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/snpRefUCSC.c src/hg/snp/snpLoad/snpRefUCSC.c
index be4176f..4649874 100644
--- src/hg/snp/snpLoad/snpRefUCSC.c
+++ src/hg/snp/snpLoad/snpRefUCSC.c
@@ -1,232 +1,232 @@
 /* snpRefUCSC - sixth step in dbSNP processing.
  * Read the nib file for a chrom into memory.
  * Lookup sequence at coordinates. 
  * Rewrite to new chrN_snpTmp tables.  
  * Rename chrMT_snpTmp to chrM_snpTmp before running this.
  * Use UCSC chromInfo.  */
 
 /* Copyright (C) 2013 The Regents of the University of California 
  * See kent/LICENSE or http://genome.ucsc.edu/license/ for licensing information. */
 
 /* Check for coords larger than chromSize; log as errors. */
 
 #include "common.h"
 
 #include "chromInfo.h"
 #include "dystring.h"
 #include "hash.h"
 #include "hdb.h"
 
 /* errAbort if larger SNP found */
 #define MAX_SNP_SIZE 1024
 
 
 static char *snpDb = NULL;
 static struct hash *chromHash = NULL;
 FILE *errorFileHandle = NULL;
 
 void usage()
 /* Explain usage and exit. */
 {
 errAbort(
     "snpRefUCSC - read nib files\n"
     "usage:\n"
     "    snpRefUCSC snpDb\n");
 }
 
 
 struct hash *loadChroms()
 /* hash from UCSC chromInfo */
 {
 struct hash *ret;
 char query[512];
 struct sqlConnection *conn = hAllocConn();
 struct sqlResult *sr;
 char **row;
 struct chromInfo *el;
 char tableName[64];
 
 ret = newHash(0);
 sqlSafef(query, sizeof(query), "select chrom, size from chromInfo");
 sr = sqlGetResult(conn, query);
 while ((row = sqlNextRow(sr)) != NULL)
     {
     safef(tableName, ArraySize(tableName), "%s_snpTmp", row[0]);
     if (!hTableExists(tableName)) continue;
     el = chromInfoLoad(row);
     hashAdd(ret, el->chrom, (void *)(& el->size));
     }
 sqlFreeResult(&sr);
 hFreeConn(&conn);
 return ret;
 }
 
 unsigned getChromSize(char *chrom)
 /* Return size of chrom.  */
 {
 struct hashEl *el = hashLookup(chromHash,chrom);
 
 if (el == NULL)
     errAbort("Couldn't find size of chrom %s", chrom);
 return *(unsigned *)el->val;
 }
 
 
 void getRefUCSC(char *chromName)
 /* get sequence for each row */
 {
 char query[512];
 struct sqlConnection *conn = hAllocConn();
 struct sqlResult *sr;
 char **row;
 char tableName[64];
 char fileName[64];
 char nibName[HDB_MAX_PATH_STRING];
 FILE *f;
 struct dnaSeq *seq;
 char *seqPtr = NULL;
 int start = 0;
 int end = 0;
 int chromSize = 0;
 char refUCSC[MAX_SNP_SIZE];
 int pos = 0;
 int snpSize = 0;
 
 safef(tableName, ArraySize(tableName), "%s_snpTmp", chromName);
 if (!hTableExists(tableName)) return;
 safef(fileName, ArraySize(fileName), "%s_snpTmp.tab", chromName);
 chromSize = getChromSize(chromName);
 
 f = mustOpen(fileName, "w");
 hNibForChrom(chromName, nibName);
 seq = hFetchSeq(nibName, chromName, 0, chromSize-1);
 touppers(seq->dna);
 seqPtr = seq->dna;
 
 sqlSafef(query, sizeof(query), 
     "select snp_id, ctg_id, chromStart, chromEnd, loc_type, orientation, allele, weight from %s", tableName);
 
 sr = sqlGetResult(conn, query);
 while ((row = sqlNextRow(sr)) != NULL)
     {
     start = sqlUnsigned(row[2]);
     end = sqlUnsigned(row[3]);
     if (start > chromSize)
         {
         fprintf(errorFileHandle, "rs%s at %s:%d-%d; chromSize=%d\n", row[0], chromName, start, end, chromSize);
 	continue;
 	}
 
