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/hgTables/hgTables.c src/hg/hgTables/hgTables.c
index 3a0df73..60071c9 100644
--- src/hg/hgTables/hgTables.c
+++ src/hg/hgTables/hgTables.c
@@ -305,31 +305,33 @@
 int dif;
 dif = chrStrippedCmp(a->chrom, b->chrom);
 if (dif == 0)
     dif = a->start - b->start;
 return dif;
 }
 
 static struct region *getRegionsFullGenomeLocal()
 /* get all the chrom ranges for a local database */
 {
 struct sqlConnection *conn = hAllocConn(database);
 struct sqlResult *sr;
 char **row;
 struct region *region, *regionList = NULL;
 
-sr = sqlGetResult(conn, NOSQLINJ "select chrom,size from chromInfo");
+char query[1024];
+sqlSafef(query, sizeof query, "select chrom,size from chromInfo");
+sr = sqlGetResult(conn, query);
 while ((row = sqlNextRow(sr)) != NULL)
     {
     AllocVar(region);
     region->chrom = cloneString(row[0]);
     region->end = sqlUnsigned(row[1]);
     region->fullChrom = TRUE;
     region->name = NULL;		/* unused for full chrom */
     slAddHead(&regionList, region);
     }
 slSort(&regionList, regionCmp);
 sqlFreeResult(&sr);
 hFreeConn(&conn);
 return regionList;
 }
 
@@ -357,31 +359,33 @@
 /* Get a region list that covers all of each chromosome. */
 {
 if (trackHubDatabase(database))
     return getRegionsFullGenomeHub();
 return getRegionsFullGenomeLocal();
 }
 
 struct region *getEncodeRegions()
 /* Get encode regions from encodeRegions table. */
 {
 struct sqlConnection *conn = hAllocConn(database);
 struct sqlResult *sr;
 char **row;
 struct region *list = NULL, *region;
 
-sr = sqlGetResult(conn, NOSQLINJ "select chrom,chromStart,chromEnd,name from encodeRegions order by name desc");
+char query[1024];
+sqlSafef(query, sizeof query, "select chrom,chromStart,chromEnd,name from encodeRegions order by name desc");
+sr = sqlGetResult(conn, query);
 while ((row = sqlNextRow(sr)) != NULL)
     {
     AllocVar(region);
     region->chrom = cloneString(row[0]);
     region->start = atoi(row[1]);
     region->end = atoi(row[2]);
     region->name = cloneString(row[3]);	/* encode region name	*/
     slAddHead(&list, region);
     }
 sqlFreeResult(&sr);
 hFreeConn(&conn);
 return list;
 }
 
 struct hgPositions *lookupPosition(struct dyString *dyWarn)
@@ -486,35 +490,35 @@
 	}
     if (region->fullChrom) /* Full chromosome. */
 	{
 	sr = hExtendedChromQuery(conn, table, region->chrom,
 		extraWhere, FALSE, fields, NULL);
 	}
     else
 	{
 	sr = hExtendedRangeQuery(conn, table, region->chrom, region->start, region->end,
 		extraWhere, TRUE, fields, NULL);
 	}
     }
 else
     {
     struct dyString *query = dyStringNew(0);
-    sqlDyStringPrintf(query, "select %-s from %s", sqlCkIl(fields), table);
+    sqlCkIl(fieldsSafe,fields)
+    sqlDyStringPrintf(query, "select %-s from %s", fieldsSafe, table);
     if (extraWhere)
          {
-	 dyStringAppend(query, " where ");
-	 dyStringAppend(query, extraWhere);
+	 sqlDyStringPrintf(query, " where %-s", extraWhere);
 	 }
     sr = sqlGetResult(conn, query->string);
     dyStringFree(&query);
     }
 return sr;
 }
 
 char *getDbTable(char *db, char *table)
 /* If table already contains its real database as a dot-prefix, then
  * return a clone of table; otherwise alloc and return db.table . */
 {
 if (sameString(table, WIKI_TRACK_TABLE))
     {
     char dbTable[256];
     safef(dbTable, sizeof(dbTable), "%s.%s", wikiDbName(), WIKI_TRACK_TABLE);
@@ -665,32 +669,33 @@
 struct hTableInfo *hti = maybeGetHti(db, table, conn);
 hFreeConn(&conn);
 return hti;
 }
 
 
 boolean isPositional(char *db, char *table)
 /* Return TRUE if it looks to be a positional table. */
 {
 boolean result = FALSE;
 struct sqlConnection *conn = hAllocConn(db);
 if (sqlTableExists(conn, "chromInfo"))
     {
     char chromName[64];
     struct hTableInfo *hti;
-    sqlQuickQuery(conn, NOSQLINJ "select chrom from chromInfo limit 1",
-	chromName, sizeof(chromName));
+    char query[1024];
+    sqlSafef(query, sizeof query, "select chrom from chromInfo limit 1");
+    sqlQuickQuery(conn, query, chromName, sizeof(chromName));
     hti = hFindTableInfo(db, chromName, table);
     if (hti != NULL)
 	{
 	result = htiIsPositional(hti);
 	}
     }
 hFreeConn(&conn);
 return result;
 }
 
 boolean isSqlStringType(char *type)
 /* Return TRUE if type is a stringish SQL type. */
 {
 return strstr(type, "char") || strstr(type, "text")
        || strstr(type, "blob");
@@ -831,35 +836,35 @@
     char *table = cartUsualString(cart, var, tableList->name);
     if (slNameInList(tableList, table))
 	return table;
     return tableList->name;
     }
 }
 
