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/bioImage/knownToBioImage/knownToBioImage.c src/hg/bioImage/knownToBioImage/knownToBioImage.c
index 86ceb70..179cc35 100644
--- src/hg/bioImage/knownToBioImage/knownToBioImage.c
+++ src/hg/bioImage/knownToBioImage/knownToBioImage.c
@@ -1,192 +1,194 @@
 /* knownToBioImage - Create knownToBioImage table by riffling through various other knownTo tables. */
 
 /* 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"
 #include "hgRelate.h"
 #include "bioImage.h"
 
 void usage()
 /* Explain usage and exit. */
 {
 errAbort(
   "knownToBioImage - Create knownToBioImage table by riffling through various other knownTo tables\n"
   "usage:\n"
   "   knownToBioImage database\n"
   "options:\n"
   "   -xxx=XXX\n"
   );
 }
 
 static struct optionSpec options[] = {
    {NULL, 0},
 };
 
 struct prioritizedImage 
     {
     int imageId;	/* ID of image */
     float priority;	/* Image priority - smaller is more urgent */
     };
 
 void createTable(struct sqlConnection *conn, char *tableName)
 /* Create our name/value table, dropping if it already exists. */
 {
 struct dyString *dy = dyStringNew(512);
 sqlDyStringPrintf(dy, 
 "CREATE TABLE  %s (\n"
 "    name varchar(255) not null,\n"
 "    value varchar(255) not null,\n"
 "              #Indices\n"
 "    PRIMARY KEY(name(16)),\n"
 "    INDEX(value(16))\n"
 ")\n",  tableName);
 sqlRemakeTable(conn, tableName, dy->string);
 dyStringFree(&dy);
 }
 
 void addPrioritizedImage(struct hash *hash, int id, float priority, char *key)
 /* Add image to hash, replacing what's already there if we have a better priority */
 {
 struct prioritizedImage *pi = hashFindVal(hash, key);
 if (pi == NULL)
     {
     AllocVar(pi);
     pi->imageId = id;
     pi->priority = priority;
     hashAdd(hash, key, pi);
     }
 else if (pi->priority > priority)
     {
     pi->imageId = id;
     pi->priority = priority;
     }
 }
 
 void foldIntoHash(struct sqlConnection *conn, char *table, char *keyField, char *valField,
 	struct hash *hash)
 /* Add key/value pairs from table into hash */
 {
 struct sqlResult *sr;
 char query[256];
 char **row;
 sqlSafef(query, sizeof(query), "select %s,%s from %s", keyField, valField, table);
 sr = sqlGetResult(conn, query);
 while ((row = sqlNextRow(sr)) != NULL)
     hashAdd(hash, row[0], cloneString(row[1]));
 sqlFreeResult(&sr);
 }
 
 int bestImage(char *kgId, struct hash *kgToHash, struct hash *imageHash)
 /* Return best image id if possible, otherwise 0 */
 {
 struct hashEl *extId = hashLookup(kgToHash, kgId);
 
 while (extId != NULL)
     {
     struct prioritizedImage *pi = hashFindVal(imageHash, extId->val);
     if (pi != NULL)
 	return pi->imageId;
     extId = hashLookupNext(extId);
     }
 return 0;
 }
 
 void knownToBioImage(char *database)
 /* knownToBioImage - Create knownToBioImage table by riffling through various other knownTo tables. */
 {
 char *tempDir = ".";
 char *outTable = "knownToBioImage";
 FILE *f = hgCreateTabFile(tempDir, outTable);
 struct sqlConnection *hConn = sqlConnect(database);
 struct sqlConnection *iConn = sqlConnect("bioImage");
 struct sqlResult *sr;
 char **row;
 struct hash *geneImageHash = newHash(18);
 struct hash *locusLinkImageHash = newHash(18);
 struct hash *refSeqImageHash = newHash(18);
 struct hash *genbankImageHash = newHash(18);
 struct hash *knownToLocusLinkHash = newHash(18);
 struct hash *knownToRefSeqHash = newHash(18);
 struct hash *knownToGeneHash = newHash(18);
 struct slName *knownList = NULL, *known;
 struct hash *dupeHash = newHash(17);
+char query[1024];
 