     snpSize = end - start;
     if (snpSize > MAX_SNP_SIZE)
 	errAbort("maximum size exceeded %s, %s:%d-%d\n", row[0], chromName, start, end);
     if (start == end)
         {
 	/* copy whatever convention dbSNP uses for insertion */
         fprintf(f, "%s\t%s\t%d\t%d\t%s\t%s\t%s\t%s\t%s\t%s\n", 
                 row[0], row[1], start, end, row[4], row[5], row[6], row[6], row[6], row[7]);
 	continue;
 	}
     verbose(5, "building refUCSC for rs%s at %s:%d-%d\n", row[0], chromName, start, end);
     // could potentially use memcpy here
     for (pos = start; pos < end; pos++)
         refUCSC[pos - start] = seqPtr[pos];
     refUCSC[snpSize] = '\0';
     verbose(5, "refUCSC = %s\n", refUCSC);
     
     fprintf(f, "%s\t%s\t%d\t%d\t%s\t%s\t%s\t%s\t", row[0], row[1], start, end, row[4], row[5], row[6], refUCSC);
     reverseComplement(refUCSC, snpSize);
     fprintf(f, "%s\t%s\n", refUCSC, row[7]);
 
     }
 sqlFreeResult(&sr);
 hFreeConn(&conn);
 carefulClose(&f);
 }
 
 
 
 
 void recreateDatabaseTable(char *chromName)
 /* create a new chrN_snpTmp table with new definition */
 /* could use enum for loc_type here */
 {
 struct sqlConnection *conn = hAllocConn();
 char tableName[64];
 char *createString =
 "CREATE TABLE %s (\n"
 "    snp_id int(11) not null,\n"
 "    ctg_id int(11) not null,\n"
 "    chromStart int(11) not null,\n"
 "    chromEnd int(11) not null,\n"
 "    loc_type tinyint(4) not null,\n"
 "    orientation tinyint(4) not null,\n"
 "    allele blob,\n"
 "    refUCSC blob,\n"
 "    refUCSCReverseComp blob,\n"
 "    weight int\n"
 ");\n";
 
-struct dyString *dy = newDyString(1024);
+struct dyString *dy = dyStringNew(1024);
 
 safef(tableName, ArraySize(tableName), "%s_snpTmp", chromName);
 sqlDyStringPrintf(dy, createString, tableName);
 sqlRemakeTable(conn, tableName, dy->string);
 dyStringFree(&dy);
 hFreeConn(&conn);
 }
 
 
 void loadDatabase(char *chromName)
 /* load one table into database */
 {
 FILE *f;
 struct sqlConnection *conn = hAllocConn();
 char tableName[64], fileName[64];
 
 safef(tableName, ArraySize(tableName), "%s_snpTmp", chromName);
 safef(fileName, ArraySize(fileName), "%s_snpTmp.tab", chromName);
 
 f = mustOpen(fileName, "r");
 hgLoadTabFile(conn, ".", tableName, &f);
 
 hFreeConn(&conn);
 }
 
 
 int main(int argc, char *argv[])
 /* read chrN_snpTmp, look up sequence, rewrite to individual chrom tables */
 {
 struct hashCookie cookie;
 char *chromName;
 char tableName[64];
 
 if (argc != 2)
     usage();
 
 snpDb = argv[1];
 hSetDb(snpDb);
 
 chromHash = loadChroms();
 if (chromHash == NULL) 
     {
     verbose(1, "couldn't get chrom info\n");
     return 1;
     }
 
 errorFileHandle = mustOpen("snpRefUCSC.errors", "w");
 
 cookie = hashFirst(chromHash);
 while ((chromName = hashNextName(&cookie)) != NULL)
     {
     safef(tableName, ArraySize(tableName), "%s_snpTmp", chromName);
     if (!hTableExists(tableName)) continue;
     verbose(1, "chrom = %s\n", chromName);
     getRefUCSC(chromName);
     recreateDatabaseTable(chromName);
     loadDatabase(chromName);
     }
 
 carefulClose(&errorFileHandle);
 return 0;
 }