 
 
 void addWhereClause(struct dyString *query, boolean *gotWhere)
 /* Add where clause to query.  If already have a where clause
  * add 'and' to it. */
 {
 if (*gotWhere)
     {
-    dyStringAppend(query, " and ");
+    sqlDyStringPrintf(query, " and ");
     }
 else
     {
-    dyStringAppend(query, " where ");
+    sqlDyStringPrintf(query, " where ");
     *gotWhere = TRUE;
     }
 }
 
 boolean htiIsPositional(struct hTableInfo *hti)
 /* Return TRUE if hti looks like it's from a positional table. */
 {
 return isCustomTrack(hti->rootName) || hti->isPos;
 #ifdef OLD
     ((hti->startField[0] && hti->endField[0]) &&
 	(hti->chromField[0] || sameString(hti->rootName, "gl")));
 #endif /* OLD */
 }
 
 char *getIdField(char *db, struct trackDb *track, char *table,
@@ -992,72 +997,72 @@
     ret = lastCol;
     }
 else
     hOrFPrintf(f, "%s\n", field);
 
 return(ret);
 }
 
 void doTabOutDb( char *db, char *dbVarName, char *table, char *tableVarName,
         FILE *f, struct sqlConnection *conn, char *fields, char outSep)
 /* Do tab-separated output on fields of a single table. */
 {
 struct region *regionList = getRegions();
 struct region *region;
 struct hTableInfo *hti = NULL;
-struct dyString *fieldSpec = newDyString(256);
+struct dyString *fieldSpec = dyStringNew(256);
 struct hash *idHash = NULL;
 int outCount = 0;
 boolean isPositional;
 int fieldCount;
 char *idField;
 boolean showItemRgb = FALSE;
 int itemRgbCol = -1;        /*        -1 means not found        */
 boolean printedColumns = FALSE;
 struct trackDb *tdb = findTdbForTable(db, curTrack, table, ctLookupName);
 
 hti = getHti(db, table, conn);
 idField = getIdField(db, curTrack, table, hti);
 
 showItemRgb=bedItemRgb(tdb);        /* should we expect itemRgb instead of "reserved" */
 
 /* If they didn't pass in a field list assume they want all fields. */
 if (fields != NULL)
     {
-    dyStringAppend(fieldSpec, sqlCkIl(fields));
+    dyStringAppend(fieldSpec, fields);
     fieldCount = countChars(fields, ',') + 1;
     }
 else
     {
     dyStringAppend(fieldSpec, "*");
     fieldCount = countTableColumns(conn, table);
     }
 
 /* If can find id field for table then get
  * uploaded list of identifiers, create identifier hash
  * and add identifier column to end of result set. */
 char *identifierFilter = NULL;
 if (idField != NULL)
     {
     idHash = identifierHash(db, table);
     if (idHash != NULL)
         {
         identifierFilter = identifierWhereClause(idField, idHash);
         if (isEmpty(identifierFilter))
             {
             dyStringAppendC(fieldSpec, ',');
-            dyStringAppend(fieldSpec, sqlCkId(idField));
+            dyStringAppend(fieldSpec, idField);
             }
         }
     }
 isPositional = htiIsPositional(hti);
 
 /* Loop through each region. */
 for (region = regionList; region != NULL; region = region->next)
     {
     struct sqlResult *sr;
     char **row;
     int colIx, lastCol = fieldCount-1;
     char *filter = filterClause(dbVarName, tableVarName, region->chrom, identifierFilter);
 
     sr = regionQuery(conn, table, fieldSpec->string,
             region, isPositional, filter);
@@ -1331,47 +1336,48 @@
 }
 
 /* Remove any meta data variables from the cart. (Copied from above!) */
 void removeMetaData()
 {
 cartRemove(cart, "hgta_metaStatus");
 cartRemove(cart, "hgta_metaVersion");
 cartRemove(cart, "hgta_metaDatabases");
 cartRemove(cart, "hgta_metaTables");
 }
 
 void doMetaData(struct sqlConnection *conn)
 /* Get meta data for a database. */
 {
 puts("Content-Type:text/plain\n");
-char *query = "";
+char query[1024];
+sqlSafef(query, sizeof query, "%s", ""); 
 if (cartVarExists(cart, hgtaMetaStatus))
     {
     printf("Table status for database %s\n", database);
-    query = NOSQLINJ "SHOW TABLE STATUS";
+    sqlSafef(query, sizeof query, "SHOW TABLE STATUS");
     }
 else if (cartVarExists(cart, hgtaMetaVersion))
     {
-    query = NOSQLINJ "SELECT @@VERSION";
+    sqlSafef(query, sizeof query, "SELECT @@VERSION");
     }
 else if (cartVarExists(cart, hgtaMetaDatabases))
     {
-    query = NOSQLINJ "SHOW DATABASES";
+    sqlSafef(query, sizeof query, "SHOW DATABASES");
     }
 else if (cartVarExists(cart, hgtaMetaTables))
     {
-    query = NOSQLINJ "SHOW TABLES";
+    sqlSafef(query, sizeof query, "SHOW TABLES");
     }
 struct sqlResult *sr;
 char **row;
 char *sep="";
 int c = 0;
 int numCols = 0;
 sr = sqlGetResult(conn, query);
 numCols = sqlCountColumns(sr);
 char *field;
 while ((field = sqlFieldName(sr)) != NULL)
     printf("%s \t", field);
 printf("\n");
 while ((row = sqlNextRow(sr)) != NULL)
     {
     sep="";