name. */
 {
 return xp->fileName;
 }
 
 void xpError(struct xp *xp, char *format, ...)
 /* Output an error message with filename and line number included. */
 {
 va_list args;
 va_start(args, format);
 vaWarn(format, args);
 errAbort("line %d of %s", xpLineIx(xp), xpFileName(xp));
 va_end(args);
 }
 
 static void xpUnexpectedEof(struct xp *xp)
 /* Squawk and die about EOF. */
 {
 xpError(xp, "Unexpected end of file.");
 }
 
 static void xpEatComment(struct xp *xp, char commentC)
 /* Skip characters until comment end. */
 {
 int startLine = xp->lineIx;
 char lastC = 0;
 char c;
 for (;;)
     {
     if ((c = xpGetChar(xp)) == 0)
         xpError(xp, "End of file in comment that started line %d", startLine);
     if (c == '\n')
         ++xp->lineIx;
     if (c == '>')
         {
 	if (lastC == commentC || commentC == '!')
 	break;
 	}
     lastC = c;
     }
 }
 
 static void xpLookup(struct xp *xp, struct dyString *temp, struct dyString *text)
 /* Parse after '&' until ';' and look up symbol.  Put result into text. */
 {
 char c;
 char *s;
 dyStringClear(temp);
 for (;;)
     {
     if ((c = xpGetChar(xp)) == 0)
 	xpError(xp, "End of file in after & and before ;");
     if (isspace(c))
         xpError(xp, "& without ;");
     if (c == ';')
         break;
     dyStringAppendC(temp, c);
     }
 s = temp->string;
 if (s[0] == '#')
     {
     c = atoi(s+1);
     dyStringAppendC(text, c);
     }
 else if ((s = hashFindVal(xp->symHash, s)) == NULL)
     {
     dyStringAppendC(text, '&');
     dyStringAppend(text, temp->string);
     dyStringAppendC(text, ';');
     }
 else
     {
     dyStringAppend(text, s);
     }
 }
 
 void xpForceMatch(struct xp *xp, char *matchString)
 /* Make sure that the next characters are match, and eat them. */
 {
 char *match = matchString, m;
 while ((m = *match++) != 0)
     {
     if (m != xpGetChar(xp))
         xpError(xp, "Expecting %s", matchString);
     }
 }
 
 void xpTextUntil(struct xp *xp, char *endPattern)
 /* Stuff xp->text with everything up to endPattern. */
 {
 int endSize = strlen(endPattern);
 int endPos = 0;
 char c;
 struct dyString *dy = xp->stack->text;
 for (;;)
     {
     if ((c = xpGetChar(xp)) == 0)
 	xpUnexpectedEof(xp);
     if (c == endPattern[endPos])
         {
 	endPos += 1;
 	if (endPos == endSize)
 	    return;
 	}
     else
         {
 	if (endPos > 0)
 	    dyStringAppendN(dy, endPattern, endPos);
 	dyStringAppendC(dy, c);
 	endPos = 0;
 	}
     }
 }
 
 
 void xpParseStartTag(struct xp *xp, 
 	int maxAttCount,		  /* Maximum attribute count. */
 	struct dyString *retName, 	  /* Returns tag name */
 	int *retAttCount, 		  /* Returns attribute count. */
 	struct dyString **retAttributes,  /* Name, value, name, value... */
 	boolean *retClosed)	  /* If true then is self-closing (ends in />) */
 /* Call this after the first '<' in a tag has been read.  It'll
  * parse out until the '>' tag. */
 {
 char c, quotC;
 int attCount = 0;
 struct dyString *dy;
 int lineStart;
 
 dyStringClear(retName);
 
 /* Skip white space after '<' and before tag name. */
 for (;;)
     {
     if ((c = xpGetChar(xp)) == 0)
 	xpUnexpectedEof(xp);
     if (isspace(c))
         {
 	if (c == '\n')
 	    ++xp->lineIx;
         }
     else
         break;
     }
 
 /* Read in tag name. */
 for (;;)
     {
     dyStringAppendC(retName, c);
     if ((c = xpGetChar(xp)) == 0)
 	xpUnexpectedEof(xp);
     if (c == '>' || c == '/' || isspace(c))
         break;
     }
 if (c == '\n')
     ++xp->lineIx;
 
