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/oneShot/cacheMergedRanges/cacheMergedRanges.c src/hg/oneShot/cacheMergedRanges/cacheMergedRanges.c
index 39fb906..ff2982e 100644
--- src/hg/oneShot/cacheMergedRanges/cacheMergedRanges.c
+++ src/hg/oneShot/cacheMergedRanges/cacheMergedRanges.c
@@ -1,540 +1,546 @@
 /* cacheMergedRanges - compare speeds of different ways to cache position 
  * ranges from a SQL table, removing overlaps. */
 
 /* Copyright (C) 2013 The Regents of the University of California 
  * See kent/LICENSE or http://genome.ucsc.edu/license/ for licensing information. */
 #include "common.h"
 #include "options.h"
 #include "jksql.h"
 #include "hash.h"
 #include "dystring.h"
 #include "portable.h"
 #include "hdb.h"
 #include "rbTree.h"
 #include "rbmTree.h"
 
 
 /* Need to get a cart in order to use hgFind. */
 struct cart *cart = NULL;
 
 /* Command line option specifications */
 static struct optionSpec optionSpecs[] = {
     {NULL, 0}
 };
 
 
 void usage()
 {
 errAbort(
 "cacheMergedRanges - compare speeds of 3 query/sort/merge/store methods.\n"
 "usage:\n"
 "  cacheMergedRanges database bedTable\n"
 /*
 "options:\n"
 */
 );
 }
 
 
 //** BEGIN STUFF COPIED FROM NETCLASS AND MODIFIED
 struct range
 /* A part of a chromosome. */
     {
     struct range *next;
     int start, end;	/* Half open zero based coordinates. */
     };
 
 int rangeCmp(void *va, void *vb)
 /* Return -1 if a before b,  0 if a and b overlap,
  * and 1 if a after b. */
 {
 struct range *a = va;
 struct range *b = vb;
 if (a->end <= b->start)
     return -1;
 else if (b->end <= a->start)
     return 1;
 else
     return 0;
 }
 
 //** END STUFF COPIED FROM NETCLASS AND MODIFIED
 
 int rangeCmpStart(const void *va, const void *vb)
 /* Return -1 if a->start before b->start,  0 if a and b equal,
  * and 1 if a after b. */
 {
 struct range *a = *(struct range **)va;
 struct range *b = *(struct range **)vb;
 return a->start - b->start;
 }
 
 rbmTreeCompareResult rangeCmpMerge(void *va, void *vb)
 /* Comparison function for use by rbTreeAddMerge, with distinct return 
  * values for complete vs. partial overlap of values:
  * Return RBMT_LESS if a is strictly less than b, 
  * RBMT_GREATER if a is strictly greater than b,
  * RBMT_COMPLETE if a is completely contained/encompassed by b 
  *   (not nec. vice versa!  mnemonic: b may be bigger),
  * RBMT_PARTIAL if a and b have a partial overlap requiring a merge. */
 {
 struct range *a = (struct range *)va;
 struct range *b = (struct range *)vb;
 if (a->end < b->start)
     return RBMT_LESS;
 else if (a->start > b->end)
     return RBMT_GREATER;
 else if (a->start >= b->start && a->end <= b->end)
     return RBMT_COMPLETE;
 else
     return RBMT_PARTIAL;
 }
 
 
 void rangeMerge(void *va, void *vb)
 /* Item value-merging function for use by rbTreeAddMerge.  
  * Change b to encompass both a and b (again, b may be bigger). */
 {
 struct range *a = (struct range *)va;
 struct range *b = (struct range *)vb;
 
 if (a->start < b->start)
     b->start = a->start;
 if (a->end > b->end)
     b->end = a->end;
 }
 
