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/lsSnpPdbChimera.c src/hg/cgilib/lsSnpPdbChimera.c
index f27d0e1..7d3e5c8 100644
--- src/hg/cgilib/lsSnpPdbChimera.c
+++ src/hg/cgilib/lsSnpPdbChimera.c
@@ -94,31 +94,31 @@
 
 fprintf(xfh, "))\n");
 
 chimeraxEnd(&xfh);
 }
 
 void lsSnpPdbChimeraSnpAnn(struct sqlConnection *conn,
                            char *pdbId, char *primarySnpId,
                            struct tempName *outName)
 /* Generate a chimerax file for the given pdb with all non-synonymous SNPs
  * that have been mapped to this protein.  If primarySnpId is not NULL, it is
  * colored differently than the other SNPs.  Fills in outName structure. */
 {
 getOutFile(pdbId, primarySnpId, outName);
 char where[512];
-sqlSafefFrag(where, sizeof(where), "(pdbId=\"%s\")", pdbId);
+sqlSafef(where, sizeof(where), "(pdbId=\"%s\")", pdbId);
 chimeraxGen(conn, pdbId, where, primarySnpId, outName->forCgi);
 }
 
 struct slName *lsSnpPdbChimeraGetSnpPdbs(struct sqlConnection *conn,
                                          char *snpId)
 /* get list of PDBs to which snpId is mapped.  */
 {
 if (!sqlTableExists(conn, "lsSnpPdb"))
     return NULL;
 char query[256];
 sqlSafef(query, sizeof(query), "SELECT distinct pdbId FROM lsSnpPdb WHERE (snpId = \"%s\")",
       snpId);
 struct slName *pdbIds = sqlQuickList(conn, query);
 slNameSort(&pdbIds);
 return pdbIds;