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/hgWaba/hgWaba.c src/hg/makeDb/hgWaba/hgWaba.c
index 7864f67..d5f5530 100644
--- src/hg/makeDb/hgWaba/hgWaba.c
+++ src/hg/makeDb/hgWaba/hgWaba.c
@@ -1,191 +1,191 @@
 /* hgWaba - load Waba alignments into database. */
 
 /* 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 "dystring.h"
 #include "xa.h"
 #include "jksql.h"
 
 
 void usage()
 /* Explain usage and exit. */
 {
 errAbort(
   "hgWaba - load Waba alignments into database\n"
   "usage:\n"
   "   hgWaba database species chromosome offset file(s).wab\n"
   "example:\n"
   "   hgWaba hg3 tet chr20 0 waba/*.wab\n");
 }
 
 
 char *wabaChromCreate = 
 /* An abbreviated table just for quick display. */
 "CREATE TABLE %s (\n"
 "    query varchar(255) not null,       # Name of foreign sequence\n"
 "    chromStart int unsigned not null,  # Start in genomic sequence\n"
 "    chromEnd int unsigned not null,    # End in genomic sequence\n"
 "    strand char(1) not null,           # Relative orientation\n"
 "    milliScore int unsigned not null,  # Identity in parts per thousand\n"
 "    squeezedSym longblob not null,     # HMM symbols with target inserts squeezed out\n"
 "           #Indices\n"
 "   INDEX(chromStart),\n"
 "   INDEX(chromEnd)\n"
 ")";
 
 char *wabaFullCreate =
 /* A full table for reference. */
 "CREATE TABLE %s (\n"
 "   query varchar(255) not null,       # Name of foreign sequence\n"
 "   qStart int unsigned not null,      # Start of alignment in query\n"
 "   qEnd int unsigned not null,        # End of alignment in query\n"
 "   qStrand char(1) not null,          # Which strand\n"
 "   chrom varchar(255) not null,       # Which chromosome.\n"
 "   chromStart int unsigned not null,  # Start in chromosome sequence\n"
 "   chromEnd int unsigned not null,    # End in chromosome sequence\n"
 "   milliScore int unsigned not null,  # Identity in parts per thousand\n"
 "   symCount int unsigned not null,    # Number of symbols in following blobs\n"
 "   qSym longblob not null,            # Query sequence and insert chars.\n"
 "   tSym longblob not null,            # Target sequence and insert chars.\n"
 "   hSym longblob not null,            # HMM symbols\n"
 "           #Indices\n"
 "   INDEX(query(16)),\n"
 "   INDEX(chrom(16), chromStart)\n"
 ")";
 
 int xaAliCmpTstart(const void *va, const void *vb)
 /* Compare two xaAli's to sort by ascending tStart positions. */
 {
 const struct xaAli *a = *((struct xaAli **)va);
 const struct xaAli *b = *((struct xaAli **)vb);
 return a->tStart - b->tStart;
 }
 
 int squeezeSym(char *tSym, char *hSym, int inCount, char *outSym)
 /* Copy hSym to outSym except where tSym has '-'s.  Return
  * size of outSym. */
 {
 int readIx, writeIx = 0;
 
 for (readIx = 0; readIx < inCount; ++readIx)
     {
     if (tSym[readIx] != '-')
 	outSym[writeIx++] = hSym[readIx];
     }
 return writeIx;
 }
 
 void hgWaba(char *database, char *species, char *chromosome, 
 	int chromOffset, int wabaFileCount, char *wabaFile[])
 /* hgWaba - load Waba alignments into database. */
 {
 struct sqlConnection *conn = sqlConnect(database);
 FILE *fullTab, *chromTab;
 FILE *in;
 struct xaAli *xa, *xaList = NULL;
 char fullTabName[512], chromTabName[512];
 char fullTable[128], chromTable[128];
 char *inFile;
 int i;
-struct dyString *query = newDyString(2048);
+struct dyString *query = dyStringNew(2048);
 
