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/hgExonerate/hgExonerate.c src/hg/makeDb/outside/hgExonerate/hgExonerate.c
index 93ecb3b..c65792e 100644
--- src/hg/makeDb/outside/hgExonerate/hgExonerate.c
+++ src/hg/makeDb/outside/hgExonerate/hgExonerate.c
@@ -1,183 +1,183 @@
 /* hgExonerate - Convert Exonerate modified GFF files to BED format and load in 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 "cheapcgi.h"
 #include "linefile.h"
 #include "hash.h"
 #include "dystring.h"
 #include "jksql.h"
 
 
 void usage()
 /* Explain usage and exit. */
 {
 errAbort(
   "hgExonerate - Convert Exonerate modified GFF files to BED format and load in database.\n"
   "usage:\n"
   "   hgExonerate database table inputFile\n"
   "options:\n"
   "   -elia    - handle Elia's 11 column GFF's");
 }
 
 char *createString = 
 "CREATE TABLE %s (\n"
     "chrom varchar(255) not null,	# Human chromosome or FPC contig\n"
     "chromStart int unsigned not null,	# Start position in chromosome\n"
     "chromEnd int unsigned not null,	# End position in chromosome\n"
     "name varchar(255) not null,	# Name of other sequence\n"
     "score int unsigned not null,	# Score from 0 to 1000\n"
     "strand char(1) not null,	# + or -\n"
     "otherStart int unsigned not null,	# Start in other sequence\n"
     "otherEnd int unsigned not null,	# End in other sequence\n"
               "#Indices\n"
     "INDEX(chrom(8),chromStart),\n"
     "INDEX(chrom(8),chromEnd),\n"
     "INDEX(name(12))\n"
 ")\n";
 
 void loadIntoDb(char *tabFile, char *database, char *table, boolean clear)
 /* Load database table from tab file. */
 {
 struct sqlConnection *conn = sqlConnect(database);
-struct dyString *dy = newDyString(2048);
+struct dyString *dy = dyStringNew(2048);
 
 sqlDyStringPrintf(dy, createString, table);
 sqlMaybeMakeTable(conn, table, dy->string);
 if (clear)
     {
     dyStringClear(dy);
     sqlDyStringPrintf(dy, "delete from %s", table);
     sqlUpdate(conn, dy->string);
     }
 dyStringClear(dy);
 sqlDyStringPrintf(dy, "LOAD data local infile '%s' into table %s", tabFile, table);
 sqlUpdate(conn, dy->string);
 sqlDisconnect(&conn);
 }
 
 struct hash *hashGroup(struct lineFile *lf, char *s)
 /* Make a little hash from group field. */
 {
 struct hash *hash = newHash(4);
 char *words[2], *e;
 int wordCount;
 
 for (;;)
     {
     s = skipLeadingSpaces(s);
     if (s == NULL || s[0] == 0)
         break;
     e = strchr(s, ';');
     if (e != NULL)
        *e++ = 0;
     wordCount = chopString(s, "=;", words, ArraySize(words));
     if (wordCount != 2)
        errAbort("malformed group line %d of %s\n", lf->lineIx, lf->fileName);
     hashAdd(hash, words[0], cloneString(words[1]));
     if (e == NULL)
        break;
     s = e;
     }
 return hash;
 }
 
 void hgExonerate(char *database, char *table, char *file)
 /* hgExonerate - Convert Exonerate modified GFF files to BED format and load in database.. */
 {
 struct lineFile *lf = lineFileOpen(file, TRUE);
 char *line;
 int lineSize;
 FILE *f;
 char tabFileName[512];
 char *row[12];
 char *parts[6];
 char *subParts[3];
 char *strand;
 int partCount;
 double score;
 int count = 0;
 boolean doElia = cgiBoolean("elia");
 int wordCount;
 
 sprintf(tabFileName, "%s.tab", table);
 f = mustOpen(tabFileName, "w");
 printf("Converting %s to %s\n", file, tabFileName);
 while (lineFileNext(lf, &line, &lineSize))
     {
     if (line[0] == '#')
         continue;
     ++count;
     wordCount = chopTabs(line, row);
     if (wordCount < 9)
         errAbort("Expecting at least 9 words line %d of %s\n", lf->lineIx, lf->fileName);
     fprintf(f, "%s\t", row[0]);				/* chromosome. */
     fprintf(f, "%d\t", lineFileNeedNum(lf, row, 3)-1);       /* chromStart. */
     fprintf(f, "%s\t", row[4]);                         /* chromEnd. */
     score = atof(row[5]) * 0.70;                               
     if (score > 1000) score = 1000;
     if (score < 0) score = 0;
     strand = row[6];
     if (doElia)
         {
 	int start, end;
 	if (wordCount < 10)
 	    errAbort("Expecting at least 10 words line %d of %s\n", lf->lineIx, lf->fileName);
 	if (strand[0] == '-')
 	    {
 	    strand = "-";
 	    start = atoi(row[9])-1;
 	    end = atoi(row[8]);
 	    }
 	else
 	    {
 	    strand = "+";
 	    start = atoi(row[8])-1;
 	    end = atoi(row[9]);
 	    }
 	fprintf(f, "%s\t%d\t%s\t%d\t%d\n", row[7], round(score), strand, start, end);
 	}
     else
 	{
 	if (startsWith("trace=", row[8]))
 	    {
 	    struct hash *hash = hashGroup(lf, row[8]);
 	    char *trace = hashMustFindVal(hash, "trace");
 	    int start = atoi(hashMustFindVal(hash, "hstart")) - 1;
 	    int end = atoi(hashMustFindVal(hash, "hend"));
 	    fprintf(f, "%s\t%d\t%s\t%d\t%d\n", trace, round(score), strand, start, end);
 	    freeHashAndVals(&hash);
 	    }
 	else
 	    {
 	    partCount = chopString(row[8], ".:", parts, ArraySize(parts));
 	    if (partCount != 4)
 	       errAbort("Unparsable field 9 line %d of %s", lf->lineIx, lf->fileName);
 	    fprintf(f, "%s.%s\t", parts[0], parts[1]);          /* name. */
 	    fprintf(f, "%d\t", round(score));			/* milliScore */
 	    fprintf(f, "%s\t", strand);				/* strand */
 	    partCount = chopByChar(parts[2], '-', subParts, ArraySize(subParts));
 	    if (partCount != 2 || !isdigit(subParts[0][0]) || !isdigit(subParts[1][0]))
 	       errAbort("Unparsable number range in field 9 line %d of %s", lf->lineIx, lf->fileName);
 	    fprintf(f, "%d\t", atoi(subParts[0])-1);		/* otherStart */
 	    fprintf(f, "%s\n", subParts[1]);			/* otherEnd */
 	    }
 	}
     }
 carefulClose(&f);
 lineFileClose(&lf);
 
 printf("Loading %d items into table %s in database %s\n", count, table, database);
 loadIntoDb(tabFileName, database, table, TRUE);
 }
 
 int main(int argc, char *argv[])
 /* Process command line. */
 {
 cgiSpoof(&argc, argv);
 if (argc != 4)
     usage();
 hgExonerate(argv[1], argv[2], argv[3]);
 return 0;
 }