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/genomeRangeTree.c src/lib/genomeRangeTree.c
index 7fb6733..a050384 100644
--- src/lib/genomeRangeTree.c
+++ src/lib/genomeRangeTree.c
@@ -1,201 +1,201 @@
 /* genomeRangeTree - This module is a way of keeping track of
  * non-overlapping ranges (half-open intervals) across a whole
  * genome (multiple chromosomes or scaffolds). 
  * It is a hash table container mapping chrom to rangeTree.
  * Most of the work is performed by rangeTree, this container
  * enables local memory and stack to be shared by many rangeTrees
  * so it should be able to handle genomes with a very large 
  * number of scaffolds. See rangeTree for more information. */
 
 /* Copyright (C) 2014 The Regents of the University of California 
  * See kent/LICENSE or http://genome.ucsc.edu/license/ for licensing information. */
 
 #include "common.h"
 #include "sig.h"
 #include "localmem.h"
 #include "rbTree.h"
 #include "hash.h"
 #include "rangeTree.h"
 #include "genomeRangeTree.h"
 #include "dystring.h"
 #include <limits.h>
 
 
 struct genomeRangeTree *genomeRangeTreeNewSize(int hashPowerOfTwoSize)
 /* Create a new, empty, genomeRangeTree. 
  * Free with genomeRangeTreeFree. */
 {
 struct genomeRangeTree *t;
 AllocVar(t); 
 t->hash = newHash(hashPowerOfTwoSize);
 t->lm = lmInit(0);
 return t;
 }
 
 struct genomeRangeTree *genomeRangeTreeNew()
 /* Create a new, empty, genomeRangeTree. Uses the default hash size.
  * Free with genomeRangeTreeFree. */
 {
 return genomeRangeTreeNewSize(0);
 }
 
 void genomeRangeTreeFree(struct genomeRangeTree **pTree)
 /* Free up genomeRangeTree.  */
 {
 struct genomeRangeTree *grt = *pTree;
 if (grt != NULL)
     {
     /* need to manually free object due to thee way rbTreeNewDetailed is done */
     struct hashCookie hc = hashFirst(grt->hash);
     struct hashEl *hel;
     while ((hel = hashNext(&hc)) != NULL)
 	freeMem(hel->val);
 
     lmCleanup(&(grt->lm));  /* clean up all the memory for all nodes for all trees */
     freeHash(&(grt->hash)); /* free the hash table including names (trees are freed by lmCleanup) */
     freez(pTree);                /* free this */
     }
 }
 
 struct rbTree *genomeRangeTreeFindRangeTree(struct genomeRangeTree *tree, char *chrom)
 /* Find the rangeTree for this chromosome, if any. Returns NULL if chrom not found. */
 {
 return hashFindVal(tree->hash, chrom);
 }
 
 struct rbTree *genomeRangeTreeFindOrAddRangeTree(struct genomeRangeTree *tree, char *chrom)
 /* Find the rangeTree for this chromosome, or add new chrom and empty rangeTree if not found. */
 {
 struct hashEl *hel;
 hel = hashStore(tree->hash, chrom);
 if (hel->val == NULL) /* need to add a new rangeTree */
     hel->val = rangeTreeNewDetailed(tree->lm, tree->stack);
 return hel->val;
 }
 
 struct range *genomeRangeTreeAdd(struct genomeRangeTree *tree, char *chrom, int start, int end)
 /* Add range to tree, merging with existing ranges if need be. 
  * Adds new rangeTree if chrom not found. */
 {
 return rangeTreeAdd(genomeRangeTreeFindOrAddRangeTree(tree,chrom), start, end);
 }
 
 struct range *genomeRangeTreeAddVal(struct genomeRangeTree *tree, char *chrom, int start, int end, void *val, void *(*mergeVals)(void *existing, void *newVal))
 /* Add range to tree, merging with existing ranges if need be. 
  * Adds new rangeTree if chrom not found. 
  * If this is a new range, set the value to this val.
  * If there are existing items for this range, and if mergeVals function is not null, 
  * apply mergeVals to the existing values and this new val, storing the result as the val
  * for this range (see rangeTreeAddValCount() and rangeTreeAddValList() below for examples). */
 {
 return rangeTreeAddVal(genomeRangeTreeFindOrAddRangeTree(tree,chrom), start, end, val, mergeVals);
 }
 
 struct range *genomeRangeTreeAddValCount(struct genomeRangeTree *tree, char *chrom, int start, int end)
 /* Add range to tree, merging with existing ranges if need be. 
  * Adds new rangeTree if chrom not found. 
  * Set range val to count of elements in the range. Counts are pointers to 
  * ints allocated in tree localmem */
 {
 return rangeTreeAddValCount(genomeRangeTreeFindOrAddRangeTree(tree,chrom), start, end);
 }
 
