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/hgc/regMotif.c src/hg/hgc/regMotif.c
index 92d667e..1b9d65e 100644
--- src/hg/hgc/regMotif.c
+++ src/hg/hgc/regMotif.c
@@ -86,31 +86,31 @@
 static void dnaMotifPrintProbTable(struct dnaMotif *motif, FILE *f)
 /* Print DNA motif probabilities. */
 {
 printProbRow(f, "A", motif->aProb, motif->columnCount);
 printProbRow(f, "C", motif->cProb, motif->columnCount);
 printProbRow(f, "G", motif->gProb, motif->columnCount);
 printProbRow(f, "T", motif->tProb, motif->columnCount);
 }
 
 struct dnaMotif *loadDnaMotif(char *motifName, char *motifTable)
 /* Load dnaMotif from table. */
 {
 struct sqlConnection *conn = hAllocConn(database);
 char query[256];
 struct dnaMotif *motif;
-sqlSafefFrag(query, sizeof query, "name = '%s'", motifName);
+sqlSafef(query, sizeof query, "name = '%s'", motifName);
 motif = dnaMotifLoadWhere(conn, motifTable, query);
 hFreeConn(&conn);
 return motif;
 }
 
 void motifLogoAndMatrix(struct dnaSeq **seqs, int count, struct dnaMotif *motif)
 /* Print out motif sequence logo and text (possibly with multiple occurences) */
 {
 // Detect inconsistent motif/pwm tables and suppress confusing display
 if (motif != NULL)
     {
     if (seqs != NULL && motif->columnCount != seqs[0]->size)
         {
         warn("Motif seq length doesn't match PWM\n");
         return;
@@ -211,31 +211,31 @@
 sqlFreeResult(&sr);
 
 if (hit != NULL)
     {
     seq = hDnaFromSeq(database, hit->chrom, hit->chromStart, hit->chromEnd, dnaLower);
     if (hit->strand[0] == '-')
 	reverseComplement(seq->dna, seq->size);
     }
 motifHitSection(seq, motif);
 printTrackHtml(tdb);
 }
 
 void doFlyreg(struct trackDb *tdb, char *item)
 /* flyreg.org: Drosophila DNase I Footprint db. */
 {
-struct dyString *query = newDyString(256);
+struct dyString *query = dyStringNew(256);
 struct sqlConnection *conn = hAllocConn(database);
 struct sqlResult *sr = NULL;
 char **row;
 int start = cartInt(cart, "o");
 int end   = cartInt(cart, "t");
 char fullTable[HDB_MAX_TABLE_STRING];
 boolean hasBin = FALSE;
 char *motifTable = "flyregMotif";
 struct dnaMotif *motif = NULL;
 boolean isVersion2 = sameString(tdb->table, "flyreg2");
 
 genericHeader(tdb, item);
 if (!hFindSplitTable(database, seqName, tdb->table, fullTable, sizeof fullTable, &hasBin))
     errAbort("track %s not found", tdb->table);
 sqlDyStringPrintf(query, "select * from %s where chrom = '%s' and ",
@@ -648,33 +648,35 @@
 	    {
 	    AllocVar(tf);
 	    hashAddSaveName(tfHash, tfName, tf, &tf->name);
 	    slAddHead(&tfList, tf);
 	    }
 	AllocVar(cond);
 	cond->name = cloneString(condition);
 	cond->binding = probe->bindVals[i];
 	slAddHead(&tf->conditionList, cond);
 	}
     slSort(&tfList, tfDataCmpName);
 
     /* Fold in motif hits in region. */
     if (sqlTableExists(conn, codeTable))
         {
+	char sqlClause[1024];
+        sqlSafef(sqlClause, sizeof sqlClause, "chipEvidence != 'none'");
 	sr = hRangeQuery(conn, codeTable,
 		probe->chrom, probe->chromStart, probe->chromEnd,
-		"chipEvidence != 'none'", &rowOffset);
+		sqlClause, &rowOffset);
 	while ((row = sqlNextRow(sr)) != NULL)
 	    {
 	    trc = transRegCodeLoad(row+rowOffset);
 	    tf = hashFindVal(tfHash, trc->name);
 	    if (tf != NULL)
 		slAddTail(&tf->trcList, trc);
 	    }
 	sqlFreeResult(&sr);
 	}
     if (tfList == NULL)
 	printf("No significant immunoprecipitation.");
     else
 	{
 	tfBindLevelSection(tfList, conn, motifTable, tfToConditionTable);
 	}