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/phyloTree.c src/lib/phyloTree.c
index 9fbe00f..f911897 100644
--- src/lib/phyloTree.c
+++ src/lib/phyloTree.c
@@ -1,512 +1,512 @@
 /* Copyright (C) 2011 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 "dystring.h"
 #include "phyloTree.h"
 
 
 struct phyloTree *phyloReadTree(struct lineFile *lf)
 /* reads a phyloTree from lineFile (first line only) */
 {
 struct phyloTree *tree = NULL;
 char *ptr;
 int len;
 
 if (lineFileNext(lf, &ptr, &len) && (len > 0))
     tree = phyloParseString(ptr);
 
 return tree;
 }
 
 struct phyloTree *phyloOpenTree(char *fileName)
 {
 struct lineFile *lf = lineFileUdcMayOpen(fileName, TRUE);
 if (lf == NULL)
     errAbort("phyloOpenTree: Can't open '%s'", fileName);
 struct phyloTree *tree = phyloReadTree(lf);
 
 lineFileClose(&lf);
 
 return tree;
 }
 
 static char *unescapeNewark(char *s)
 /* unescape backslashed Newark punctuation chars */
 {
 char out[strlen(s)+1];
 char *o = out;
 boolean escaped = FALSE;
 while(TRUE)
     {
     char c = *s++;
     if (escaped)
 	{
 	if (c == '(' || c == ')' || c == ',' || c == ':' || c == ';' || c == '\\')
 	    {
 	    *o++ = c;
 	    }
 	else  
 	    {
 	    errAbort("Expected Newark punctuation characters or backslash after a backslash.");
 	    }
 	escaped = FALSE;
 	}
     else
 	{
 	if (c == '\\')
 	    {
 	    escaped = TRUE;
 	    }
 	else
 	    {
 	    if (c == '(' || c == ')' || c == ',' || c == ':' || c == ';' || c == '\\')
 		errAbort("Expected a backslash before Newark punctuation characters or backslash.");
 	    *o++ = c;
 	    }
 	}
     if (c == 0)
 	break;
     }
 return cloneString(out);
 }
 
 
 static struct phyloName *parseIdent(char **ptrPtr)
 /* read a node name with possibile branch length */
 {
 struct phyloName *pName;
 char *start = *ptrPtr;
 char *ptr = *ptrPtr;
 
 AllocVar(pName);
 
 
 /* legal id's are anything except Newick punctuation chars */
 char prev = ' ';
 char c;
 while((c = *ptr))
     {
     if (c == '(' || c == ')' || c == ',' || c == ':' || c == ';')
 	{
 	if (prev != '\\') // backslash escape char?
     	    break;
 	}
     ptr++;
     prev = c;
     }
 
 /* did we read something? */
 if(ptr > start)
     {
     char val;
 
     val = *ptr;
     *ptr = 0;
     pName->name = cloneString(start);
     pName->name = trimSpaces(pName->name);
     pName->name = unescapeNewark(pName->name);
     *ptr = val;
     }
 
 /* is there some branch length info */
 if (*ptr == ':')
     {
     ptr++;
     char *lStart = ptr;
     while (isdigit(*ptr) || *ptr == '.' || *ptr == 'e' || *ptr == 'E' || *ptr == '+' || *ptr == '-')
         ptr++;
     int lSize = ptr - lStart;
     if (lSize)
         pName->length = strtod(lStart, NULL);
     while ((*ptr != '[') && (*ptr != ')') && (*ptr != ',') && (*ptr != ';'))
 	ptr++;
     }
 
 *ptrPtr = ptr;
 
 return pName;
 }
 
 static struct phyloTree *newEdge(struct phyloTree *parent, struct phyloTree *child)
 {
 parent->numEdges++;
 
 if (parent->numEdges > parent->allocedEdges)
     {
     int oldSize = parent->allocedEdges * sizeof (struct phyloTree *);
     int newSize;
 
     parent->allocedEdges += 5;
     newSize = parent->allocedEdges * sizeof (struct phyloTree *);
     parent->edges = needMoreMem(parent->edges, oldSize, newSize);
     }
 
 if (!child)
     errAbort("unexpected error: child is null in phyloTree.c::newEdge()");
 
 child->parent = parent;
 return parent->edges[parent->numEdges -1 ] = child;
 }
 
 struct phyloTree *phyloAddEdge(struct phyloTree *parent, struct phyloTree *child)
 /* add an edge to a phyloTree node */
 {
 return newEdge(parent, child);
 }
 
 static struct phyloTree *parseSubTree(char **ptrPtr)
 /* the recursive workhorse function, parses a tree from ptr */
 {
 struct phyloTree *node = NULL;
 char *ptr = *ptrPtr;
 
 /* trees are terminated by one of these three chars */
 if ((*ptr == ';') || (*ptr == ',') || (*ptr == ')') )
     return NULL;
 
