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/snpReadFasta.c src/hg/snp/snpLoad/snpReadFasta.c
index c4f2148..3238ae2 100644
--- src/hg/snp/snpLoad/snpReadFasta.c
+++ src/hg/snp/snpLoad/snpReadFasta.c
@@ -1,267 +1,267 @@
 /* snpReadFasta - seventh step in dbSNP processing.
  * Hash the snpFasta contents (by chrom, and also chrMulti).
  * Serially read the chrN_snpTmp tables.
  * Do lookups into snpFasta hashes for class, observed, molType. 
  * 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. */
 
 /* Could drop refUCSCReverseComp here. */
 /* Dropping ctg_id at this point. */
 
 /* Look in chrMulti_snpFasta if no match found in chrN_snpFasta. */
 /* Write to error file if no match found in chrN_snpFasta or chrMulti_snpFasta. */
 /* Also write to error file if matches found in chrN_snpFasta AND chrMulti_snpFasta. */
 /* Give preference to chrMulti_snpFasta data. (Don't bother checking for difference). */
 
 #include "common.h"
 
 #include "hash.h"
 #include "hdb.h"
 
 
 struct snpFasta
     {
     /* I don't think I need next */
     struct snpFasta *next;
     char *molType;
     char *class;
     char *observed;
     };
 
 static struct hash *multiFastaHash = NULL;
 static struct hash *chromFastaHash = NULL;
 
 static char *snpDb = NULL;
 FILE *errorFileHandle = NULL;
 
 void usage()
 /* Explain usage and exit. */
 {
 errAbort(
     "snpReadFasta - lookup molType, class and observed in chrN_snpFasta and chrMulti_snpFasta\n"
     "check for errors in observed\n"
     "recreate chrN_snpTmp\n"
     "usage:\n"
     "    snpReadFasta snpDb \n");
 }
 
 
 struct hash *readFasta(char *chromName)
 /* read contents of chrN_fasta into hash. */
 /* Read again for random */
 /* Also called to create the chrN_multi hash. */
 {
 struct snpFasta *fel;
 char query[512];
 struct sqlConnection *conn = hAllocConn();
 struct sqlResult *sr;
 char **row;
 char fastaTableName[64];
 struct hash *newChromHash = NULL;
 char *adjustedChromName = cloneString(chromName);
 char *randomSubstring = NULL;
 
 newChromHash = newHash(0);
 
 randomSubstring = strstr(chromName, "random");
 if (randomSubstring != NULL) 
     stripString(adjustedChromName, "_random");
 
 safef(fastaTableName, ArraySize(fastaTableName), "%s_snpFasta", adjustedChromName);
 if(!hTableExistsDb(snpDb, fastaTableName)) 
     errAbort("can't get table %s\n", fastaTableName);
 
 sqlSafef(query, sizeof(query), "select rsId, molType, class, observed from %s", fastaTableName);
 sr = sqlGetResult(conn, query);
 while ((row = sqlNextRow(sr)) != NULL)
     {
     AllocVar(fel);
     fel->molType = cloneString(row[1]);
     fel->class = cloneString(row[2]);
     fel->observed = cloneString(row[3]);
     /* could check for duplicates here */
     hashAdd(newChromHash, cloneString(row[0]), fel);
     }
 
 sqlFreeResult(&sr);
 hFreeConn(&conn);
 
 return newChromHash;
 }
 
 struct snpFasta *getFastaElement(char *snp_id, char *chromName)
 /* look first in the chromFastaHash */
 /* also look in the multiFastaHash */
 {
 struct snpFasta *felChrom = NULL;
 struct snpFasta *felMulti = NULL;
 char snpName[32];
 
 safef(snpName, sizeof(snpName), "rs%s", snp_id);
 felChrom = hashFindVal(chromFastaHash, snpName);
 felMulti = hashFindVal(multiFastaHash, snpName);
 
 if (felChrom == NULL && felMulti == NULL)
     {
     fprintf(errorFileHandle, "no snpFasta for %s in %s\n", snpName, chromName);
     return NULL;
     }
     
 if (felChrom != NULL && felMulti != NULL)
     {
     fprintf(errorFileHandle, "duplicate snpFasta for %s in %s\n", snpName, chromName);
     return felMulti;
     }
 
 if (felChrom != NULL) 
     return felChrom;
 
 return felMulti;
 