 
 char *makeQuery(char *table, boolean sortByChromStart)
 /* Make a query to get chrom,chromStart,chromEnd (or whatever the appropriate 
  * field names are for table), ordered by chrom and possibly by start. */
 {
 char query[512];
 char *db = hGetDb();
 struct hTableInfo *hti = hFindTableInfo(NULL, table);
 if (hti == NULL)
     errAbort("Can't find table info for %s.%s", db, table);
 if (! hti->isPos)
     errAbort("Table must be positional, but looks like %s.%s isn't",
 	     db, table);
 if (sortByChromStart)
     sqlSafef(query, sizeof(query), "select %s,%s,%s from %s order by %s,%s",
 	  hti->chromField, hti->startField, hti->endField, table,
 	  hti->chromField, hti->startField);
 else
     sqlSafef(query, sizeof(query), "select %s,%s,%s from %s order by %s",
 	  hti->chromField, hti->startField, hti->endField, table,
 	  hti->chromField);
 return(cloneString(query));
 }
 
 
 void addRbTree(char *chrom, struct hash *chromHash, struct rbTree *tree)
 /* Add tree to chromHash. */
 {
 struct hashEl *hel = hashLookup(chromHash, chrom);
 if (hel != NULL)
     errAbort("resultsToMergedTreesMergeInline: need results ordered by chrom, "
 	     "but looks like they weren't for %s.", chrom);
 hashAdd(chromHash, chrom, tree);
 }
 
 
 struct hash *resultsToTreesMergeInline(struct sqlResult *sr)
 /* Given results of a sorted query on chrom,chromStart,chromEnd, store results 
  * as rbTrees hashed by chrom. */
 {
 struct hash *chromHash = newHash(18);
 char **row = NULL;
 struct rbTree *t = rbTreeNew(rangeCmp);
 char *prevChrom = NULL;
 struct range *prevR = NULL;
 while ((row = sqlNextRow(sr)) != NULL)
     {
     struct range *r = NULL;
     AllocVar(r);
     r->start = sqlUnsigned(row[1]);
     r->end   = sqlUnsigned(row[2]);
     if (prevChrom == NULL)
 	prevChrom = cloneString(row[0]);
     else if (! sameString(prevChrom, row[0]))
 	{
 	rbTreeAdd(t, prevR);
 	addRbTree(prevChrom, chromHash, t);
 	prevR = NULL;
 	freeMem(prevChrom);
 	prevChrom = cloneString(row[0]);
 	t = rbTreeNew(rangeCmp);
 	}
     if (prevR == NULL)
 	prevR = r;
     else if (r->start <= prevR->end && prevR->start <= r->end)
 	{
 	/* Overlap: merge r into prevR & discard; prevR gets passed forward. */
 	if (r->end > prevR->end)
 	    prevR->end = r->end;
 	if (r->start < prevR->start)
 	    prevR->start = r->start;
 	freez(&r);
 	}
     else
 	{
 	rbTreeAdd(t, prevR);
 	prevR = r;
 	}
     }
 if (prevChrom != NULL)
     {
     rbTreeAdd(t, prevR);
     addRbTree(prevChrom, chromHash, t);
     freeMem(prevChrom);
     }
 return chromHash;
 }
 
 void mergeOverlaps(struct range **pRangeList)
 /* Given a pointer to an *already sorted by start* list of ranges, 
  * merge overlapping ranges together and set the pointer to the new 
  * *reverse sorted* list. */
 {
 struct range *r = *pRangeList, *nextR = NULL, *newList = NULL;
 while (r != NULL)
     {
     nextR = r->next;
     if (nextR != NULL && (nextR->start <= r->end) && (r->start <= nextR->end))
 	{
 	/* Overlap: merge r into nextR & discard; nextR gets passed forward. */
 	if (r->end > nextR->end)
 	    nextR->end = r->end;
 	if (r->start < nextR->start)
 	    nextR->start = r->start;
 	freez(&r);
 	}
     else
 	slAddHead(&newList, r);
     r = nextR;
     }
 *pRangeList = newList;
 }
 
 
 void addRangeListAsRbTree(char *chrom, struct hash *chromHash,
 			  struct range *rangeList, boolean doSort)
 /* Given a list of ranges for a chrom, sort if specified, merge overlapping
  * ranges, create a non-merging rbTree of ranges and store it in chromHash. */
 {
 struct rbTree *t = rbTreeNew(rangeCmp);
 struct range *r = NULL;
 struct hashEl *hel = hashLookup(chromHash, chrom);
 