 /* Loop through each waba file grabbing sequence into
  * memory, then sort. */
 for (i = 0; i < wabaFileCount; ++i)
     {
     inFile = wabaFile[i];
     printf("Processing %s\n", inFile);
     in = xaOpenVerify(inFile);
 
     while ((xa = xaReadNext(in, FALSE)) != NULL)
         {
 	xa->tStart += chromOffset;
 	xa->tEnd += chromOffset;
 	slAddHead(&xaList, xa);
 	}
     carefulClose(&in);
     }
 printf("Sorting %d alignments by chromosome position\n", slCount(xaList));
 slSort(&xaList, xaAliCmpTstart);
 
 /* Create names of tables and the tables themselves. 
  * Clear anything in the chrom table. */
 sprintf(fullTable, "waba%s", species);
 sprintf(chromTable, "%s_waba%s", chromosome, species);
 dyStringClear(query);
 sqlDyStringPrintf(query, wabaFullCreate, fullTable);
 sqlMaybeMakeTable(conn, fullTable, query->string);
 dyStringClear(query);
 sqlDyStringPrintf(query, wabaChromCreate, chromTable);
 sqlMaybeMakeTable(conn, chromTable, query->string);
 if (chromOffset == 0)
     {
     dyStringClear(query);
     sqlDyStringPrintf(query, "DELETE from %s", chromTable);
     sqlUpdate(conn, query->string);
     }
 
 /* Make a temp file for each table we'll update. */
 strcpy(fullTabName, "full_waba.tab");
 fullTab = mustOpen(fullTabName, "w");
 strcpy(chromTabName, "chrom_waba.tab");	
 chromTab = mustOpen(chromTabName, "w");
 
 /* Write out tab-delimited files. */
 printf("Writing tab-delimited files\n");
 for (xa = xaList; xa != NULL; xa = xa->next)
     {
     int squeezedSize;
     squeezedSize = squeezeSym(xa->tSym, xa->hSym, xa->symCount, xa->hSym);
     if( squeezedSize != xa->tEnd - xa->tStart ) {
 		printf("%s squeezedSize: %d, tEnd, tStart: %d, %d, diff: %d\n", xa->query, squeezedSize, xa->tEnd, xa->tStart, xa->tEnd - xa->tStart );
         } else {
     fprintf(fullTab, "%s\t%d\t%d\t%c\t%s\t%d\t%d\t%d\t%d\t%s\t%s\t%s\n",
     	/*xa->query, xa->qStart, xa->qEnd, xa->qStrand,*/
     	xa->name, xa->qStart, xa->qEnd, xa->qStrand,
 	chromosome, xa->tStart, xa->tEnd,
 	xa->milliScore, xa->symCount, 
 	xa->qSym, xa->tSym, xa->hSym);
     assert(squeezedSize == xa->tEnd - xa->tStart);
     fprintf(chromTab, "%s\t%d\t%d\t%c\t%d\t%s\n",
         /*xa->query, xa->tStart, xa->tEnd, xa->qStrand,*/
         xa->name, xa->tStart, xa->tEnd, xa->qStrand,
 	xa->milliScore, xa->hSym);
         }
     }
 fclose(fullTab);
 fclose(chromTab);
 
 printf("Loading %s table in %s\n", chromTable, database);
 dyStringClear(query);
 sqlDyStringPrintf(query, 
    "LOAD data local infile '%s' into table %s", chromTabName, chromTable);
 sqlUpdate(conn, query->string);
 
 printf("Loading %s table in %s\n", fullTable, database);
 dyStringClear(query);
 sqlDyStringPrintf(query, 
    "LOAD data local infile '%s' into table %s", fullTabName, fullTable);
 sqlUpdate(conn, query->string);
 
 printf("Done!\n");
 
 // remove(fullTabName);
 // remove(chromTabName);
 sqlDisconnect(&conn);
-freeDyString(&query);
+dyStringFree(&query);
 }
 
 
 
 int main(int argc, char *argv[])
 /* Process command line. */
 {
 if (argc < 6)
     usage();
 if (!isdigit(argv[4][0]))
     usage();
 hgWaba(argv[1], argv[2], argv[3], atoi(argv[4]), argc-5, argv+5);
 return 0;
 }