 /* Parse attributes. */
 if (c != '>' && c != '/')
     {
     for (;;)
 	{
 	/* Skip leading white space. */
 	for (;;)
 	    {
 	    if ((c = xpGetChar(xp)) == 0)
 		xpUnexpectedEof(xp);
 	    if (isspace(c))
 		{
 		if (c == '\n')
 		    ++xp->lineIx;
 		}
 	    else
 		break;
 	    }
 	if (c == '>' || c == '/')
 	    break;
 
 	/* Allocate space in attribute table. */
 	if (attCount >= maxAttCount - 2)
 	    xpError(xp, "Attribute stack overflow");
 	dy = retAttributes[attCount];
 	if (dy == NULL)
-	    dy = retAttributes[attCount] = newDyString(64);
+	    dy = retAttributes[attCount] = dyStringNew(64);
 	else
 	    dyStringClear(dy);
 	++attCount;
 
 	/* Read until not a label character. */
 	for (;;)
 	    {
 	    dyStringAppendC(dy, c);
 	    if ((c = xpGetChar(xp)) == 0)
 		xpUnexpectedEof(xp);
 	    if (isspace(c))
 		{
 		if (c == '\n')
 		    ++xp->lineIx;
 		break;
 		}
 	    if (c == '=')
 		break;
 	    if (c == '/' || c == '>')
 		xpError(xp, "Expecting '=' after attribute name");
 	    }
 
 	/* Skip white space until '=' */
 	if (c != '=')
 	    {
 	    for (;;)
 		{
 		if ((c = xpGetChar(xp)) == 0)
 		    xpUnexpectedEof(xp);
 		if (isspace(c))
 		    {
 		    if (c == '\n')
 			++xp->lineIx;
 		    }
 		else
 		    break;
 		}
 	    if (c != '=')
 		xpError(xp, "Expecting '=' after attribute name");
 	    }
 
 	/* Skip space until quote. */
 	for (;;)
 	    {
 	    if ((c = xpGetChar(xp)) == 0)
 		xpUnexpectedEof(xp);
 	    else if (isspace(c))
 		{
 		if (c == '\n')
 		    ++xp->lineIx;
 		}
 	    else
 		break;
 	    }
 	if (c != '\'' && c != '"')
 	    xpError(xp, "Expecting quoted string after =");
 
 	/* Allocate space in attribute table. */
 	if (attCount >= maxAttCount - 2)
 	    xpError(xp, "Attribute stack overflow");
 	dy = retAttributes[attCount];
 	if (dy == NULL)
-	    dy = retAttributes[attCount] = newDyString(64);
+	    dy = retAttributes[attCount] = dyStringNew(64);
 	else
 	    dyStringClear(dy);
 	++attCount;
 
 	/* Read until next quote. */
 	quotC = c;
 	lineStart = xp->lineIx;
 	for (;;)
 	    {
 	    if ((c = xpGetChar(xp)) == 0)
 	       xpError(xp, "End of file inside literal string that started at line %d", lineStart);
 	    if (c == quotC)
 		break;
 	    if (c == '&')
 	       xpLookup(xp, xp->endTag, dy);
 	    else
 		{
 		if (c == '\n')
 		    ++xp->lineIx;
 		dyStringAppendC(dy, c);
 		}
 	    }
 	}
     }
 if (c == '/')
     {
     *retClosed = TRUE;
     c = xpGetChar(xp);
     if (c != '>')
         xpError(xp, "Expecting '>' after '/'");
     }
 else
     *retClosed = FALSE;
 *retAttCount = attCount;
 }
 
 void xpParseEndTag(struct xp *xp, char *tagName)
 /* Call this after have seen </.  It will parse through
  * > and make sure that the tagName matches. */
 {
 struct dyString *dy = xp->endTag;
 char c;
 
 dyStringClear(dy);
 
 /* Skip leading space. */
 for (;;)
     {
     if ((c = xpGetChar(xp)) == 0)
 	xpUnexpectedEof(xp);
     if (isspace(c))
 	{
 	if (c == '\n')
 	    ++xp->lineIx;
 	}
     else
 	break;
     }
 
 /* Read end tag. */
 for (;;)
     {
     dyStringAppendC(dy, c);
     if ((c = xpGetChar(xp)) == 0)
 	xpUnexpectedEof(xp);
     if (isspace(c))
 	{
 	if (c == '\n')
 	    ++xp->lineIx;
 	break;
 	}
     if (c == '>')
 	break;
     }
 