 if (hel != NULL)
     errAbort("resultsToTrees: need results ordered by chrom, "
 	     "but looks like they weren't for %s.", chrom);
 if (doSort)
     slSort(&rangeList, rangeCmpStart);
 mergeOverlaps(&rangeList);
 for (r = rangeList;  r != NULL;  r = r->next)
     {
     rbTreeAdd(t, r);
     }
 hashAdd(chromHash, chrom, t);
 }
 
 
 struct hash *resultsToTrees(struct sqlResult *sr, boolean doSort)
 /* Given results of a query on chrom,chromStart,chromEnd, store results 
  * as range lists (reversed!) hashed by chrom. */
 {
 struct hash *chromHash = newHash(18);
 char **row = NULL;
 struct range *rangeList = NULL;
 char *prevChrom = NULL;
 while ((row = sqlNextRow(sr)) != NULL)
     {
     struct range *r = NULL;
     AllocVar(r);
     r->start = sqlUnsigned(row[1]);
     r->end   = sqlUnsigned(row[2]);
     /* Merging overlaps from a sorted query here would be more efficient. */
     if (prevChrom == NULL)
 	prevChrom = cloneString(row[0]);
     else if (! sameString(prevChrom, row[0]))
 	{
 	addRangeListAsRbTree(prevChrom, chromHash, rangeList, doSort);
 	freeMem(prevChrom);
 	prevChrom = cloneString(row[0]);
 	rangeList = NULL;
 	}
     slAddHead(&rangeList, r);
     }
 if (prevChrom != NULL)
     {
     addRangeListAsRbTree(prevChrom, chromHash, rangeList, doSort);
     freeMem(prevChrom);
     }
 return chromHash;
 }
 
 struct hash *sqlSorting(struct sqlConnection *conn, char *table)
 /* Grab contents of bed table into chrom-hashed range lists, 
  * using SQL to sort by chromStart; then merge ranges and 
  * convert to chrom-hashed rbTrees with normal rbTreeAdd. */
 {
 char *query = makeQuery(table, TRUE);
 struct sqlResult *sr = NULL;
 struct hash *chromTrees = NULL;
 int startMs = 0, endMs = 0, totalMs = 0;
 
-sqlUpdate(conn, NOSQLINJ "reset query cache");
+char query2[1024];
+sqlSafef(query, sizeof query2, "reset query cache");
+sqlUpdate(conn, query2);
 startMs = clock1000();
 sr = sqlGetResult(conn, query);
 endMs = clock1000();
 verbose(1, "sqlSorting: Took %dms to do sorting query.\n", endMs - startMs);
 printf("%d\t", endMs - startMs);
 totalMs += (endMs - startMs);
 
 startMs = clock1000();
 chromTrees = resultsToTreesMergeInline(sr);
 endMs = clock1000();
 verbose(1, "sqlSorting: Took %dms to build, merge and convert.\n",
        endMs - startMs);
 printf("%d\t", endMs - startMs);
 totalMs += (endMs - startMs);
 
 verbose(1, "sqlSorting: Took %dms total.\n\n", totalMs);
 printf("%d\t", totalMs);
 freeMem(query);
 sqlFreeResult(&sr);
 return chromTrees;
 }
 
 
 struct hash *jkSorting(struct sqlConnection *conn, char *table)
 /* Grab contents of bed table into chrom-hashed range lists, 
  * using slSort() to sort by start; then merge ranges and 
  * convert to chrom-hashed rbTrees with normal rbTreeAdd. */
 {
 char *query = makeQuery(table, FALSE);
 struct sqlResult *sr = NULL;
 struct hash *chromTrees = NULL;
 int startMs = 0, endMs = 0, totalMs = 0;
 
