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/hgVisiGene/fullTextExperiment.c src/hg/visiGene/hgVisiGene/fullTextExperiment.c
index 55b3ceb..85575d0 100644
--- src/hg/visiGene/hgVisiGene/fullTextExperiment.c
+++ src/hg/visiGene/hgVisiGene/fullTextExperiment.c
@@ -1,167 +1,169 @@
 /* fullTextExperiment - VisiGene search using full text.
  * This ends up not working so well - it's not specific
  * enough.  I'm checking it in in case want to try another
  * pass at it later. */
 
 /* 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 "options.h" 
 #include "dystring.h"
 #include "bits.h"
 #include "obscure.h"
 #include "rbTree.h"
 #include "jksql.h"
 #include "visiGene.h"
 #include "visiSearch.h"
 #include "trix.h"
 
 void visiMatchFree(struct visiMatch **pMatch)
 /* Free up memory associated with visiMatch */
 {
 struct visiMatch *match = *pMatch;
 if (match != NULL)
     {
 #ifdef OLD
     bitFree(&match->wordBits);
 #endif /* OLD */
     freez(pMatch);
     }
 }
 
 void visiMatchFreeList(struct visiMatch **pList)
 /* Free up memory associated with list of visiMatch */
 {
 struct visiMatch *el, *next;
 
 for (el = *pList; el != NULL; el = next)
     {
     next = el->next;
     visiMatchFree(&el);
     }
 *pList = NULL;
 }
 
 static int visiMatchCmpImageId(void *va, void *vb)
 /* rbTree comparison function to tree on imageId. */
 {
 struct visiMatch *a = va, *b = vb;
 return a->imageId - b->imageId;
 }
 
 int visiMatchCmpWeight(const void *va, const void *vb)
 /* Compare to sort based on match. */
 {
 const struct visiMatch *a = *((struct visiMatch **)va);
 const struct visiMatch *b = *((struct visiMatch **)vb);
 double dif = b->weight - a->weight;
 if (dif > 0)
    return 1;
 else if (dif < 0)
    return -1;
 else
    return 0;
 }
 
 static struct hash *makePrivateHash(struct sqlConnection *conn)
 /* Build up hash of all submission sets that are private.
  * This is keyed by the ascii version of submissionSet.id */
 {
 struct hash *hash = hashNew(0);
 if (sqlFieldIndex(conn, "submissionSet", "privateUser") >= 0)
     {
     struct sqlResult *sr;
     char **row;
-    sr = sqlGetResult(conn, NOSQLINJ "select id from submissionSet where privateUser!=0");
+    char query[1024];
+    sqlSafef(query, sizeof query, "select id from submissionSet where privateUser!=0");
+    sr = sqlGetResult(conn, query);
     while ((row = sqlNextRow(sr)) != NULL)
         hashAdd(hash, row[0], NULL);
     sqlFreeResult(&sr);
     }
 return hash;
 }
 
 static boolean isPrivate(struct sqlConnection *conn,
 	struct hash *privateHash, char *imageId)
 /* Return TRUE if image is associated with private submissionSet. */
 {
 char *src, buf[16];
 char query[256];
 sqlSafef(query, sizeof(query), "select submissionSet from image where id='%s'",
 	imageId);
 src = sqlQuickQuery(conn, query, buf, sizeof(buf));
 if (src != NULL && hashLookup(privateHash, src) != NULL)
     return TRUE;
 return FALSE;
 }
 
 static struct visiMatch *matchGeneName(struct sqlConnection *conn, 
 	char *symbol, struct hash *privateHash)
 /* Return matching list if it's a gene symbol. */
 {
 struct visiMatch *matchList = NULL, *match;
 struct slInt *imageList, *image;
 char *sqlPat = sqlLikeFromWild(symbol);
 if (sqlWildcardIn(sqlPat))
     imageList = visiGeneSelectNamed(conn, sqlPat, vgsLike);
 else
     imageList = visiGeneSelectNamed(conn, sqlPat, vgsExact);
 for (image = imageList; image != NULL; image = image->next)
     {
     char asciiId[16];
     safef(asciiId, sizeof(asciiId), "%d", image->val);
     if (!isPrivate(conn, privateHash, asciiId))
 	{
 	AllocVar(match);
 	match->imageId = image->val;
 	slAddHead(&matchList, match);
 	}
     }
 slReverse(&matchList);
 return matchList;
 }
 
 
 struct visiMatch *visiSearch(struct sqlConnection *conn, char *searchString)
 /* visiSearch - return list of images that match searchString sorted
  * by how well they match. This will search most fields in the
  * database. */
 {
 char *dupe = cloneString(searchString);
 struct trix *trix = trixOpen("visiGeneData/visiGene.ix");
 struct trixSearchResult *tsrList, *tsr;
 struct visiMatch *matchList = NULL, *match;
 int wordCount = chopByWhite(dupe, NULL, 0);
 char **words;
 boolean hasWild;
 struct hash *privateHash = makePrivateHash(conn);
 
 tolowers(dupe);
 hasWild = (strchr(searchString, '*') != NULL);
 if (hasWild)
     stripChar(dupe, '*');
 AllocArray(words, wordCount);
 chopByWhite(dupe, words, wordCount);
 /* if (wordCount != 1 || 
 	(matchList = matchGeneName(conn, words[0],privateHash)) == NULL) */
     {
     tsrList = trixSearch(trix, wordCount, words, hasWild ? tsmExpand : tsmExact);
     for (tsr = tsrList; tsr != NULL; tsr = tsr->next)
 	{
 	if (!isPrivate(conn, privateHash, tsr->itemId))
 	    {
 	    AllocVar(match);
 	    match->imageId = sqlUnsigned(tsr->itemId);
 	    slAddHead(&matchList, match);
 	    }
 	}
     trixSearchResultFreeList(&tsrList);
     trixClose(&trix);
     slReverse(&matchList);
     }
 freeMem(dupe);
 return matchList;
 }