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/visiGene/vgRemoveSubmission/vgRemoveSubmission.c src/hg/visiGene/vgRemoveSubmission/vgRemoveSubmission.c
index 314f82c..9757f0d 100644
--- src/hg/visiGene/vgRemoveSubmission/vgRemoveSubmission.c
+++ src/hg/visiGene/vgRemoveSubmission/vgRemoveSubmission.c
@@ -1,170 +1,177 @@
 /* vgRemoveSubmission - Remove submissionSet and associated images.. */
 
 /* 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 "options.h"
 #include "jksql.h"
 
 
 boolean testOnly = FALSE;
 
 void usage()
 /* Explain usage and exit. */
 {
 errAbort(
   "vgRemoveSubmission - Remove submissionSet and associated images.\n"
   "usage:\n"
   "   vgRemoveSubmission database submissionSetId\n"
   "example:\n"
   "   vgRemoveSubmission visiGene 704\n"
   "options:\n"
   "   -testOnly  Report how many records would delete, but don't delete them\n"
   "   -verbose=N Set verbosity level.  0 for silent.  1 (default) for record counts\n"
   "              2 to see sql statements\n"
   "Note: submission contributors, probes, and genes will still be listed in\n"
   "      respective tables, since these are shared with other submission sets.\n"
   );
 }
 
 static struct optionSpec options[] = {
    {"testOnly", OPTION_BOOLEAN},
    {NULL, 0},
 };
 
 void maybeUpdate(struct sqlConnection *conn, char *sql)
 /* Update database if not in testing only mode. */
 {
 verbose(2, "%s\n", sql);
 if (!testOnly)
     sqlUpdate(conn, sql);
 }
 
 void intInClause(struct dyString *query, struct slInt *list)
 /* Add in clause to query for all integers in list. */
 {
 struct slInt *el;
 sqlDyStringPrintf(query, " in (");
 for (el = list; el != NULL; el = el->next)
     {
     sqlDyStringPrintf(query, "%d", el->val);
     if (el->next != NULL)
 	sqlDyStringPrintf(query, ",");
     }
 sqlDyStringPrintf(query, ") ");
 }
 
 void vgRemoveSubmission(char *database, char *submissionSetId)
 /* vgRemoveSubmission - Remove submissionSet and associated images.. */
 {
 struct sqlConnection *conn = sqlConnect(database);
 int submitId = atoi(submissionSetId);
 char *submitName;
 struct dyString *query = dyStringNew(0);
 struct slInt *imageList = NULL, *imageProbeList = NULL;
 int imageFileCount, contributorCount;
 
 /* As a sanity check get the name of submission set and print it */
 sqlDyStringPrintf(query, "select name from submissionSet where id=%d",
 	submitId);
 submitName = sqlQuickString(conn, query->string);
 if (submitName == NULL)
     errAbort("No submissionSetId %s in %s", submissionSetId, database);
 verbose(1, "Removing submissionSet named %s\n", submitName);
 
 /* Figure out how many submissionContributors we'll delete. */
 dyStringClear(query);
 sqlDyStringPrintf(query, 
 	"select count(*) from submissionContributor where submissionSet=%d",
 	submitId);
 contributorCount = sqlQuickNum(conn, query->string);
 
 /* Actually delete submissionContributors. */
 dyStringClear(query);
 sqlDyStringPrintf(query, 
     "delete from submissionContributor where submissionSet=%d", submitId);
 maybeUpdate(conn, query->string);
 verbose(1, "Deleted %d submissionContributors\n", contributorCount);
 
 /* Get list of images we'll delete. */
 dyStringClear(query);
 sqlDyStringPrintf(query, 
     "select id from image where submissionSet=%d", submitId);
 imageList = sqlQuickNumList(conn, query->string);
 
 /* Get list of imageProbes. */
 if (imageList != NULL)
     {
     dyStringClear(query);
     sqlDyStringPrintf(query, 
 	"select id from imageProbe where image ");
     intInClause(query, imageList);
     imageProbeList = sqlQuickNumList(conn, query->string);
     }
 
 
 /* Delete expressionLevel's tied to imageProbes. */
 if (imageProbeList != NULL)
     {
-    int oldExpLevel = sqlQuickNum(conn, NOSQLINJ "select count(*) from expressionLevel");
+
+    dyStringClear(query);
+    sqlDyStringPrintf(query, 
+	"select count(*) from expressionLevel");
+    int oldExpLevel = sqlQuickNum(conn, query->string);
     int newExpLevel;
     dyStringClear(query);
     sqlDyStringPrintf(query, 
 	"delete from expressionLevel where imageProbe ");
     intInClause(query, imageProbeList);
     maybeUpdate(conn, query->string);
-    newExpLevel = sqlQuickNum(conn, NOSQLINJ "select count(*) from expressionLevel");
+    dyStringClear(query);
+    sqlDyStringPrintf(query, 
+	"select count(*) from expressionLevel");
+    newExpLevel = sqlQuickNum(conn, query->string);
     verbose(1, "Deleted %d expressionLevels\n", oldExpLevel - newExpLevel);
     }
 
 /* Delete image probes. */
 if (imageProbeList != NULL)
     {
     dyStringClear(query);
     sqlDyStringPrintf(query, 
 	"delete from imageProbe where image ");
     intInClause(query, imageList);
     maybeUpdate(conn, query->string);
     }
 verbose(1, "Deleted %d image probes.\n", slCount(imageProbeList));
 
 /* Delete images. */
 dyStringClear(query);
 sqlDyStringPrintf(query, "delete from image where submissionSet=%d", submitId);
 maybeUpdate(conn, query->string);
 verbose(1, "Deleted %d images.\n", slCount(imageList));
 
 /* Delete imageFiles. */
 dyStringClear(query);
 sqlDyStringPrintf(query, "select count(*) from imageFile where submissionSet=%d", 
 	submitId);
 imageFileCount = sqlQuickNum(conn, query->string);
 dyStringClear(query);
 sqlDyStringPrintf(query, "delete from imageFile where submissionSet=%d", 
 	submitId);
 maybeUpdate(conn, query->string);
 verbose(1, "Deleted %d imageFile records.\n", imageFileCount);
 
 /* Delete submissionSet record. */
 dyStringClear(query);
 sqlDyStringPrintf(query, "delete from submissionSet where id=%d", submitId);
 maybeUpdate(conn, query->string);
 
 dyStringFree(&query);
 slFreeList(&imageList);
 sqlDisconnect(&conn);
 }
 
 int main(int argc, char *argv[])
 /* Process command line. */
 {
 optionInit(&argc, argv, options);
 if (argc != 3)
     usage();
 testOnly = optionExists("testOnly");
 vgRemoveSubmission(argv[1], argv[2]);
 return 0;
 }