-sqlUpdate(conn, NOSQLINJ "reset query cache");
+char query2[1024];
+sqlSafef(query2, sizeof query2, "reset query cache");
+sqlUpdate(conn, query2);
 startMs = clock1000();
 sr = sqlGetResult(conn, query);
 endMs = clock1000();
 verbose(1, "jkSorting: Took %dms to do plain query.\n", endMs - startMs);
 printf("%d\t", endMs - startMs);
 totalMs += (endMs - startMs);
 
 startMs = clock1000();
 chromTrees = resultsToTrees(sr, TRUE);
 endMs = clock1000();
 verbose(1, "jkSorting: Took %dms to build, sort, merge, and convert.\n",
        endMs - startMs);
 printf("%d\t", endMs - startMs);
 totalMs += (endMs - startMs);
 
 verbose(1, "jkSorting: Took %dms total.\n\n", totalMs);
 printf("%d\t", totalMs);
 freeMem(query);
 sqlFreeResult(&sr);
 return chromTrees;
 }
 
 
 void addRbmTree(char *chrom, struct hash *chromHash, struct rbmTree *tree)
 /* Add tree to chromHash. */
 {
 struct hashEl *hel = hashLookup(chromHash, chrom);
 if (hel != NULL)
     errAbort("resultsToMergedTrees: need results ordered by chrom, "
 	     "but looks like they weren't for %s.", chrom);
 hashAdd(chromHash, chrom, tree);
 }
 
 
 struct hash *resultsToMergedTrees(struct sqlResult *sr)
 /* Given results of a query on chrom,chromStart,chromEnd, store results 
  * in chrom-hashed rbmTrees of non-overlapping (merged) ranges. */
 {
 struct hash *chromHash = newHash(18);
 struct rbmTree *t = rbmTreeNew(rangeCmpMerge, rangeMerge, NULL, freeMem);
 char **row = NULL;
 char *prevChrom = NULL;
 while ((row = sqlNextRow(sr)) != NULL)
     {
     struct range *r = NULL;
     AllocVar(r);
     r->start = sqlUnsigned(row[1]);
     r->end   = sqlUnsigned(row[2]);
     if (prevChrom == NULL)
 	prevChrom = cloneString(row[0]);
     else if (! sameString(prevChrom, row[0]))
 	{
 	addRbmTree(prevChrom, chromHash, t);
 	freeMem(prevChrom);
 	t = rbmTreeNew(rangeCmpMerge, rangeMerge, NULL, freeMem);
 	prevChrom = cloneString(row[0]);
 	}
     rbmTreeAdd(t, r);
     }
 if (prevChrom != NULL)
     {
     addRbmTree(prevChrom, chromHash, t);
     freeMem(prevChrom);
     }
 return chromHash;
 }
 
 
 struct hash *rbMerging(struct sqlConnection *conn, char *table)
 /* Grab contents of bed table ordered by chrom but not sorted, 
  * then convert to chrom-hashed rbmTrees to handle merging of 
  * overlapping ranges. */
 {
 char *query = makeQuery(table, FALSE);
 struct sqlResult *sr = NULL;
 struct hash *chromTrees = NULL;
 int startMs = 0, endMs = 0, totalMs = 0;
 
-sqlUpdate(conn, NOSQLINJ "reset query cache");
+char query2[1024];
+sqlSafef(query2, sizeof query2, "reset query cache");
+sqlUpdate(conn, query2);
 startMs = clock1000();
 sr = sqlGetResult(conn, query);
 endMs = clock1000();
 verbose(1, "rbMerging: Took %dms to do plain query.\n", endMs - startMs);
 printf("%d\t", endMs - startMs);
 totalMs += (endMs - startMs);
 
 startMs = clock1000();
 chromTrees = resultsToMergedTrees(sr);
 endMs = clock1000();
 verbose(1, "rbMerging: Took %dms to make merged trees.\n", endMs - startMs);
 printf("%d\t", endMs - startMs);
 totalMs += (endMs - startMs);
 
 verbose(1, "rbMerging: Took %dms total.\n\n", totalMs);
 printf("%d\n", totalMs);
 freeMem(query);
 sqlFreeResult(&sr);
 return chromTrees;
 }
 