 /* Go through and make up hashes of images keyed by various fields. */
-sr = sqlGetResult(iConn, 
-	NOSQLINJ "select id,priority,gene,locusLink,refSeq,genbank from image");
+sqlSafef(query, sizeof query, "select id,priority,gene,locusLink,refSeq,genbank from image");
+sr = sqlGetResult(iConn, query);
 while ((row = sqlNextRow(sr)) != NULL)
     {
     int id = sqlUnsigned(row[0]);
     float priority = atof(row[1]);
     addPrioritizedImage(geneImageHash, id, priority, row[2]);
     addPrioritizedImage(locusLinkImageHash, id, priority, row[3]);
     addPrioritizedImage(refSeqImageHash, id, priority, row[4]);
     addPrioritizedImage(genbankImageHash, id, priority, row[5]);
     }
 uglyf("Made hashes of image: geneImageHash %d, locusLinkImageHash %d, refSeqImageHash %d, genbankImageHash %d\n", geneImageHash->elCount, locusLinkImageHash->elCount, refSeqImageHash->elCount, genbankImageHash->elCount);
 sqlFreeResult(&sr);
 
 /* Build up list of known genes. */
-sr = sqlGetResult(hConn, NOSQLINJ "select name from knownGene");
+sqlSafef(query, sizeof query, "select name from knownGene");
+sr = sqlGetResult(hConn, query);
 while ((row = sqlNextRow(sr)) != NULL)
     {
     char *name = row[0];
     if (!hashLookup(dupeHash, name))
         {
 	hashAdd(dupeHash, name, NULL);
 	known = slNameNew(name);
 	slAddHead(&knownList, known);
 	}
     }
 slReverse(&knownList);
 sqlFreeResult(&sr);
 
 /* Build up hashes from knownGene to other things. */
 foldIntoHash(hConn, "knownToLocusLink", "name", "value", knownToLocusLinkHash);
 foldIntoHash(hConn, "knownToRefSeq", "name", "value", knownToRefSeqHash);
 foldIntoHash(hConn, "kgAlias", "kgID", "alias", knownToGeneHash);
 foldIntoHash(hConn, "kgProtAlias", "kgID", "alias", knownToGeneHash);
 uglyf("knownToLocusLink %d, knownToRefSeq %d, knownToGene %d\n", knownToLocusLinkHash->elCount, knownToRefSeqHash->elCount, knownToGeneHash->elCount);
 
 /* Try and find an image for each gene. */
 for (known = knownList; known != NULL; known = known->next)
     {
     char *name = known->name;
     int imageId = 0;
 
     imageId = bestImage(name, knownToLocusLinkHash, locusLinkImageHash);
     if (imageId == 0)
         imageId = bestImage(name, knownToRefSeqHash, refSeqImageHash);
     if (imageId == 0)
 	{
 	struct prioritizedImage *pi = hashFindVal(genbankImageHash, name);
 	if (pi != NULL)
 	    imageId = pi->imageId;
 	}
     if (imageId == 0)
         imageId = bestImage(name, knownToGeneHash, geneImageHash);
     if (imageId != 0)
         {
 	fprintf(f, "%s\t%d\n", name, imageId);
 	}
     }
 
 createTable(hConn, outTable);
 hgLoadTabFile(hConn, tempDir, outTable, &f);
 hgRemoveTabFile(tempDir, outTable);
 }
 
 int main(int argc, char *argv[])
 /* Process command line. */
 {
 optionInit(&argc, argv, options);
 if (argc != 2)
     usage();
 knownToBioImage(argv[1]);
 return 0;
 }