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/lib/chainNetDbLoad.c src/hg/lib/chainNetDbLoad.c
index 5b2fe16..1528c2f 100644
--- src/hg/lib/chainNetDbLoad.c
+++ src/hg/lib/chainNetDbLoad.c
@@ -1,358 +1,358 @@
 /* chainNetDbLoad - This will load a database representation of
  * a net into a chainNet representation.  Also helps database
  * representation of chain into chain. */
 
 /* 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 "hash.h"
 #include "linefile.h"
 #include "jksql.h"
 #include "hdb.h"
 #include "chain.h"
 #include "chainDb.h"
 #include "chainLink.h"
 #include "chainNet.h"
 #include "netAlign.h"
 #include "chainNetDbLoad.h"
 #include "chromAlias.h"
 
 
 struct cnFill *cnFillFromNetAlign(struct netAlign *na, struct hash *nameHash)
 /* Convert netAlign to cnFill. Name hash is a place to store
  * the strings. */
 {
 struct cnFill *fill;
 AllocVar(fill);
 fill->tStart = na->tStart;
 fill->tSize = na->tEnd - na->tStart;
 fill->qName = hashStoreName(nameHash, na->qName);
 fill->qStrand = na->strand[0];
 fill->qStart = na->qStart;
 fill->qSize = na->qEnd - na->qStart;
 fill->chainId = na->chainId;
 fill->score = na->score;
 fill->ali = na->ali;
 fill->qOver = na->qOver;
 fill->qFar = na->qFar;
 fill->qDup = na->qDup;
 if (!sameString(na->type, "gap"))
     fill->type = hashStoreName(nameHash, na->type);
 fill->tN = na->tN;
 fill->qN = na->qN;
 fill->tR = na->tR;
 fill->qR = na->qR;
 fill->tNewR = na->tNewR;
 fill->qNewR = na->qNewR;
 fill->tOldR = na->tOldR;
 fill->qOldR = na->qOldR;
 fill->tTrf = na->tTrf;
 fill->qTrf = na->qTrf;
 return fill;
 }
 
 struct cnlHelper
 /* Structure to help us make tree from flattened database
  * representation. */
     {
     struct cnlHelper *next;	/* Next in list. */
     char *tName;		/* Name of target.  Not allocated here. */
     struct hash *nameHash;	/* Place to keep names. */
     struct cnFill **levels;	/* Array to sort leaves by depth. */
     int maxDepth;		/* Maximum depth allowed. */
     };
 
 struct chainNet *helpToNet(struct cnlHelper **pHelp)
 /* Make a chainNet from cnlHelper.  This will destroy
  * *pHelp in the process. */
 {
 struct chainNet *net;
 struct cnlHelper *help = *pHelp;
 struct cnFill *parentList, *childList, *parent, *child, *nextChild;
 struct cnFill **levels = help->levels;
 int depth, maxDepth = 0;
 
 /* Note that level 0 is always empty. */
 
 /* Sort everybody by target start. */
 for (depth=1; ; ++depth)
     {
     if (levels[depth] == NULL && depth != 0)
         break;
     maxDepth = depth;
     slSort(&levels[depth], cnFillCmpTarget);
     }
 
 /* Assign children to parents. */
 for (depth=maxDepth; depth >= 2; --depth)
     {
     childList = levels[depth];
     parentList = levels[depth-1];
     child = childList;
     for (parent = parentList; parent != NULL; parent = parent->next)
         {
 	while (child != NULL && 
 		child->tStart + child->tSize <= parent->tStart + parent->tSize)
 	    {
 	    nextChild = child->next;
 	    slAddHead(&parent->children, child);
 	    child = nextChild;
 	    }
 	slReverse(&parent->children);
 	}
     }
 
 /* Make up net structure and fill it in. */
 AllocVar(net);
 net->name = cloneString(help->tName);
 net->fillList = levels[1];
 net->nameHash = help->nameHash;
 
 /* Cleanup what's left of help and go home. */
 freeMem(help->levels);
 freez(pHelp);
 return net;
 }
 
 struct chainNet *chainNetLoadResult(struct sqlResult *sr, int rowOffset)
 /* Given a query result that returns a bunch netAligns, make up
  * a list of chainNets that has the equivalent information. 
  * Note the net->size field is not filled in. */
 {
 char **row;
 struct netAlign na;
 struct cnFill *fill;
 struct cnlHelper *helpList = NULL, *help, *nextHelp;
 struct chainNet *netList = NULL, *net;
 struct hash *helpHash = hashNew(0);
 
