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/geneBounds/eisenInput/eisenInput.c src/hg/geneBounds/eisenInput/eisenInput.c
index 63459ed..db15f01 100644
--- src/hg/geneBounds/eisenInput/eisenInput.c
+++ src/hg/geneBounds/eisenInput/eisenInput.c
@@ -1,343 +1,345 @@
 /* eisenInput - Create input for Eisen-style cluster program. */
 #include "common.h"
 #include "linefile.h"
 #include "hash.h"
 #include "options.h"
 #include "jksql.h"
 #include "binRange.h"
 #include "hdb.h"
 #include "bed.h"
 #include "genePred.h"
 #include "refLink.h"
 #include "expRecord.h"
 
 
 /* Some variables we should probably let people set from the
  * command line. */
 char *expTrack = "affyRatio";	/* Values positioned on chromosome. */
 char *expRecordTable = "affyExps";  /* Extra expression info . */
 
 void usage()
 /* Explain usage and exit. */
 {
 errAbort(
   "eisenInput - Create input for Eisen-style cluster program\n"
   "usage:\n"
   "   eisenInput database output.txt\n"
   );
 }
 
 struct expRecord * loadExpRecord(char *table, char *database)
 /* Load everything from an expRecord table in the
    specified database, usually hgFixed instead of hg7, hg8, etc. */
 {
 struct sqlConnection *conn = sqlConnect(database);
 char query[256];
 struct expRecord *erList = NULL;
 sqlSafef(query, sizeof(query), "select * from %s", table);
 erList = expRecordLoadByQuery(conn, query);
 sqlDisconnect(&conn);
 return erList;
 }
 
 
 struct bed *loadBed(char *database, char *chrom, char *track, int bedN, struct binKeeper *bk)
 /* Load in info from a bed track to bk. */
 {
 struct sqlConnection *conn = hAllocConn(database);
 struct sqlResult *sr;
 char **row;
 int rowOffset;
 struct bed *list = NULL, *el;
 
 sr = hChromQuery(conn, track, chrom, NULL, &rowOffset);
 while ((row = sqlNextRow(sr)) != NULL)
     {
     el = bedLoadN(row + rowOffset, bedN);
     binKeeperAdd(bk, el->chromStart, el->chromEnd, el);
     slAddHead(&list, el);
     }
 sqlFreeResult(&sr);
 hFreeConn(&conn);
 slReverse(&list);
 return list;
 }
 
 struct genePred *loadGenePred(char *database, char *chrom, char *track, struct binKeeper *bk)
 /* Load in a gene prediction track to bk. */
 {
 struct sqlConnection *conn = hAllocConn(database);
 struct sqlResult *sr;
 char **row;
 int rowOffset;
 struct genePred *list = NULL, *el;
 
 sr = hChromQuery(conn, track, chrom, NULL, &rowOffset);
 while ((row = sqlNextRow(sr)) != NULL)
     {
     el = genePredLoad(row + rowOffset);
     binKeeperAdd(bk, el->txStart, el->txEnd, el);
     slAddHead(&list, el);
     }
 sqlFreeResult(&sr);
 hFreeConn(&conn);
 slReverse(&list);
 return list;
 }
 
 struct refLink *loadRefLink(char *database, struct hash *hash)
 /* Load refLink into hash keyed by mrna accession and
  * return list too. */
 {
 struct sqlConnection *conn = hAllocConn(database);
 struct sqlResult *sr;
 char **row;
 struct refLink *list = NULL, *el;
 