 /* Skip until '>' */
 while (c != '>')
     {
     dyStringAppendC(dy, c);
     if ((c = xpGetChar(xp)) == 0)
 	xpUnexpectedEof(xp);
     if (isspace(c))
 	{
 	if (c == '\n')
 	    ++xp->lineIx;
 	}
     else if (c != '>')
 	xpError(xp, "Unexpected characters past first word in /%s tag", dy->string);
     }
 
 if (!sameString(dy->string, tagName))
     xpError(xp, "Mismatch between start tag %s and end tag %s",  tagName, dy->string);
 }
 
 boolean xpParseNext(struct xp *xp, char *tag)
 /* Skip through file until get given tag.  Then parse out the
  * tag and all of it's children (calling atStartTag/atEndTag).
  * You can call this repeatedly to process all of a given tag
  * in file. */
 
 {
 char c;
 int i, attCount = 0;
 struct dyString *text = NULL;
 boolean isClosed;
 boolean inside = (tag == NULL);
 struct xpStack *initialStack = xp->stack;
 
 for (;;)
     {
     /* Load up text until next tag. */
     for (;;)
         {
 	if ((c = xpGetChar(xp)) == 0)
 	    return FALSE;
 	if (c == '<')
 	    break;
 	if (c == '&')
 	   xpLookup(xp, xp->endTag, text);
 	else 
 	    {
 	    if (c == '\n')
 		++xp->lineIx;
 	    if (text != NULL)
 		dyStringAppendC(text, c);
 	    }
 	}
 
     /* Get next character to figure out what type of tag. */
     c = xpGetChar(xp);
     if (c == 0)
        xpError(xp, "End of file inside tag");
     else if (c == '?' || c == '!')
         xpEatComment(xp, c);
     else if (c == '/')  /* Closing tag. */
         {
 	struct xpStack *stack = xp->stack;
 	if (stack >= xp->stackBufEnd)
 	    xpError(xp, "Extra end tag");
 	xpParseEndTag(xp, stack->tag->string);
 	if (inside)
 	    xp->atEndTag(xp->userData, stack->tag->string, stack->text->string);
 	xp->stack += 1;
 	if (xp->stack == initialStack)
 	    return TRUE;
 	}
     else	/* Start tag. */
         {
 	/* Push new frame on stack and check for overflow and unallocated strings. */
 	struct xpStack *stack = --xp->stack;
 	if (stack < xp->stackBuf)
 	    xpError(xp, "Stack overflow");
 	if (stack->tag == NULL)
-	    stack->tag = newDyString(32);
+	    stack->tag = dyStringNew(32);
 	else
 	    dyStringClear(stack->tag);
 	if (stack->text == NULL)
-	    stack->text = newDyString(256);
+	    stack->text = dyStringNew(256);
 	else
 	    dyStringClear(stack->text);
 	text = stack->text;
 
 	/* Parse the start tag. */
 	xpUngetChar(xp);
 	xpParseStartTag(xp, ArraySize(xp->attDyBuf), stack->tag, 
 		&attCount, xp->attDyBuf, &isClosed);
 
 	if (!inside && sameString(stack->tag->string, tag))
 	    {
 	    inside = TRUE;
 	    initialStack = xp->stack + 1;
 	    }
 
 	/* Call user start function, and if closed tag, end function too. */
 	if (inside)
 	    {
 	    /* Unpack attributes into simple array of strings. */
 	    for (i=0; i<attCount; ++i)
 		xp->attBuf[i] = xp->attDyBuf[i]->string;
 	    xp->attBuf[attCount] = NULL;
 	    xp->atStartTag(xp->userData, stack->tag->string, xp->attBuf);
 	    }
 	if (isClosed)
 	    {
 	    if (inside)
 		xp->atEndTag(xp->userData, stack->tag->string, stack->text->string);
 	    xp->stack += 1;
 	    if (xp->stack == initialStack)
 		return TRUE;
 	    }
 	}
     }
 }
 
 void xpParse(struct xp *xp)
 /* Parse from start tag to end tag.  Throw error if a problem. */
 {
 xpParseNext(xp, NULL);
 }