 /* Convert database rows to cnFills, and store
  * them in help->levels. */
 while ((row = sqlNextRow(sr)) != NULL)
     {
     netAlignStaticLoad(row + rowOffset, &na);
     help = hashFindVal(helpHash, na.tName);
     if (help == NULL)
         {
 	AllocVar(help);
 	hashAddSaveName(helpHash, na.tName, help, &help->tName);
 	help->nameHash = hashNew(8);
 	help->maxDepth = 40;
 	slAddHead(&helpList, help);
 	AllocArray(help->levels, help->maxDepth);
 	}
     fill = cnFillFromNetAlign(&na, help->nameHash);
     if (na.level >= help->maxDepth)
         errAbort("can't handle level %d, only go up to %d", 
 		na.level, help->maxDepth-1);
     slAddHead(&help->levels[na.level], fill);
     }
 
 /* Convert helps to nets. */
 for (help = helpList; help != NULL; help = nextHelp)
     {
     nextHelp = help->next;
     net = helpToNet(&help);
     slAddHead(&netList, net);
     }
 helpList = NULL;
 
 /* Clean up and go home. */
 hashFree(&helpHash);
 return netList;
 }
 
 struct chainNet *chainNetLoadRange(char *database, char *track,
 	char *chrom, int start, int end, char *extraWhere)
 /* Load parts of a net track that intersect range. */
 {
 int rowOffset;
 struct sqlConnection *conn;
 struct sqlResult *sr;
 struct chainNet *net;
 
 conn = sqlConnect(database);
 sr = hRangeQuery(conn, track, chrom, start, end, extraWhere, &rowOffset);
 net = chainNetLoadResult(sr, rowOffset);
 sqlFreeResult(&sr);
 if (net != NULL)
     net->size = hChromSize(database, chrom);
 sqlDisconnect(&conn);
 return net;
 }
 
 struct chainNet *chainNetLoadChrom(char *database, char *track,
 	char *chrom, char *extraWhere)
 /* Load net on whole chromosome. */
 {
 int rowOffset;
 struct sqlConnection *conn;
 struct sqlResult *sr;
 struct chainNet *net;
 
 conn = sqlConnect(database);
 sr = hChromQuery(conn, track, chrom, extraWhere, &rowOffset);
 net = chainNetLoadResult(sr, rowOffset);
 sqlFreeResult(&sr);
 net->size = hChromSize(database, chrom);
 sqlDisconnect(&conn);
 return net;
 }
 
 static void chainLinkAddResult(struct sqlResult *sr, int rowOffset, struct chain *chain)
 /* Add links that we get from sr to chain. */
 {
 char **row;
 struct cBlock *list = NULL, *b;
 struct chainLink link;
 while ((row = sqlNextRow(sr)) != NULL)
     {
     chainLinkStaticLoad(row+rowOffset, &link);
     AllocVar(b);
     b->tStart = link.tStart;
     b->tEnd = link.tEnd;
     b->qStart = link.qStart;
     b->qEnd = link.qStart + (link.tEnd - link.tStart);
     slAddHead(&list, b);
     }
 slSort(&list, cBlockCmpTarget);
 chain->blockList = list;
 }
 
 struct chain *chainLoadIdRangeHub(char *db, char *fileName, char *linkFileName,   char *chrom, int start, int end, int id)
 /* Load parts of chain of given ID from bigChain file.  Note the chain header
  * including score, tStart, tEnd, will still reflect the whole chain,
  * not just the part in range.  However only the blocks of the chain
  * overlapping the range will be loaded. */
 {
 struct lm *lm = lmInit(0);
 struct bbiFile *bbi =  bigBedFileOpenAlias(fileName, chromAliasFindAliases);
 struct bigBedInterval *bb, *bbList =  bigBedIntervalQuery(bbi, chrom, start, end, 0, lm);
 char *bedRow[12];
 char startBuf[16], endBuf[16];
 bbiFileClose(&bbi);
 boolean loadAll = FALSE;
 
 struct chain *chain;
 AllocVar(chain);
 
 for (bb = bbList; bb != NULL; bb = bb->next)
     {
     bigBedIntervalToRow(bb, chrom, startBuf, endBuf, bedRow, ArraySize(bedRow));
 
