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/outside/hgLsSnpPdbLoad/hgLsSnpPdbLoad.c src/hg/makeDb/outside/hgLsSnpPdbLoad/hgLsSnpPdbLoad.c
index 35a5e13..5c68f64 100644
--- src/hg/makeDb/outside/hgLsSnpPdbLoad/hgLsSnpPdbLoad.c
+++ src/hg/makeDb/outside/hgLsSnpPdbLoad/hgLsSnpPdbLoad.c
@@ -1,176 +1,177 @@
 /* hgLsSnpPdbLoad - fetch data from LS-SNP PDB mysql server and load table for browser. */
 
 /* Copyright (C) 2013 The Regents of the University of California 
  * See kent/LICENSE or http://genome.ucsc.edu/license/ for licensing information. */
 #include "common.h"
 #include "options.h"
 #include "jksql.h"
 #include "lsSnpPdb.h"
 #include "linefile.h"
 #include "portable.h"
 
 
 void usage(char *msg)
 /* Explain usage and exit. */
 {
 errAbort("Error: %s:\n"
   "hgLsSnpPdbLoad - fetch data from LS-SNP/PDB mysql server or\n"
   "                 load an lsSnpPdb format table or file\n"
   "usage:\n"
   "   hgLsSnpPdbLoad fetch lsSnpDb tabOut\n"
   "   hgLsSnpPdbLoad load db table tabIn\n"
   "\n"
   "lsSnpDb can be either a local database name or profile:database,\n"
   "to use a profile in ~/.hg.conf to access a remote database.\n",
   msg);
 }
 
 static struct optionSpec options[] = {
     {NULL, 0},
 };
 
 static char *createSql =
     "CREATE TABLE %s ("
     "    protId varchar(255) not null,"
     "    pdbId varchar(255) not null,"
     "    structType enum(\"XRay\", \"NMR\") not null,"
     "    chain char(1) not null,"
     "    snpId varchar(255) not null,"
     "    snpPdbLoc int not null,"
     "    index(protId),"
     "    index(pdbId),"
     "    index(snpId));";
 
 
 static void buildLsSnpPdb(char *lsSnpProf, char *lsSnpDb, char *tabFile)
 /* fetch LSSNP data and create an lsSnpPdb format tab file  */
 {
 struct sqlConnection *conn = sqlConnectProfile(lsSnpProf, lsSnpDb);
 FILE *fh = mustOpen(tabFile, "w");
-char *query =
-    NOSQLINJ "SELECT distinct pr.accession,ps.pdb_id,pstr.struct_type,ps.chain,SNP.name,ps.snp_position "
+char query[1024];
+sqlSafef(query, sizeof query, 
+    "SELECT distinct pr.accession,ps.pdb_id,pstr.struct_type,ps.chain,SNP.name,ps.snp_position "
     "FROM Protein pr,PDB_SNP ps, SNP, PDB_Structure pstr "
     "WHERE (ps.snp_id = SNP.snp_id) AND (pr.prot_id = ps.prot_id) "
-    "AND (pstr.pdb_id = ps.pdb_id)";
+    "AND (pstr.pdb_id = ps.pdb_id)");
 struct sqlResult *sr = sqlGetResult(conn, query);
 char **row;
 struct lsSnpPdb rec;
 while ((row = sqlNextRow(sr)) != NULL)
     {
     // translate struct_type
     char *hold = row[2];
     if (sameString(row[2], "X-Ray"))
         row[2] = "XRay";
     else if (sameString(row[2], "NMR"))
         row[2] = "NMR";
     else
         errAbort("unknown struct_type field value: \"%s\"", row[2]);
     lsSnpPdbStaticLoad(row, &rec);
     lsSnpPdbTabOut(&rec, fh);
     row[2] = hold;
     }
 sqlFreeResult(&sr);
 carefulClose(&fh);
 sqlDisconnect(&conn);
 }
 
 static char *parseLsSnpDb(char **lsSnpDbPtr)
 /* parse lsSnpDb spec, updating ptr and returning profile or null */
 {
 char *lsSnpProf = NULL;
 char *sep = strchr(*lsSnpDbPtr, ':');
 if (sep != NULL)
     {
     lsSnpProf = *lsSnpDbPtr;
     *sep = '\0';
     *lsSnpDbPtr = sep+1;
     }
 return lsSnpProf;
 }
 
 static void fetchLsSnpPdb(char *lsSnpDb, char *tabOut)
 /* fetch data from LS-SNP/PDB mysql server */
 {
 char *lsSnpProf = parseLsSnpDb(&lsSnpDb);
 buildLsSnpPdb(lsSnpProf, lsSnpDb, tabOut);
 }
 
 /* get a temporary copy of the tab input file, possibly decompressing it */
 static void getTmpTabFile(char *inFile, char *tmpFileName, int tmpFileNameSize)
 {
 char *tmpDir = getenv("TMPDIR");
 if (tmpDir == NULL)
     tmpDir = "/var/tmp";
 safef(tmpFileName, tmpFileNameSize, "%s/lsSnpPdb.%s.%d.tab", tmpDir, getHost(), getpid());
 struct lineFile *inLf = lineFileOpen(inFile, TRUE);
 FILE *outFh = mustOpen(tmpFileName, "w");
 char *line;
 while (lineFileNext(inLf, &line, NULL))
     {
     fputs(line, outFh);
     fputc('\n', outFh);
     }
 carefulClose(&outFh);
 lineFileClose(&inLf);
 }
 
 static void loadLsSnpPdb(char *db, char *table, char *inFile)
 /* load lsSnpPdb table.  A temporary table is created and then
  * an atomic rename is done once it is loaded. */
 {
 char tmpTabFile[PATH_LEN];
 getTmpTabFile(inFile, tmpTabFile, sizeof(tmpTabFile));
 
 char newTbl[256], oldTbl[256], query[1024];
 safef(newTbl, sizeof(newTbl), "%s_new", table);
 safef(oldTbl, sizeof(oldTbl), "%s_old", table);
 
 struct sqlConnection * conn = sqlConnect(db);
 
 // clean up droppings from previous runs
 sqlDropTable(conn, newTbl);
 sqlDropTable(conn, oldTbl);
 
 // load into tmp table
 sqlSafef(query, sizeof(query), createSql, newTbl);
 sqlUpdate(conn, query);
 sqlLoadTabFile(conn, tmpTabFile, newTbl, 0);
 
 // rename into place
 if (sqlTableExists(conn, table))
     sqlSafef(query, sizeof(query), "rename table %s to %s, %s to %s",
           table, oldTbl, newTbl, table);
 else
     sqlSafef(query, sizeof(query), "rename table %s to %s",
           newTbl, table);
 sqlUpdate(conn, query);
 
 sqlDropTable(conn, oldTbl);
 sqlDisconnect(&conn);
 unlink(tmpTabFile);  // ignore failures
 }
 
 int main(int argc, char *argv[])
 /* Process command line. */
 {
 static char *wrongArgsMsg = "wrong number of arguments";
 optionInit(&argc, argv, options);
 if (argc < 2)
     usage(wrongArgsMsg);
 if (sameString(argv[1], "fetch"))
     {
     if (argc != 4)
         usage(wrongArgsMsg);
     fetchLsSnpPdb(argv[2], argv[3]);
     }
 else if (sameString(argv[1], "load"))
     {
     if (argc != 5)
         usage(wrongArgsMsg);
     loadLsSnpPdb(argv[2], argv[3], argv[4]);
     }
 else
     usage("invalid action");
 
 return 0;
 }