-sr = sqlGetResult(conn, NOSQLINJ "select * from refLink");
+char query[1024];
+sqlSafef(query, sizeof query, "select * from refLink"); 
+sr = sqlGetResult(conn, query);
 while ((row = sqlNextRow(sr)) != NULL)
     {
     el = refLinkLoad(row);
     hashAdd(hash, el->mrnaAcc, el);
     slAddHead(&list, el);
     }
 sqlFreeResult(&sr);
 hFreeConn(&conn);
 slReverse(&list);
 return list;
 }
 
 struct rangeInfo
 /* Information on a range. */
     {
     struct rangeInfo *next;	/* Next in list. */
     char *id;			/* Unique id string, no allocated here. */
     char *commonName;		/* Associated gene name if any. Not allocated here. */
     struct bed *range;	/* Underlying range. Not allocated here.*/
     boolean isSplit;		/* True if one exp hits this and another. */
     };
 
 char *findCommonName(struct bed *range, struct binKeeper *knownBk,
 	struct hash *refLinkHash)
 /* Try and find a common name for range based on overlap with
  * known genes. */
 {
 struct binElement *beList=NULL, *be;
 struct refLink *link = NULL;
 struct genePred *gp;
 int matchCount = 0;
 
 beList = binKeeperFind(knownBk, range->chromStart, range->chromEnd);
 for (be = beList; be != NULL; be = be->next)
     {
     gp = be->val;
     if (gp->strand[0] == range->strand[0])
         {
 	++matchCount;
 	link = hashFindVal(refLinkHash, gp->name);
 	}
     }
 slFreeList(&beList);
 if (matchCount == 1 && link != 0)
     return link->name;
 else
     return range->name;
 }
 
 void writeHeader(FILE *f, struct bed *exp, struct hash *erHash)
 /* Write out expression data header. */
 {
 int i;
 struct expRecord *er;
 fprintf(f, "YORF\tNAME\tGWEIGHT");
 for (i=0; i< exp->expCount; ++i)
     {
     char sid[16];
     snprintf(sid, sizeof(sid), "%u", exp->expIds[i]);
     er = hashMustFindVal(erHash, sid);
     fprintf(f, "\t%s", er->name);
     }
 fprintf(f, "\n");
 }
 
 void outputAveraged(FILE *f, struct rangeInfo *ri, struct hash *erHash,
 	struct binElement *beList)
 /* Write out average expresssion value. */
 {
 static FILE *oldFile = NULL;
 static int colCount = 0;
 float *scores = NULL;
 struct binElement *be;
 struct bed *exp;
 int elCount = 0;
 float elScale;
 int i;
 
 if (beList == NULL)
     return;
 
 
 /* Calculate score averages. */
 for (be = beList; be != NULL; be = be->next)
     {
     ++elCount;
     exp = be->val;
 
     /* Write header if this is the first time through. */
     if (f != oldFile)
 	{
 	writeHeader(f, exp, erHash);
 	oldFile = f;
 	colCount = exp->expCount;
 	}
 
     if (scores == NULL)
         AllocArray(scores, colCount);
 	
     /* Make sure number of columns are consistent. */
     if (colCount != exp->expCount)
 	errAbort("Not all column counts are the same (%d vs %d)", 
 	    colCount, exp->expCount);
 
     for (i=0; i<colCount; ++i)
 	scores[i] += exp->expScores[i];
     }
 
 /* Write line of output. */
 fprintf(f, "%s\t%s\t1", ri->id, ri->commonName);
 elScale = 1.0/elCount;
 for (i=0; i<colCount; ++i)
     fprintf(f, "\t%f", scores[i] * elScale);
 fprintf(f, "\n");
 
 /* Clean up. */
 freez(&scores);
 }
 
 void oneChromInput(char *database, char *chrom, int chromSize, 	
 	char *rangeTrack, char *expTrack, 
 	struct hash *refLinkHash, struct hash *erHash, FILE *f)
 /* Read in info for one chromosome. */
 {
 struct binKeeper *rangeBk = binKeeperNew(0, chromSize);
 struct binKeeper *expBk = binKeeperNew(0, chromSize);
 struct binKeeper *knownBk = binKeeperNew(0, chromSize);
 struct bed *rangeList = NULL, *range;
 struct bed *expList = NULL;
 struct genePred *knownList = NULL;
 struct rangeInfo *riList = NULL, *ri;
 struct hash *riHash = hashNew(0); /* rangeInfo values. */
 struct binElement *rangeBeList = NULL, *rangeBe, *beList = NULL, *be;
 