 AllocVar(node);
 
 while(*ptr == ' ')
     ptr++;
 
 if (*ptr == '(') 
     {
     struct phyloTree *edge;
 
     ptr++;
 
     do
 	{
 	struct phyloTree *child = parseSubTree(&ptr);
 	if (!child)
 	    errAbort("missing child/subTree at (%s)",ptr-1);
 	edge = newEdge(node,child);
 	edge->parent = node;
 	} while (*ptr++ == ',');
     --ptr;
     if (*ptr++ != ')') 
 	errAbort("unbalanced parenthesis at (%s)",ptr-1);
     node->ident = parseIdent(&ptr);
     }
 else 
     if ((*ptr == ':') || (isalpha(*ptr))|| (isdigit(*ptr)) || (*ptr == '_')
 	 || (*ptr == '\'') || (*ptr == '.')) 
 	node->ident = parseIdent(&ptr);
 else
     errAbort("illegal char '%c' in phyloString",*ptr);
 
 if (*ptr == '[')
     {
     if (startsWith("[&&NHX:D=Y]",ptr))
 	node->isDup = TRUE;
 
     while(*ptr != ']')
 	ptr++;
 
     ptr++;
 
     }
 
 *ptrPtr = ptr;
 
 
 return node;
 }
 
 static void replaceWhitespaceWithSpaces(char *s)
 /* Replace all whitespace chars with a space char */
 {
 char c;
 for(c=*s; c != 0; c = *(++s))
     {
     if (isspace(c))
 	{
 	*s = ' ';
 	}
     }
 }
 
 
 struct phyloTree *phyloParseString(char *string)
 /* build a phyloTree from a string */
 {
 struct phyloTree *tree = NULL;
 
 replaceWhitespaceWithSpaces(string);
 
 char *ptr = string;
 tree = parseSubTree(&ptr);
 
 if (tree == NULL)
     errAbort("expecting properly formatted tree");
 if (*ptr != ';')
     errAbort("expecting tree terminator ';', found '%s'", ptr);
 
 return tree;
 }
 
 
 /*  some static stuff for printing out trees */
 static int recurseCount = 0;
 
 static void tabOut(FILE *f)
 {
 int i;
 
 for(i=0; i < recurseCount; i++)
     fputc(' ',f);
 }
 
 static void pTree( struct phyloTree *tree,FILE *f, boolean noDups)
 /* print out phylogenetic tree in Newick format */
 {
 if (tree)
     {
     int ii;
     if (noDups && (tree->numEdges == 1))
 	pTree(tree->edges[0], f, noDups);
     else 
 	{
 	if (tree->numEdges)
 	    {
 	    fprintf(f,"(");
 	    for (ii= 0; ii < tree->numEdges; ii++)
 		{
 		pTree(tree->edges[ii], f, noDups);
 		if (ii + 1 < tree->numEdges)
 		    fprintf(f,",");
 		}
 	    fprintf(f,")");
 	    }
 	if (tree->ident->name)
 	    fprintf(f,"%s",tree->ident->name);
 	//if (tree->ident->length != 0.0)
 	    fprintf(f,":%0.04g", tree->ident->length);
 	if (tree->isDup)
 	    fprintf(f,"[&&NHX:D=Y]");
 	}
     }
 }
 
 void phyloPrintTreeNoDups( struct phyloTree *tree,FILE *f)
 /* print out phylogenetic tree in Newick format (only speciation nodes) */
 {
 pTree(tree, f, TRUE);
 fprintf(f, ";\n");
 }
 
 void phyloPrintTree( struct phyloTree *tree,FILE *f)
 /* print out phylogenetic tree in Newick format */
 {
 pTree(tree, f, FALSE);
 fprintf(f, ";\n");
 }
 
 void phyloDebugTree( struct phyloTree *tree,FILE *f)
 /* print out phylogenetic tree */
 {
 if (tree)
     {
     int ii;
     fprintf(f,"%s:%g numEdges %d\n",tree->ident->name, tree->ident->length, tree->numEdges);
     recurseCount++;
     for (ii= 0; ii < tree->numEdges; ii++)
 	{
 	tabOut(f);
 	phyloDebugTree(tree->edges[ii], f);
 	}
     recurseCount--;
     }
 }
 
 struct phyloTree *phyloFindName( struct phyloTree *tree,char *name )
 /* find the node with this name */
 {
 struct phyloTree *subTree = NULL;
 int ii;
 
 if (tree->ident->name && sameString(tree->ident->name, name))
     return tree;
 
 for (ii=0; ii < tree->numEdges; ii++)
     {
     if ((subTree = phyloFindName( tree->edges[ii], name)) != NULL)
 	break;
     }
 
 return subTree;
 }
 
 void phyloClearTreeMarks(struct phyloTree *tree)
 /* clear the favorite child marks */
 {
 int ii;
 
 tree->mark = 0;
 