 struct range *genomeRangeTreeAddValList(struct genomeRangeTree *tree, char *chrom, int start, int end, void *val)
 /* Add range to tree, merging with existing ranges if need be. 
  * Adds new rangeTree if chrom not found. 
  * Add val to the list of values (if any) in each range.
  * val must be valid argument to slCat (ie, be a struct with a 'next' pointer as its first member) */
 {
 return rangeTreeAddValList(genomeRangeTreeFindOrAddRangeTree(tree,chrom), start, end, val);
 }
 
 boolean genomeRangeTreeOverlaps(struct genomeRangeTree *tree, char *chrom, int start, int end)
 /* Return TRUE if start-end overlaps anything in tree */
 {
 struct rbTree *t;
 return (t=genomeRangeTreeFindRangeTree(tree,chrom)) ? rangeTreeOverlaps(t, start, end) : FALSE;
 }
 
 int genomeRangeTreeOverlapSize(struct genomeRangeTree *tree, char *chrom, int start, int end)
 /* Return the total size of intersection between interval
  * from start to end, and items in range tree. Sadly not
  * thread-safe. */
 {
 struct rbTree *t;
 return (t=genomeRangeTreeFindRangeTree(tree,chrom)) ? rangeTreeOverlapSize(t, start, end) : 0;
 }
 
 struct range *genomeRangeTreeFindEnclosing(struct genomeRangeTree *tree, char *chrom, int start, int end)
 /* Find item in range tree that encloses range between start and end 
  * if there is any such item. */
 {
 struct rbTree *t;
 return (t=genomeRangeTreeFindRangeTree(tree,chrom)) ? rangeTreeFindEnclosing(t, start, end) : NULL;
 }
 
 struct range *genomeRangeTreeAllOverlapping(struct genomeRangeTree *tree, char *chrom, int start, int end)
 /* Return list of all items in range tree that overlap interval start-end.
  * Do not free this list, it is owned by tree.  However it is only good until
  * next call to rangeTreeFindInRange or rangeTreeList. Not thread safe. */
 {
 struct rbTree *t;
 return (t=genomeRangeTreeFindRangeTree(tree,chrom)) ? rangeTreeAllOverlapping(t, start, end) : NULL;
 }
 
 struct range *genomeRangeTreeMaxOverlapping(struct genomeRangeTree *tree, char *chrom, int start, int end)
 /* Return item that overlaps most with start-end. Not thread safe.  Trashes list used
  * by rangeTreeAllOverlapping. */
 {
 struct rbTree *t;
 return (t=genomeRangeTreeFindRangeTree(tree,chrom)) ? rangeTreeMaxOverlapping(t, start, end) : NULL;
 }
 
 struct range *genomeRangeTreeList(struct genomeRangeTree *tree, char *chrom)
 /* Return list of all ranges in single rangeTree in order.  Not thread safe. 
  * No need to free this when done, memory is local to tree. */
 {
 struct rbTree *t;
 return (t=genomeRangeTreeFindRangeTree(tree,chrom)) ? rangeTreeList(t) : NULL;
 }
 
 /* globals used for genomeRangeTreeToString */
 struct dyString *tmpTreeToString = NULL;
 char *tmpTreeToStringCurChrom = NULL;
 void tmpNodeToString(void *item)
 {
 struct range *r = item;
 dyStringPrintf(tmpTreeToString, " (%d,%d)", r->start, r->end);
 }
 
 struct dyString *genomeRangeTreeToString(struct genomeRangeTree *tree)
 /* Return a string representation of the genomeRangeTree.
  * Useful for testing.
  * Not thread-safe; uses globals */
 {
 struct hashEl *chrom, *chromList = hashElListHash(tree->hash);
 slSort(&chromList, hashElCmp); /* alpha sort on chrom */
 dyStringFree(&tmpTreeToString);
-tmpTreeToString = newDyString(0);
+tmpTreeToString = dyStringNew(0);
 dyStringAppend(tmpTreeToString, "[tree");
 for (chrom = chromList ; chrom ; chrom = chrom->next)
     {
     dyStringPrintf(tmpTreeToString, " [%s:", chrom->name);
     rbTreeTraverse(genomeRangeTreeFindRangeTree(tree, chrom->name), tmpNodeToString);
     dyStringAppend(tmpTreeToString, "]");
     }
 dyStringAppend(tmpTreeToString, "]");
 hashElFreeList(&chromList);
 return tmpTreeToString;
 }
 
 long long genomeRangeTreeSumRanges(struct genomeRangeTree *grt)
 /* Sum up all ranges in tree. */
 {
 long long sum = 0;
 struct hashEl *chrom, *chromList = hashElListHash(grt->hash);
 for (chrom = chromList; chrom != NULL; chrom = chrom->next)
     rbTreeTraverseWithContext(chrom->val, rangeTreeSumRangeCallback, &sum);
 hashElFreeList(&chromList);
 return sum;
 }