 }
 
 void processSnps(char *chromName)
 /* read through all rows in snpTmp */
 /* look up molType/class/observed */
 /* write to output file */
 {
 char query[512];
 struct sqlConnection *conn = hAllocConn();
 struct sqlResult *sr;
 char **row;
 char tableName[64];
 char fileName[64];
 char *classString = NULL;
 FILE *f;
 struct snpFasta *fel = NULL;
 int loc_type = 0;
 
 safef(tableName, ArraySize(tableName), "%s_snpTmp", chromName);
 safef(fileName, ArraySize(fileName), "%s_snpTmp.tab", chromName);
 f = mustOpen(fileName, "w");
 
 sqlSafef(query, sizeof(query), 
      "select snp_id, chromStart, chromEnd, loc_type, orientation, allele, refUCSC, refUCSCReverseComp, weight from %s ", tableName);
 sr = sqlGetResult(conn, query);
 while ((row = sqlNextRow(sr)) != NULL)
     {
     loc_type = sqlUnsigned(row[3]);
     fel = getFastaElement(row[0], chromName);
     if (fel == NULL)
         {
         fprintf(f, "%s\t%s\t%s\t%d\t", row[0], row[1], row[2], loc_type);
 	fprintf(f, "%s\t%s\t%s\t%s\t", "unknown", row[4], "unknown", row[5]);
 	fprintf(f, "%s\t%s\t%s\t%s\n", row[6], row[7], "n/a", row[8]);
 	continue;
 	}
     classString = fel->class;
     /* special handling for class = in-del; split into classes of our own construction */
     if (sameString(classString, "in-del"))
         {
         if (loc_type == 3) 
 	    classString = cloneString("insertion");
 	if (loc_type == 1 || loc_type == 2) 
 	    classString = cloneString("deletion");
 	}
     fprintf(f, "%s\t%s\t%s\t%d\t", row[0], row[1], row[2], loc_type);
     fprintf(f, "%s\t%s\t%s\t%s\t", classString, row[4], fel->molType, row[5]);
     fprintf(f, "%s\t%s\t%s\t%s\n", row[6], row[7], fel->observed, row[8]);
     }
 
 sqlFreeResult(&sr);
 hFreeConn(&conn);
 carefulClose(&f);
 }
 
 
 void recreateDatabaseTable(char *chromName)
 /* create a new chrN_snpTmp table with new definition */
 {
 struct sqlConnection *conn = hAllocConn();
 char tableName[64];
 char *createString =
 "CREATE TABLE %s (\n"
 "    snp_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"
 "    class varchar(255) not null,\n"
 "    orientation tinyint(4) not null,\n"
 "    molType varchar(255) not null,\n"
 "    allele blob,\n"
 "    refUCSC blob,\n"
 "    refUCSCReverseComp blob,\n"
 "    observed 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 closes the file handle */
 hgLoadTabFile(conn, ".", tableName, &f);
 
 hFreeConn(&conn);
 }
 
 
 
 int main(int argc, char *argv[])
 /* hash snpFasta, read through chrN_snpTmp, rewrite with extensions to individual chrom tables */
 {
 struct slName *chromList, *chromPtr;
 char tableName[64];
 
 if (argc != 2)
     usage();
 
 snpDb = argv[1];
 hSetDb(snpDb);
 chromList = hAllChromNamesDb(snpDb);
 
 errorFileHandle = mustOpen("snpReadFasta.errors", "w");
 
 multiFastaHash = readFasta("chrMulti");
 
 for (chromPtr = chromList; chromPtr != NULL; chromPtr = chromPtr->next)
     {
     safef(tableName, ArraySize(tableName), "%s_snpTmp", chromPtr->name);
     if (!hTableExists(tableName)) continue;
     verbose(1, "chrom = %s\n", chromPtr->name);
     chromFastaHash = readFasta(chromPtr->name);
     processSnps(chromPtr->name);
     }
 
 for (chromPtr = chromList; chromPtr != NULL; chromPtr = chromPtr->next)
     {
     safef(tableName, ArraySize(tableName), "%s_snpTmp", chromPtr->name);
     if (!hTableExists(tableName)) continue;
     recreateDatabaseTable(chromPtr->name);
     verbose(1, "loading chrom = %s\n", chromPtr->name);
     loadDatabase(chromPtr->name);
     }
 
 carefulClose(&errorFileHandle);
 
 return 0;
 }