 /* Load up data from database. */
 rangeList = loadBed(database, chrom, rangeTrack, 12, rangeBk);
 expList = loadBed(database, chrom, expTrack, 15, expBk);
 knownList = loadGenePred(database, chrom, "refGene", knownBk);
 
 /* Build range info basics. */
 rangeBeList = binKeeperFindAll(rangeBk);
 for (rangeBe = rangeBeList; rangeBe != NULL; rangeBe = rangeBe->next)
     {
     range = rangeBe->val;
     AllocVar(ri);
     slAddHead(&riList, ri);
     hashAddSaveName(riHash, range->name, ri, &ri->id);
     ri->range = range;
     ri->commonName = findCommonName(range, knownBk, refLinkHash);
     }
 slReverse(&riList);
 
 /* Mark split ones. */
 beList = binKeeperFindAll(expBk);
 for (be = beList; be != NULL; be = be->next)
     {
     struct bed *exp = be->val;
     struct binElement *subList = binKeeperFind(rangeBk, 
     	exp->chromStart, exp->chromEnd);
     if (slCount(subList) > 1)
         {
 	struct binElement *sub;
 	for (sub = subList; sub != NULL; sub = sub->next)
 	    {
 	    struct bed *range = sub->val;
 	    struct rangeInfo *ri = hashMustFindVal(riHash, range->name);
 	    ri->isSplit = TRUE;
 	    }
 	}
     slFreeList(&subList);
     }
 
 /* Output the nice ones: not split and having some expression info. */
 for (ri = riList; ri != NULL; ri = ri->next)
     {
     if (!ri->isSplit)
         {
 	struct bed *range =  ri->range;
 	beList = binKeeperFind(expBk, range->chromStart, range->chromEnd);
 	if (beList != NULL)
 	    outputAveraged(f, ri, erHash, beList);
 	slFreeList(&beList);
 	}
     }
 
 /* Clean up time! */
 freeHash(&riHash);
 genePredFreeList(&knownList);
 bedFree(&rangeList);
 bedFree(&expList);
 slFreeList(&rangeBeList);
 slFreeList(&beList);
 slFreeList(&riList);
 binKeeperFree(&rangeBk);
 binKeeperFree(&expBk);
 binKeeperFree(&knownBk);
 }
 
 void eisenInput(char *database, char *outFile)
 /* eisenInput - Create input for Eisen-style cluster program. */
 {
 struct slName *chromList = NULL, *chromEl;
 FILE *f = mustOpen(outFile, "w");
 char *chrom;
 struct hash *refLinkHash = hashNew(0);
 struct refLink *refLinkList;
 struct hash *erHash = hashNew(0);
 struct expRecord *erList = NULL, *er;
 
 
 /* Load info good for all chromosomes. */
 refLinkList = loadRefLink(database, refLinkHash);
 erList = loadExpRecord(expRecordTable, "hgFixed");
 for (er = erList; er != NULL; er = er->next)
     {
     char sid[16];
     snprintf(sid, sizeof(sid), "%u", er->id);
     hashAdd(erHash, sid, er);
     }
 
 /* Do it chromosome by chromosome. */
 chromList = hAllChromNames(database);
 for (chromEl = chromList; chromEl != NULL; chromEl = chromEl->next)
     {
     chrom = chromEl->name;
     uglyf("%s\n", chrom);
     oneChromInput(database, chrom, hChromSize(database, chrom), "rnaCluster", expTrack, 
     	refLinkHash, erHash, f);
     }
 
 /* Cleanup time! */
 expRecordFreeList(&erList);
 freeHash(&erHash);
 refLinkFreeList(&refLinkList);
 freeHash(&refLinkHash);
 }
 
 int main(int argc, char *argv[])
 /* Process command line. */
 {
 optionHash(&argc, argv);
 if (argc != 3)
     usage();
 eisenInput(argv[1], argv[2]);
 return 0;
 }