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/cgilib/transMapSrc.c src/hg/cgilib/transMapSrc.c
index 596212e..129fe97 100644
--- src/hg/cgilib/transMapSrc.c
+++ src/hg/cgilib/transMapSrc.c
@@ -1,173 +1,171 @@
 /* transMapSrc.c was originally generated by the autoSql program, which also 
  * generated transMapSrc.h and transMapSrc.sql.  This module links the database and
  * the RAM representation of objects. */
 
 /* Copyright (C) 2014 The Regents of the University of California 
  * See kent/LICENSE or http://genome.ucsc.edu/license/ for licensing information. */
 
 #include "common.h"
 #include "linefile.h"
 #include "dystring.h"
 #include "jksql.h"
 #include "transMapSrc.h"
 
 
-char *transMapSrcCommaSepFieldNames = "db,id,chrom,chromStart,chromEnd,strand,ident,aligned";
-
 void transMapSrcStaticLoad(char **row, struct transMapSrc *ret)
 /* Load a row from transMapSrc table into ret.  The contents of ret will
  * be replaced at the next call to this function. */
 {
 
 safecpy(ret->db, sizeof(ret->db), row[0]);
 ret->id = row[1];
 ret->chrom = row[2];
 ret->chromStart = sqlUnsigned(row[3]);
 ret->chromEnd = sqlUnsigned(row[4]);
 ret->strand = row[5][0];
 ret->ident = sqlFloat(row[6]);
 ret->aligned = sqlFloat(row[7]);
 }
 
 struct transMapSrc *transMapSrcLoad(char **row)
 /* Load a transMapSrc from row fetched with select * from transMapSrc
  * from database.  Dispose of this with transMapSrcFree(). */
 {
 struct transMapSrc *ret;
 
 AllocVar(ret);
 safecpy(ret->db, sizeof(ret->db), row[0]);
 ret->id = cloneString(row[1]);
 ret->chrom = cloneString(row[2]);
 ret->chromStart = sqlUnsigned(row[3]);
 ret->chromEnd = sqlUnsigned(row[4]);
 ret->strand = row[5][0];
 ret->ident = sqlFloat(row[6]);
 ret->aligned = sqlFloat(row[7]);
 return ret;
 }
 
 struct transMapSrc *transMapSrcLoadAll(char *fileName) 
 /* Load all transMapSrc from a whitespace-separated file.
  * Dispose of this with transMapSrcFreeList(). */
 {
 struct transMapSrc *list = NULL, *el;
 struct lineFile *lf = lineFileOpen(fileName, TRUE);
 char *row[8];
 
 while (lineFileRow(lf, row))
     {
     el = transMapSrcLoad(row);
     slAddHead(&list, el);
     }
 lineFileClose(&lf);
 slReverse(&list);
 return list;
 }
 
 struct transMapSrc *transMapSrcLoadAllByChar(char *fileName, char chopper) 
 /* Load all transMapSrc from a chopper separated file.
  * Dispose of this with transMapSrcFreeList(). */
 {
 struct transMapSrc *list = NULL, *el;
 struct lineFile *lf = lineFileOpen(fileName, TRUE);
 char *row[8];
 
 while (lineFileNextCharRow(lf, chopper, row, ArraySize(row)))
     {
     el = transMapSrcLoad(row);
     slAddHead(&list, el);
     }
 lineFileClose(&lf);
 slReverse(&list);
 return list;
 }
 
 struct transMapSrc *transMapSrcCommaIn(char **pS, struct transMapSrc *ret)
 /* Create a transMapSrc out of a comma separated string. 
  * This will fill in ret if non-null, otherwise will
  * return a new transMapSrc */
 {
 char *s = *pS;
 
 if (ret == NULL)
     AllocVar(ret);
 sqlFixedStringComma(&s, ret->db, sizeof(ret->db));
 ret->id = sqlStringComma(&s);
 ret->chrom = sqlStringComma(&s);
 ret->chromStart = sqlUnsignedComma(&s);
 ret->chromEnd = sqlUnsignedComma(&s);
 sqlFixedStringComma(&s, &(ret->strand), sizeof(ret->strand));
 ret->ident = sqlFloatComma(&s);
 ret->aligned = sqlFloatComma(&s);
 *pS = s;
 return ret;
 }
 
 void transMapSrcFree(struct transMapSrc **pEl)
 /* Free a single dynamically allocated transMapSrc such as created
  * with transMapSrcLoad(). */
 {
 struct transMapSrc *el;
 
 if ((el = *pEl) == NULL) return;
 freeMem(el->id);
 freeMem(el->chrom);
 freez(pEl);
 }
 
 void transMapSrcFreeList(struct transMapSrc **pList)
 /* Free a list of dynamically allocated transMapSrc's */
 {
 struct transMapSrc *el, *next;
 
 for (el = *pList; el != NULL; el = next)
     {
     next = el->next;
     transMapSrcFree(&el);
     }
 *pList = NULL;
 }
 
 void transMapSrcOutput(struct transMapSrc *el, FILE *f, char sep, char lastSep) 
 /* Print out transMapSrc.  Separate fields with sep. Follow last field with lastSep. */
 {
 if (sep == ',') fputc('"',f);
 fprintf(f, "%s", el->db);
 if (sep == ',') fputc('"',f);
 fputc(sep,f);
 if (sep == ',') fputc('"',f);
 fprintf(f, "%s", el->id);
 if (sep == ',') fputc('"',f);
 fputc(sep,f);
 if (sep == ',') fputc('"',f);
 fprintf(f, "%s", el->chrom);
 if (sep == ',') fputc('"',f);
 fputc(sep,f);
 fprintf(f, "%u", el->chromStart);
 fputc(sep,f);
 fprintf(f, "%u", el->chromEnd);
 fputc(sep,f);
 if (sep == ',') fputc('"',f);
 fprintf(f, "%c", el->strand);
 if (sep == ',') fputc('"',f);
 fputc(sep,f);
 fprintf(f, "%g", el->ident);
 fputc(sep,f);
 fprintf(f, "%g", el->aligned);
 fputc(lastSep,f);
 }
 
 /* -------------------------------- End autoSql Generated Code -------------------------------- */
 
 
 struct transMapSrc *transMapSrcQuery(struct sqlConnection *srcConn,
                                      char *table, char *srcDb, char *srcId)
 /* load a single transMapSrc object for an srcDb and srcId from a table,
  * or error if not found */
 {
 return sqlQueryObjs(srcConn, (sqlLoadFunc)transMapSrcLoad,
                     sqlQueryMust|sqlQuerySingle,
-                    "SELECT %-s FROM %s WHERE (db=\"%s\") and (id = \"%s\")",
-                    transMapSrcCommaSepFieldNames, table, srcDb, srcId);
+                    "SELECT db,id,chrom,chromStart,chromEnd,strand,ident,aligned FROM %s WHERE (db=\"%s\") and (id = \"%s\")",
+                    table, srcDb, srcId);
 }