     unsigned chainId = sqlUnsigned(bedRow[3]);
     if (chainId == id)
         break;
     }
 
 if (bb == NULL)
     errAbort("chain %d is not in %s", id, fileName);
 
 chain->tName = cloneString(chrom);
 chain->tSize = sqlUnsigned(bedRow[6]);
 chain->tStart = sqlUnsigned(bedRow[1]);
 chain->tEnd = sqlUnsigned(bedRow[2]);
 chain->qName = cloneString(bedRow[7]);
 chain->qSize = sqlUnsigned(bedRow[8]);
 chain->qStrand = *bedRow[5];
 chain->qStart = sqlUnsigned(bedRow[9]);
 chain->qEnd = sqlUnsigned(bedRow[10]);
 chain->score = sqlUnsigned(bedRow[11]);
 chain->id = id;
 
 // Now load the links.
 bbi =  bigBedFileOpenAlias(linkFileName, chromAliasFindAliases);
 if (loadAll)
     {
     start = chain->tStart;
     end = chain->tEnd;
     }
 bbList =  bigBedIntervalQuery(bbi, chrom, start, end, 0, lm);
 bbiFileClose(&bbi);
 
 for (bb = bbList; bb != NULL; bb = bb->next)
     {
     bigBedIntervalToRow(bb, chrom, startBuf, endBuf, bedRow, ArraySize(bedRow));
     unsigned chainId = sqlUnsigned(bedRow[3]);
     if (chainId == id)
         {
         struct cBlock *cBlock;
 
         AllocVar(cBlock);
         slAddHead(&chain->blockList, cBlock);
         cBlock->tStart = sqlUnsigned(bedRow[1]);
         cBlock->tEnd = sqlUnsigned(bedRow[2]);
         unsigned size = cBlock->tEnd - cBlock->tStart;
         cBlock->qStart = sqlUnsigned(bedRow[4]);
         cBlock->qEnd = cBlock->qStart + size;
         }
     }
 slReverse(&chain->blockList);
 
 lmCleanup(&lm);
 return chain;
 }
 
 static struct chain *chainLoadIdSome(char *database, char *track, char *chrom, 
         int start, int end, int id, boolean loadAll)
 /* Load some or all of chain. */
 {
 struct sqlConnection *conn;
 struct sqlResult *sr;
 char **row;
 char table[HDB_MAX_TABLE_STRING];
 boolean hasBin;
 struct chain *chain;
 char query[256];
-struct dyString *dy = newDyString(128);
+struct dyString *dy = dyStringNew(128);
 
 /* Load chain header. */
 if (!hFindSplitTable(database, chrom, track, table, sizeof table, &hasBin))
    errAbort("%s table is not in %s", track, database);
 conn = sqlConnect(database);
 sqlSafef(query, sizeof(query),
 	"select * from %s where id = %d", table, id);
 sr = sqlGetResult(conn, query);
 if ((row = sqlNextRow(sr)) == NULL)
     errAbort("chain %d is not in %s", id, table);
 chain = chainHeadLoad(row+hasBin);
 sqlFreeResult(&sr);
 
 /* Load links. */
 if (loadAll)
     {
     sqlDyStringPrintf(dy, 
 	 "select * from %sLink where chainId = %d", table, id);
     }
 else
     {
     sqlDyStringPrintf(dy, 
 	 "select * from %sLink where ",table );
     hAddBinToQuery(start, end, dy);
     sqlDyStringPrintf(dy," chainId = %d and tStart < %d and tEnd > %d", id, end, start);
     }
 sr = sqlGetResult(conn, dy->string);
 chainLinkAddResult(sr, hasBin, chain);
 sqlFreeResult(&sr);
 sqlDisconnect(&conn);
-freeDyString(&dy);
+dyStringFree(&dy);
 return chain;
 }
 
 struct chain *chainLoadIdRange(char *database, char *track, char *chrom, 
 	int start, int end, int id)
 /* Load parts of chain of given ID from database.  Note the chain header
  * including score, tStart, tEnd, will still reflect the whole chain,
  * not just the part in range.  However only the blocks of the chain
  * overlapping the range will be loaded. */
 {
 return chainLoadIdSome(database, track, chrom, start, end, id, FALSE);
 }
 
 struct chain *chainLoadId(char *database, char *track, char *chrom, int id)
 /* Load chain of given ID from database. */
 {
 return chainLoadIdSome(database, track, chrom, 0, 0, id, TRUE);
 }