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/snp/snpLoad/snpGetSimple.c src/hg/snp/snpLoad/snpGetSimple.c
index a3def3b..073e253 100644
--- src/hg/snp/snpLoad/snpGetSimple.c
+++ src/hg/snp/snpLoad/snpGetSimple.c
@@ -1,201 +1,201 @@
 /* snpGetSimple - get simple SNPs. */
 /* create a hash of chrom names that contains output file handles */
 
 /* 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 "hash.h"
 #include "hdb.h"
 
 
 static struct hash *chromHash = NULL;
 static struct hash *annotationsHash = NULL;
 FILE *tabFileHandle = NULL;
 
 void usage()
 /* Explain usage and exit. */
 {
 errAbort(
     "snpGetSimple - get simple SNPs, divided by chrom\n"
     "usage:\n"
     "    snpGetSimple database snpTable annotationsTable\n");
 }
 
 void loadChroms()
 /* hash all chromNames, create file handles */
 {
 char query[512];
 struct sqlConnection *conn = hAllocConn();
 struct sqlResult *sr;
 char **row;
 FILE *f;
 char fileName[64];
 char *randomString = NULL;
 char *hapString = NULL;
 
 chromHash = newHash(0);
 sqlSafef(query, sizeof(query), "select chrom from chromInfo");
 sr = sqlGetResult(conn, query);
 while ((row = sqlNextRow(sr)) != NULL)
     {
     randomString = strstr(row[0], "random");
     if (randomString != NULL) continue;
     hapString = strstr(row[0], "hap");
     if (hapString != NULL) continue;
     safef(fileName, sizeof(fileName), "snpGetSimple.%s", row[0]);
     f = mustOpen(fileName, "w");
     hashAdd(chromHash, cloneString(row[0]), f);
     }
 sqlFreeResult(&sr);
 hFreeConn(&conn);
 }
 
 void loadMultiples(char *tableName)
 /* create a hash of SNPs that align more than once, so we can exclude these */
 {
 char query[512];
 struct sqlConnection *conn = hAllocConn();
 struct sqlResult *sr;
 char **row;
 struct hashEl *hel = NULL;
 char *snpId = NULL;
 char *annotation = NULL;
 
 annotationsHash = newHash(0);
 sqlSafef(query, sizeof(query), "select name, exception from %s", tableName);
 sr = sqlGetResult(conn, query);
 while ((row = sqlNextRow(sr)) != NULL)
     {
     annotation = cloneString(row[1]);
     if (!sameString(annotation, "MultipleAlignments")) continue;
     snpId = cloneString(row[0]);
     hel = hashLookup(annotationsHash, snpId);
     if (hel == NULL)
         hashAdd(annotationsHash, snpId, NULL);
     }
 }
 
 boolean triAllelic(char *observed)
 {
 if (sameString(observed, "A/C/G")) return TRUE;
 if (sameString(observed, "A/C/T")) return TRUE;
 if (sameString(observed, "A/G/T")) return TRUE;
 if (sameString(observed, "C/G/T")) return TRUE;
 return FALSE;
 }
 
 void getSnps(char *tableName)
 /* spew out simple SNPs */
 /* exclude SNPs on random chroms */
 /* exclude SNPs that align multiple places */
 {
 char query[512];
 struct sqlConnection *conn = hAllocConn();
 struct sqlResult *sr;
 char **row;
 struct hashCookie cookie;
 char *randomString = NULL;
 struct hashEl *hel = NULL;
 
 sqlSafef(query, sizeof(query), 
     "select name, chrom, chromStart, chromEnd, strand, refUCSC, observed, class, locType, weight from %s", tableName);
 sr = sqlGetResult(conn, query);
 while ((row = sqlNextRow(sr)) != NULL)
     {
     randomString = strstr(row[1], "random");
     if (randomString != NULL) continue;
     if (!sameString(row[7], "single")) continue;
     if (!sameString(row[8], "exact")) continue;
     if (triAllelic(row[6])) continue;
     if (sameString(row[6], "A/C/G/T")) continue;
     // if (!sameString(row[9], "1")) continue;
     hel = hashLookup(annotationsHash, row[0]);
     if (hel != NULL) continue;
     hel = hashLookup(chromHash, row[1]);
     if (hel == NULL)
         verbose(1, "%s not found\n", row[1]);
     else
         {
         fprintf(hel->val, "%s %s %s %s 0 %s %s %s\n", row[1], row[2], row[3], row[0], row[4], row[5], row[6]);
         fprintf(tabFileHandle, "%s\t%s\t%s\t%s\t0\t%s\t%s\t%s\n", row[1], row[2], row[3], row[0], row[4], row[5], row[6]);
 	}
     }
 sqlFreeResult(&sr);
 cookie = hashFirst(chromHash);
 while ((hel = hashNext(&cookie)))
     fclose(hel->val);
 }
 
 void createTable(char *tableName)
 /* create simple SNP table */
 {
 struct sqlConnection *conn = hAllocConn();
 char *createString =
 "CREATE TABLE %s (\n"
 "    chrom varchar(15) not null default '',\n"
 "    chromStart int(10) not null default '0',\n"
 "    chromEnd int(10) not null default '0',\n"
 "    name varchar(15) not null default '',\n"
 "    score smallint(5) not null default '0',\n"
 "    strand enum('?','+','-') not null default '?',\n"
 "    refUCSC enum('A','C','G','T'),\n"
 "    observed varchar(255)\n"
 ");\n";
 
-struct dyString *dy = newDyString(1024);
+struct dyString *dy = dyStringNew(1024);
 
 sqlDyStringPrintf(dy, createString, tableName);
 sqlRemakeTable(conn, tableName, dy->string);
 dyStringFree(&dy);
 hFreeConn(&conn);
 }
 
 void loadDatabase(char *tableName, char *fileName)
 /* load tab file into database */
 /* This little wrapper is a good candidate for a library. */
 {
 FILE *f; 
 struct sqlConnection *conn = hAllocConn(); 
 
 f = mustOpen(fileName, "r");
 hgLoadTabFile(conn, ".", tableName, &f);
 hFreeConn(&conn);
 }
 
 
 int main(int argc, char *argv[])
 {
 
 char *snpDb = NULL;
 char *snpTableName = NULL;
 char simpleTableName[64];
 char simpleFileName[64];
 
 if (argc != 4)
     usage();
 
 snpDb = argv[1];
 hSetDb(snpDb);
 
 snpTableName = argv[2];
 safef(simpleTableName, ArraySize(simpleTableName), "%ssimple", snpTableName);
 safef(simpleFileName, ArraySize(simpleFileName), "%s.tab", simpleTableName);
 
 /* check that tables exist */
 if (!hTableExists(snpTableName))
     errAbort("no %s table in %s\n", snpTableName, snpDb);
 if (!hTableExists("chromInfo"))
     errAbort("no chromInfo table in %s\n", snpDb);
 
 loadChroms();
 loadMultiples(argv[3]);
 tabFileHandle = mustOpen(simpleFileName, "w");
 getSnps(snpTableName);
 carefulClose(&tabFileHandle);
 createTable(simpleTableName);
 loadDatabase(simpleTableName, simpleFileName);
 
 return 0;
 }