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/recycleDb/bedUp/bedUp.c src/hg/recycleDb/bedUp/bedUp.c
index 5654d0a..0caa5f9 100644
--- src/hg/recycleDb/bedUp/bedUp.c
+++ src/hg/recycleDb/bedUp/bedUp.c
@@ -1,305 +1,307 @@
 /* bedUp - Load bed submissions after conversion back into new database.. */
 
 /* 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 "hash.h"
 #include "jksql.h"
 #include "psl.h"
 #include "clonePos.h"
 
 
 void usage()
 /* Explain usage and exit. */
 {
 errAbort(
   "bedUp - Load bed submissions after conversion back into new database.\n"
   "usage:\n"
   "   bedUp oldDb table newDb old.tab convert.psl missing\n");
 }
 
 struct bedExt
 /* Extended bed structure. */
     {
     struct bedExt *next;     /* Next in singly linked list. */
     char *chrom;	  /* Human chromosome or FPC contig */
     unsigned chromStart;  /* Start position in chromosome */
     unsigned chromEnd;	  /* End position in chromosome */
     char *name;           /* Name. */
     char **extraWords;    /* Other words in this row of database. */
     char *id;             /* Unique ID - allocated in hash. */
     struct psl *pslList;  /* Conversion psl. */
     char *oldClone;       /* Old clone this used to be at. */
     bool converted;       /* TRUE if converted to new coors. */
     };
 
 char *bedIdS(char *name, char *chrom, char *chromStart)
 /* Return unique identifier for bed treating number as string. */
 {
 static char buf[128];
 sprintf(buf, "%s.%s.%s", name, chrom, chromStart);
 return buf;
 }
 
 char *bedId(char *name, char *chrom, int chromStart)
 /* Return unique identifier for bed. */
 {
 char num[16];
 sprintf(num, "%d", chromStart);
 return bedIdS(name, chrom, num);
 }
 
 void unpackPslName(struct lineFile *lf, char *pslName, char **retName, char **retDb, char **retChrom, int *retStart)
 /* Unpack name in convert psl file. */
 {
 static char buf[128];
 char *words[8];
 int i;
 char *e;
 
 strncpy(buf, pslName, sizeof(buf));
 for (i=0; i<3; ++i)
     {
     e = strrchr(buf, '.');
     if (e == NULL)
         errAbort("Expecting name.db.chrom.start line %d of %s", lf->lineIx, lf->fileName);
     *e++ = 0;
     words[i] = e;
     }
 *retDb = words[2];
 *retChrom = words[1];
 *retStart = atoi(words[0]);
 *retName = buf;
 }
 
 struct bedExt *loadTable(char *fileName, struct hash *bedHash, struct hash *chromHash, struct hash *cloneHash)
 /* Make list and load up tables from file. */
 {
 struct lineFile *lf = lineFileOpen(fileName, TRUE);
 struct bedExt *bedList = NULL, *bed;
 char *words[16];
 int wordCount;
 int width;
 char *s;
 struct hashEl *hel;
 
 while ((wordCount = lineFileChop(lf, words)) != 0)
     {
     lineFileExpectWords(lf, 10, wordCount);
     AllocVar(bed);
     bed->chrom = hashStoreName(chromHash, words[2]);
     bed->chromStart = bed->chromEnd = lineFileNeedNum(lf, words, 3);
     width = lineFileNeedNum(lf, words, 4);
     bed->chromEnd += width;
     s = words[5];
     chopSuffix(s);
     bed->oldClone = hashStoreName(cloneHash, s);
     bed->name = cloneString(words[0]);
     s = bedId(bed->name, bed->chrom, bed->chromStart);
     if (hashLookup(bedHash, s))
        {
        warn("%s duplicated, ignoring all but first.", s);
        freez(&bed);
        }
     else
        {
 	hel = hashAddUnique(bedHash, s, bed);
 	bed->id = hel->name;
 	slAddHead(&bedList, bed);
        }
     }
 lineFileClose(&lf);
 slReverse(&bedList);
 return bedList;
 }
 
 void addPsls(char *fileName, char *oldDb, struct hash *bedHash)
 /* Add relevant psls to beds. */
 {
 struct bedExt *bed;
 struct lineFile *lf = pslFileOpen(fileName);
 struct psl *psl;
 char *s;
 char *name, *db, *chrom;
 int chromStart;
 int total = 0, uniq = 0;
 
 while ((psl = pslNext(lf)) != NULL)
     {
     unpackPslName(lf, psl->qName, &name, &db, &chrom, &chromStart);
     if (!sameString(db, oldDb))
         errAbort("Old database mismatch %s in command line %s in %s", oldDb, db, fileName);
     s = bedId(name, chrom, chromStart);
     bed = hashMustFindVal(bedHash, s);
     if (bed->pslList == NULL)
         uniq += 1;
     slAddHead(&bed->pslList, psl);
     ++total;
     }
 lineFileClose(&lf);
 printf("%d psls int %s added to %d beds\n", total, fileName, uniq);
 }
 
 void fixFishChrom(char *s)
 /* Fix chrna_random to chrNA_random, etc for fish. */
 {
 char *e;
 s += 3;
 if (islower(s[0]))
     {
     e = strchr(s, '_');
     if (e == NULL)
        e = s + strlen(s);
     toUpperN(s, e-s);
     }
 }
 
