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/hgSoftberryHom/hgSoftberryHom.c src/hg/makeDb/outside/hgSoftberryHom/hgSoftberryHom.c
index 22bed92..9114810 100644
--- src/hg/makeDb/outside/hgSoftberryHom/hgSoftberryHom.c
+++ src/hg/makeDb/outside/hgSoftberryHom/hgSoftberryHom.c
@@ -1,107 +1,110 @@
 /* hgSoftberryHom - Make table storing Softberry protein homology information. */
 
 /* 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 "jksql.h"
 
 
 void usage()
 /* Explain usage and exit. */
 {
 errAbort(
   "hgSoftberryHom - Make table storing Softberry protein homology information\n"
   "usage:\n"
   "   hgSoftberryHom database file(s).pro\n");
 }
 
 void makeTabLines(char *fileName, FILE *f)
 /* Loop through file and write out tab-separated records to f. */
 {
 struct lineFile *lf = lineFileOpen(fileName, TRUE);
 char *line, *s, *e, *protParts[128];
 int lineSize, protCount;
 int i;
 char *label, *gi;
 
 while (lineFileNext(lf, &line, &lineSize))
     {
     if (line[0] != '>')
         continue;
     line += 1;
     label = nextWord(&line);
     if (label == NULL)
 	errAbort("Bad format A line %d of %s\n", lf->lineIx, lf->fileName);
     if ((s = strstr(line, "##")) == NULL)
         continue;
     s += 2;
     if ((e = strstr(line, "##")) != NULL)
         *e = 0;
     s = trimSpaces(s);
     protCount = chopString(s, "\001", protParts, ArraySize(protParts));
     if (protCount < 1)
 	errAbort("Bad format C line %d of %s\n", lf->lineIx, lf->fileName);
     for (i=0; i<protCount; ++i)
         {
 	s = protParts[i];
 	gi = nextWord(&s);
 	if (s == NULL) s = "";
 	fprintf(f, "%s\t%s\t%s\n", label, gi, s);
 	}
     }
 lineFileClose(&lf);
 }
 
-/* #Protein homologies behind Softberry genes */
-char *createTable = NOSQLINJ "CREATE TABLE softberryHom (\n"
-    "name varchar(255) not null,	# Softberry gene name\n"
-    "giString varchar(255) not null,	# String with Genbank gi and accession\n"
-    "description longblob not null,	# Freeform (except for no tabs) description\n"
-              "#Indices\n"
-    "PRIMARY KEY(name)\n"
-")\n";
-
 void hgSoftberryHom(char *database, int fileCount, char *files[])
 /* hgSoftberryHom - Make table storing Softberry protein homology information. */
 {
 int i;
 char *fileName;
 char *table = "softberryHom";
 char *tabFileName = "softberryHom.tab";
 FILE *f = mustOpen(tabFileName, "w");
 struct sqlConnection *conn = NULL;
-struct dyString *ds = newDyString(2048);
+struct dyString *ds = dyStringNew(2048);
 
 for (i=0; i<fileCount; ++i)
     {
     fileName = files[i];
     printf("Processing %s\n", fileName);
     makeTabLines(fileName, f);
     }
 carefulClose(&f);
 
 /* Create table if it doesn't exist, delete whatever is
  * already in it, and fill it up from tab file. */
 conn = sqlConnect(database);
 printf("Loading %s table\n", table);
-sqlMaybeMakeTable(conn, table, createTable);
+/* #Protein homologies behind Softberry genes */
+dyStringClear(ds);
+sqlDyStringPrintf(ds, 
+"CREATE TABLE softberryHom (\n"
+    "name varchar(255) not null,	# Softberry gene name\n"
+    "giString varchar(255) not null,	# String with Genbank gi and accession\n"
+    "description longblob not null,	# Freeform (except for no tabs) description\n"
+              "#Indices\n"
+    "PRIMARY KEY(name)\n"
+")\n");
+
+sqlMaybeMakeTable(conn, table, ds->string);
+dyStringClear(ds);
 sqlDyStringPrintf(ds, "DELETE from %s", table);
 sqlUpdate(conn, ds->string);
 dyStringClear(ds);
 sqlDyStringPrintf(ds, "LOAD data local infile '%s' into table %s", 
     tabFileName, table);
 sqlUpdate(conn, ds->string);
 sqlDisconnect(&conn);
 }
 
 int main(int argc, char *argv[])
 /* Process command line. */
 {
 if (argc < 3)
     usage();
 hgSoftberryHom(argv[1], argc-2, argv+2);
 return 0;
 }