 
 /* Globals for use by hash-traversed rbTree-dumping function: */
 FILE *dumpTreesF = NULL;
 char *dumpChrom = NULL;
 int dumpSeq = 0;
 
 void dumpRange(void *item)
 /* Dump one range to f as bed 4. */
 {
 struct range *r = (struct range *)(item);
 fprintf(dumpTreesF, "%s\t%d\t%d\t%s.%d\n",
 	dumpChrom, r->start, r->end, dumpChrom, ++dumpSeq);
 }
 
 void dumpOneRbTree(struct hashEl *hel)
 /* Given a hel that associates a chrom name with an rbTree of non-overlapping 
  * ranges, dump out bed 4 like featureBits -bed. */
 {
 struct rbTree *t = (struct rbTree *)hel->val;
 dumpChrom = hel->name;
 dumpSeq = 0;
 rbTreeTraverse(t, dumpRange);
 }
 
 void dumpOneRbmTree(struct hashEl *hel)
 /* Given a hel that associates a chrom name with an rbmTree of non-overlapping 
  * ranges, dump out bed 4 like featureBits -bed. */
 {
 struct rbmTree *t = (struct rbmTree *)hel->val;
 dumpChrom = hel->name;
 dumpSeq = 0;
 rbmTreeTraverse(t, dumpRange);
 }
 
 void dumpRbTrees(struct hash *chromTrees, char *table, char *suffix)
 /* Dump out chrom-hashed rbTrees of non-overlapping ranges as bed 4 
  * for comparison with featureBits -bed output. */
 {
 char fname[512];
 safef(fname, sizeof(fname), "%s.%s.%s.bed", hGetDb(), table, suffix);
 dumpTreesF = mustOpen(fname, "w");
 hashTraverseEls(chromTrees, dumpOneRbTree);
 carefulClose(&dumpTreesF);
 }
 
 
 void dumpRbmTrees(struct hash *chromTrees, char *table, char *suffix)
 /* Dump out chrom-hashed rbmTrees of non-overlapping ranges as bed 4 
  * for comparison with featureBits -bed output. */
 {
 char fname[512];
 safef(fname, sizeof(fname), "%s.%s.%s.bed", hGetDb(), table, suffix);
 dumpTreesF = mustOpen(fname, "w");
 hashTraverseEls(chromTrees, dumpOneRbmTree);
 carefulClose(&dumpTreesF);
 }
 
 
 void hashElFreeRbTree(struct hashEl *hel)
 /* Free up an rbTree's contents and the tree itself. */
 {
 rbTreeFreeAll((struct rbTree **)(&(hel->val)), freeMem);
 }
 
 void hashElFreeRbmTree(struct hashEl *hel)
 /* Free up an rbmTree's contents and the tree itself. */
 {
 rbmTreeFreeAll((struct rbmTree **)(&(hel->val)));
 }
 
 void freeRbTreeHash(struct hash **pTreeHash)
 /* Free up a whole hash of rbTrees of ranges. */
 {
 hashTraverseEls(*pTreeHash, hashElFreeRbTree);
 hashFree(pTreeHash);
 }
 
 void freeRbmTreeHash(struct hash **pTreeHash)
 /* Free up a whole hash of rbmTrees of ranges. */
 {
 hashTraverseEls(*pTreeHash, hashElFreeRbmTree);
 hashFree(pTreeHash);
 }
 
 
 void cacheMergedRanges(char *db, char *table)
 /* cacheMergedRanges - compare speeds of different ways to cache position 
  * ranges from a SQL table, removing overlaps. */
 {
 struct sqlConnection *conn = NULL;
 struct hash *chromTrees = NULL;
 
 hSetDb(db);
 conn = hAllocConn();
 
 chromTrees = sqlSorting(conn, table);
 dumpRbTrees(chromTrees, table, "sqlSorting");
 freeRbTreeHash(&chromTrees);
 
 chromTrees = jkSorting(conn, table);
 dumpRbTrees(chromTrees, table, "jkSorting");
 freeRbTreeHash(&chromTrees);
 
 chromTrees = rbMerging(conn, table);
 dumpRbmTrees(chromTrees, table, "rbMerging");
 freeRbmTreeHash(&chromTrees);
 }
 
 
 int main(int argc, char *argv[])
 {
 optionInit(&argc, argv, optionSpecs);
 if (argc != 3)
     usage();
 
 cacheMergedRanges(argv[1], argv[2]);
 return 0;
 }