 void addOther(char *oldDb, char *oldTable, struct hash *bedHash)
 /* Add extra rows to beds. */
 {
 struct sqlConnection *conn = sqlConnect(oldDb);
 struct sqlResult *sr;
 char **row;
 char query[256];
 int columnCount;
 int extraCount, i;
 char *s;
 struct bedExt *bed;
 enum {definedCol = 4};
 int rowCount = 0;
 
 
 sqlSafef(query, sizeof query, "select * from %s", oldTable);
 sr = sqlGetResult(conn, query);
 columnCount = sqlCountColumns(sr);
 extraCount = columnCount - definedCol;
 while ((row = sqlNextRow(sr)) != NULL)
     {
     fixFishChrom(row[0]);
     s = bedIdS(row[3], row[0], row[1]);
     bed = hashMustFindVal(bedHash, s);
     if (bed->extraWords != NULL)
 	{
         warn("Duplicate %s in database, ignoring all but first.", s);
 	continue;
 	}
     AllocArray(bed->extraWords, extraCount);
     for (i=definedCol; i<columnCount; ++i)
         bed->extraWords[i-definedCol] = cloneString(row[i]);
     ++rowCount;
     }
 sqlFreeResult(&sr);
 sqlDisconnect(&conn);
 printf("Added %d extra columns to %d rows\n", extraCount, rowCount);
 }
 
 struct clonePos *loadClonePos(char *db, struct hash *clonePosHash)
 /* Load up clonePos list/hash from database table. */
 {
 struct sqlConnection *conn = sqlConnect(db);
 struct sqlResult *sr;
 char **row;
 char name[128];
 struct clonePos *el, *list = NULL;
 
-sr = sqlGetResult(conn, NOSQLINJ "select * from clonePos");
+char query[1024];
+sqlSafef(query, sizeof query, "select * from clonePos");
+sr = sqlGetResult(conn, query);
 while ((row = sqlNextRow(sr)) != NULL)
     {
     el = clonePosLoad(row);
     strcpy(name, el->name);
     chopSuffix(name);
     hashAdd(clonePosHash, name, el);
     slAddHead(&list,el);
     }
 sqlFreeResult(&sr);
 sqlDisconnect(&conn);
 slReverse(&list);
 printf("Loaded %d clonePos from %s\n", slCount(list), db);
 return list;
 }
 
 
 void convertOne(struct bedExt *bed, struct hash *clonePosHash)
 /* Convert a single bed if possible. */
 {
 int bestScore = 0, score;
 struct psl *psl, *bestPsl = NULL;
 int milliBad;
 struct clonePos *clonePos;
 
 /* Find best psl in list. */
 for (psl = bed->pslList; psl != NULL; psl = psl->next)
     {
     score = psl->match + psl->repMatch;
     if (score < round(0.80*psl->qSize))
         continue;
     if ((milliBad = pslCalcMilliBad(psl, FALSE)) > 30)
         continue;
     score = round( 0.02*(50-milliBad)*score);
     clonePos = hashFindVal(clonePosHash, bed->oldClone);
     if (clonePos != NULL)
 	{
 	if (sameString(clonePos->chrom, psl->tName))
 	    {
 	    if (rangeIntersection(psl->tStart, psl->tEnd, clonePos->chromStart, clonePos->chromEnd) > 0)
 		score += 100;
 	    }
 	}
     if (score > bestScore)
         {
 	bestScore = score;
 	bestPsl = psl;
 	}
     }
 if (bestPsl)
     {
     bed->converted = TRUE;
     }
 }
 
 void convertList(struct bedExt *bedList, struct hash *clonePosHash)
 /* Convert list to new coordinates if possible. */
 {
 struct bedExt *bed;
 int convertCount = 0;
 int totalCount = 0;
 for (bed = bedList; bed != NULL; bed = bed->next)
     if (bed->extraWords && bed->pslList)
 	{
 	convertOne(bed, clonePosHash);
 	++totalCount;
 	if (bed->converted)
 	    ++convertCount;
 	}
 printf("%d of %d converted\n", convertCount, totalCount);
 }
 
 void bedUp(char *oldDb, char *oldTable, char *newDb, char *tableFile, char *pslFile, 
 	char *missing)
 /* bedUp - Load bed submissions after conversion back into new database.. */
 {
 struct bedExt *bedList = NULL;
 struct hash *bedHash = newHash(0);
 struct hash *chromHash = newHash(5);
 struct hash *cloneHash = newHash(0);
 struct hash *clonePosHash = newHash(0);
 // struct clonePos *clonePosList = NULL;
 
 bedList = loadTable(tableFile, bedHash, chromHash, cloneHash);
 printf("Loaded %d items from %s\n", slCount(bedList), tableFile);
 addPsls(pslFile, oldDb, bedHash);
 addOther(oldDb, oldTable, bedHash);
 // clonePosList = loadClonePos(newDb, clonePosHash);
 //   answer is returned in clonePosHash
 (void) loadClonePos(newDb, clonePosHash);  // ignore returned has pointer
 convertList(bedList, clonePosHash);
 }
 
 int main(int argc, char *argv[])
 /* Process command line. */
 {
 if (argc != 7)
     usage();
 bedUp(argv[1], argv[2], argv[3], argv[4], argv[5], argv[6]);
 return 0;
 }