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/hgSanger20/hgSanger20.c src/hg/makeDb/hgSanger20/hgSanger20.c
index 29d162f..78a5048 100644
--- src/hg/makeDb/hgSanger20/hgSanger20.c
+++ src/hg/makeDb/hgSanger20/hgSanger20.c
@@ -1,194 +1,194 @@
 /* hgSanger20 - Load extra info from Sanger Chromosome 20 annotations.. */
 
 /* 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 "linefile.h"
 #include "hash.h"
 #include "dystring.h"
 #include "cheapcgi.h"
 #include "obscure.h"
 #include "jksql.h"
 #include "sanger22extra.h"
 #include "gff.h"
 #include "genePred.h"
 
 
 
 void usage()
 /* Explain usage and exit. */
 {
 errAbort(
   "hgSanger20 - Load extra info from Sanger Chromosome 20 annotations.\n"
   "usage:\n"
   "   hgSanger20 database sanger20.gff sanger20.info\n"
   "options:\n"
   "   -xxx=XXX\n"
   );
 }
 
 void finishRecord(struct sanger22extra *sx, struct dyString *dy)
 /* Finish off record. */
 {
 if (sx != NULL)
     {
     sx->description = cloneString(dy->string);
     dyStringClear(dy);
     }
 }
 
 struct hash *readInfoFile(char *fileName)
 /* Read in 'info' file into hash keyed by gene field and
  * containing a partial sanger22extra. */
 {
 struct hash *infoHash = newHash(0);
 struct lineFile *lf = lineFileOpen(fileName, TRUE);
 char *line, *type, *val;
-struct dyString *dy = newDyString(512);
+struct dyString *dy = dyStringNew(512);
 struct sanger22extra *sx = NULL;
 
 while (lineFileNext(lf, &line, NULL))
     {
     line = skipLeadingSpaces(line);
     if (line[0] == 0)
         {
 	finishRecord(sx, dy);
 	sx = NULL;
 	}
     else 
         {
 	if (sx == NULL)
 	    AllocVar(sx);
 	type = nextWord(&line);
 	val = strchr(line, '"');
 	if (val == NULL)
 	   errAbort("No quoted value line %d of %s\n", lf->lineIx, lf->fileName);
 	parseQuotedString(val, val, &line);
 	if (sameString("Gene", type))
 	    {
 	    sx->name = cloneString(val);
 	    hashAdd(infoHash, val, sx);
 	    }
 	else if (sameString("Remark", type))
 	    {
 	    dyStringAppend(dy, val);
 	    dyStringAppend(dy, ". ");
 	    }
 	}
     }
 finishRecord(sx, dy);
 lineFileClose(&lf);
 return infoHash;
 }
 
 char *needNextWord(char **pLine, struct lineFile *lf)
 /* Get next word or die. */
 {
 char *res = nextWord(pLine);
 if (res == NULL)
     errAbort("Bad line %d in %s\n", lf->lineIx, lf->fileName);
 return res;
 }
 
 void chopSemi(char *s)
 /* Remove trailing semicolon. */
 {
 int len = strlen(s);
 if (s[len-1] == ';')
    s[len-1] = 0;
 }
 
 struct sanger22extra *processGff(char *fileName, struct hash *infoHash)
 /* Process gff file and return a list of sanger22 extras. */
 {
 struct lineFile *lf = lineFileOpen(fileName, TRUE);
 struct hash *hash = newHash(0);
 struct sanger22extra *sxList = NULL, *sx, *info;
 char *line, *source, *type, *word;
 
 while (lineFileNext(lf, &line, NULL))
     {
     char *gene = NULL, *transcript = NULL;
     line = skipLeadingSpaces(line);
     if (line[0] == 0 || line[0] == '#')
         continue;
     word = needNextWord(&line, lf);	/* Skip chr20 */
     source = needNextWord(&line, lf);	
     type = needNextWord(&line, lf);
     if (sameString(type, "CDS") || sameString(type, "Exon"))
 	{
 	while (gene == NULL || transcript == NULL)
 	    {
 	    word = needNextWord(&line, lf);
 	    if (sameString(word, "gene_id"))
 		{
 		gene = needNextWord(&line, lf);
 		chopSemi(gene);
 		}
 	    else if (sameString(word, "transcript_id"))
 		{
 		transcript = needNextWord(&line, lf);
 		chopSemi(transcript);
 		}
 	    }
 	sx = hashFindVal(hash, transcript);
 	if (sx == NULL)
 	    {
 	    AllocVar(sx);
 	    sx->name = cloneString(transcript);
 	    sx->locus = cloneString(gene);
 	    sx->geneType = cloneString(source);
 	    sx->cdsType = cloneString("");
 	    if ((info = hashFindVal(infoHash, gene)) == NULL)
 	       sx->description = "";
 	    else
 	       sx->description = cloneString(info->description);
 	    hashAdd(hash, transcript, sx);
 	    slAddHead(&sxList, sx);
 	    }
 	}
     }
 hashFree(&hash);
 lineFileClose(&lf);
 slReverse(&sxList);
 return sxList;
 }
 
 void loadIntoDatabase(char *database, char *createString, char *table, char *tabName)
 /* Load tabbed file into database table. */
 {
 struct sqlConnection *conn = sqlConnect(database);
-struct dyString *ds = newDyString(2048);
+struct dyString *ds = dyStringNew(2048);
 dyStringPrintf(ds, createString, table);
 sqlRemakeTable(conn, table, ds->string);
 dyStringClear(ds);
 sqlDyStringPrintf(ds, 
    "LOAD data local infile '%s' into table %s", tabName, table);
 sqlUpdate(conn, ds->string);
 sqlDisconnect(&conn);
-freeDyString(&ds);
+dyStringFree(&ds);
 }
 
 void hgSanger20(char *database, char *gffFile, char *infoFile)
 /* Process chromosome 20 gff file. */
 {
 struct hash *infoHash = readInfoFile(infoFile);
 struct sanger22extra *sxList = processGff(gffFile, infoHash), *sx;
 char *tabName = "extra.tab";
 FILE *f = mustOpen(tabName, "w");
 for (sx = sxList; sx != NULL; sx = sx->next)
     sanger22extraTabOut(sx, f);
 carefulClose(&f);
 loadIntoDatabase(database, sanger22extraCreate, "sanger20extra", tabName);
 }
 
 
 int main(int argc, char *argv[])
 /* Process command line. */
 {
 cgiSpoof(&argc, argv);
 if (argc != 4)
     usage();
 hgSanger20(argv[1], argv[2], argv[3]);
 return 0;
 }