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/makeDb/hgLoadWiggle/hgLoadWiggle.c src/hg/makeDb/hgLoadWiggle/hgLoadWiggle.c
index ce3251a..ebf2b96 100644
--- src/hg/makeDb/hgLoadWiggle/hgLoadWiggle.c
+++ src/hg/makeDb/hgLoadWiggle/hgLoadWiggle.c
@@ -75,31 +75,33 @@
 static struct hash *loadAllChromInfo(char *database)
 /* Load up all chromosome infos. */
 {
 struct chromInfo *el;
 struct sqlConnection *conn = NULL;
 struct sqlResult *sr = NULL;
 struct hash *ret;
 char **row;
 
 /*	be wary of customTrack db loader pipeline which has special
  *	environment variables for HGDB_HOST and so forth
  */
 conn = hAllocConn(database);
 ret = newHash(0);
 
-sr = sqlGetResult(conn, NOSQLINJ "select * from chromInfo");
+char query[1024];
+sqlSafef(query, sizeof query, "select * from chromInfo");
+sr = sqlGetResult(conn, query);
 while ((row = sqlNextRow(sr)) != NULL)
     {
     el = chromInfoLoad(row);
     verbose(4, "Add hash %s value %u (%#lx)\n", el->chrom, el->size, (unsigned long)&el->size);
     hashAdd(ret, el->chrom, (void *)(& el->size));
     }
 sqlFreeResult(&sr);
 hFreeConn(&conn);
 return ret;
 }
 
 static unsigned chromosomeSize(char *chromosome)
 /* Return full extents of chromosome.  Warn and fill in if none. */
 {
 if (noChromInfo)
@@ -276,82 +278,83 @@
 		}
 	    if (i == wordCount-1)
 		fputc('\n', f);
 	    else
 		fputc('\t', f);
 	    }
 	}
     }
 fclose(f);
 }
 
 static void loadDatabase(char *database, char *track, struct wiggleStub *wiggleList)
 /* Load database from wiggleList. */
 {
 struct sqlConnection *conn = (struct sqlConnection *)NULL;
-struct dyString *dy = newDyString(1024);
+struct dyString *dy = dyStringNew(1024);
 char *tab = (char *)NULL;
 
 if (! noLoad)
     {
     conn = hAllocConn(database);
     verbose(1, "Connected to database %s for track %s\n", database, track);
     }
 
 if ((char *)NULL != tmpDir)
     tab = cloneString(rTempName(tmpDir,"loadWig",".tab"));
 else
     tab = cloneString("wiggle.tab");
 
 /* First make table definition. */
 if ((!oldTable) && (!noLoad))
     {
     int indexLen = 0;
 
     if (maxChromNameLength)
 	indexLen = maxChromNameLength;
     else
 	indexLen = hGetMinIndexLength(database);
     verbose(2, "INDEX chrom length: %d\n", indexLen);
 
     /* Create definition statement. */
     verbose(1, "Creating wiggle table definition in %s.%s\n",
 	    database, track);
     sqlDyStringPrintf(dy, "CREATE TABLE %s (\n", track);
     if (!noBin)
-       dyStringAppend(dy, "  bin smallint unsigned not null,\n");
-    dyStringAppend(dy, "  chrom varchar(255) not null,\n");
-    dyStringAppend(dy, "  chromStart int unsigned not null,\n");
-    dyStringAppend(dy, "  chromEnd int unsigned not null,\n");
-    dyStringAppend(dy, "  name varchar(255) not null,\n");
-    dyStringAppend(dy, "  span int unsigned not null,\n");
-    dyStringAppend(dy, "  count int unsigned not null,\n");
-    dyStringAppend(dy, "  `offset` int unsigned not null,\n");
-    dyStringAppend(dy, "  file varchar(255) not null,\n");
-    dyStringAppend(dy, "  lowerLimit double not null,\n");
-    dyStringAppend(dy, "  dataRange double not null,\n");
-    dyStringAppend(dy, "  validCount int unsigned not null,\n");
-    dyStringAppend(dy, "  sumData double not null,\n");
-    dyStringAppend(dy, "  sumSquares double not null,\n");
-    dyStringAppend(dy, "#Indices\n");
+       sqlDyStringPrintf(dy, "  bin smallint unsigned not null,\n");
+    sqlDyStringPrintf(dy, 
+    "  chrom varchar(255) not null,\n"
+    "  chromStart int unsigned not null,\n"
+    "  chromEnd int unsigned not null,\n"
+    "  name varchar(255) not null,\n"
+    "  span int unsigned not null,\n"
+    "  count int unsigned not null,\n"
+    "  `offset` int unsigned not null,\n"
+    "  file varchar(255) not null,\n"
+    "  lowerLimit double not null,\n"
+    "  dataRange double not null,\n"
+    "  validCount int unsigned not null,\n"
+    "  sumData double not null,\n"
+    "  sumSquares double not null,\n"
+    "#Indices\n");
     if (!noBin)
-	dyStringPrintf(dy, "  INDEX(chrom(%d),bin)\n", indexLen);
+	sqlDyStringPrintf(dy, "  INDEX(chrom(%d),bin)\n", indexLen);
     else
 	{
-	dyStringPrintf(dy, "  INDEX(chrom(%d),chromStart)\n", indexLen);
+	sqlDyStringPrintf(dy, "  INDEX(chrom(%d),chromStart)\n", indexLen);
 	}
-    dyStringAppend(dy, ")\n");
+    sqlDyStringPrintf(dy, ")\n");
     verbose(2, "%s", dy->string);
     sqlRemakeTable(conn, track, dy->string);
     }
 
 verbose(1, "Saving %s\n", tab);
 writeWiggleTab(tab, wiggleList, database);
 
 if (! noLoad)
     {
     char comment[256];
     char pathAdded[192];
     verbose(1, "Loading %s\n", database);
     dyStringClear(dy);
     sqlDyStringPrintf(dy, "load data local infile '%s' into table %s", tab, track);
     sqlUpdate(conn, dy->string);