 for (ii=0; ii < tree->numEdges; ii++)
     phyloClearTreeMarks(tree->edges[ii]);
 }
 
 struct phyloTree *phyloFindMarkUpTree(struct phyloTree *tree)
 /* find a marked node somewhere above this node */
 {
 do
     {
     if (tree->mark)
 	return tree;
     tree = tree->parent;
     } while (tree);
 
 return NULL;
 }
 
 void phyloMarkUpTree(struct phyloTree *tree)
 /* mark all the nodes from this one up to the top of the tree */
 {
     tree->mark = tree;
     for(;tree->parent; tree = tree->parent)
 	tree->parent->mark = tree;
 }
 
 char *phyloFindPath(struct phyloTree *tree, char *ref, char *cross)
 /* find the shortest path from ref to cross (returns a list
  * of the node names separated by spaces) */
 {
 struct phyloTree *treeRef, *treeCross, *parent;
-struct dyString *ds = newDyString(0);
+struct dyString *ds = dyStringNew(0);
 
 if ((treeRef = phyloFindName(tree,ref)) == NULL)
     return NULL;
 
 if ((treeCross = phyloFindName(tree,cross)) == NULL)
     return NULL;
 
 phyloClearTreeMarks(tree);
 phyloMarkUpTree(treeCross);
 if ((parent = phyloFindMarkUpTree(treeRef)) == NULL)
     return NULL;
 
 /* walk up the tree till we hit the common parent */
 while(treeRef != parent)
     {
     treeRef = treeRef->parent;
     if (ds->stringSize)
 	dyStringAppendC(ds, ' ');
     if (treeRef->ident->name)
 	dyStringAppendN(ds, treeRef->ident->name, strlen(treeRef->ident->name));
     }
 
 /* now walk down the tree till we come to the target species */
 while (parent != treeCross)
     {
     parent = parent->mark;
     dyStringAppendC(ds, ' ');
     if (parent->ident->name)
 	dyStringAppendN(ds, parent->ident->name, strlen(parent->ident->name));
     }
 
 return ds->string;
 }
 
 
 static void nodeNames(struct phyloTree *tree, struct dyString *ds)
 /* recursive workhorse to add all the node names to a string */
 {
 int ii;
 
 if (tree->ident->name)
     {
     dyStringAppendN(ds, tree->ident->name, strlen(tree->ident->name));
     dyStringAppendC(ds, ' ');
     }
 
 for (ii=0; ii < tree->numEdges; ii++)
     nodeNames(tree->edges[ii],ds);
 }
 
 char *phyloNodeNames(struct phyloTree *tree)
 /* add all the node names to a dy string */
 {
-struct dyString *ds = newDyString(0);
+struct dyString *ds = dyStringNew(0);
 
 nodeNames(tree, ds);
 
 ds->string[ds->stringSize-1]=0;
 
 return ds->string;
 }
 
 
 static void reParent(struct phyloTree *tree)
 {
 if (tree->parent)
     {
     struct phyloTree *edge, *saveParent = tree->parent;
 
     reParent(saveParent); /* make the parent into the root */
     phyloDeleteEdge(saveParent, tree); /* remove this tree from the
 					  parent tree */
     tree->parent = NULL; /* make this tree the root */
     edge = newEdge(tree, saveParent); /* add the old parent tree as a
 					child of the new root */
     edge->parent = tree; /* set the parent in the new child */
 
     edge->ident->length = tree->ident->length;
     }
 }
 
 struct phyloTree *phyloReRoot(struct phyloTree *tree)
 /* return a tree whose root is tree and what were parents are now "right" children */
 {
 reParent(tree);
 tree->ident->length = 0;
 
 return tree;
 }
 
 void phyloDeleteEdge(struct phyloTree *tree, struct phyloTree *edge)
 /* delete an edge from a node.  Aborts on error */
 {
 int ii;
 
 for (ii=0; ii < tree->numEdges; ii++)
     if (tree->edges[ii] == edge)
 	{
 	memcpy(&tree->edges[ii], &tree->edges[ii+1], sizeof(tree) * (tree->numEdges - ii - 1));
 	tree->numEdges--;
 	//phyloFreeTree(edge);
 	return;
 	}
 
 errAbort("tried to delete non-existant edge");
 }
 
 int phyloCountLeaves(struct phyloTree *tree)
 {
 int ii, count = 0;
 
 if (tree->numEdges == 0)
     return 1;
 
 for (ii=0; ii < tree->numEdges; ii++)
     count += phyloCountLeaves(tree->edges[ii]);
 
 return count;
 }
 
 int phyloCountInternalNodes(struct phyloTree *node)
 /* Return the number of internal nodes (not leaf nodes) in tree. */
 {
 int count = 0;
 if (node->numEdges > 0)
     {
     count = 1;
     int ii;
     for (ii = 0;  ii < node->numEdges;  ii++)
         count += phyloCountInternalNodes(node->edges[ii]);
     }
 return count;
 }