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/hgLinkIn/handlerList.c src/hg/hgLinkIn/handlerList.c
index 3e6dcec..2e5901a 100644
--- src/hg/hgLinkIn/handlerList.c
+++ src/hg/hgLinkIn/handlerList.c
@@ -1,214 +1,214 @@
 /* Copyright (C) 2017 The Regents of the University of California
  * See kent/LICENSE or http://genome.ucsc.edu/license/ for licensing information. */
 
 /* handlerList - a list of handler functions for translating identifiers
  * from different external databases to browser positions.  Used by
  * linkInHandlers.c. */
 
 #include "common.h"
 #include "hdb.h"
 #include "jksql.h"
 #include "handlerList.h"
 
 /********************************************
  *      UniProtKB Handler
  *******************************************/
 
 /* Databases whose IDs we can link to using the position parameter.  ... this varies by database,
  * so be restrictive.  Ordered by preference. */
 /* 1 = EMBL, 2 = RefSeq, */
 #define UniProtExtRefSeqId 2
 #define UniProtExtEMBLId 1
 
 /*
  * +---------+--------------+----+-----+------+--+
  * |     acc |     char(12) | NO | MUL | NULL |  |
  * |   extDb |      int(11) | NO |     | NULL |  |
  * | extAcc1 | varchar(255) | NO | MUL | NULL |  |
  * | extAcc2 | varchar(255) | NO |     | NULL |  |
  * | extAcc3 | varchar(255) | NO |     | NULL |  |
  * +---------+--------------+----+-----+------+--+
  *
  * Looks like UniProt marks the end of the IDs list on
  * each line with a '-'.  Supplementary material may follow
  * in the extra field(s), e.g.
  * P01892  1       M86404  -       NOT_ANNOTATED_CDS
  */
 
 
 void addIdsToList(struct slName **listPtr, char **ids, int count)
 /* Given a list of alternate identifiers taken from the uniProt
  * table, add them to the supplied list.  The identifiers list is
  * terminated with a '-' */
 {
 int i=0;
 for (i=0; i<count; i++)
     {
     if (sameString(ids[i], "-"))
         break;
     slNameStore(listPtr, ids[i]);
     }
 }
 
 
 char *uniProtAccToDb(char *id, struct sqlConnection *conn)
 /* Searches the uniProt database (which conn must be connected to)
  * for the given identifier and returns the name of the database
  * that is most relevant.  This is usually the default assembly
  * for the genome that the identifier is on. */
 {
 char *db = NULL;
 char query[4096];
 sqlSafef(query, sizeof(query), "select taxon from accToTaxon where acc = '%s'", id);
 int taxon = sqlQuickNum(conn, query);
 if (taxon != 0)
     db = hDbForTaxon(taxon);
 return db;
 }
 
 
 struct linkInResult *getEmblList(char *db, struct slName *emblNames, struct sqlConnection *conn)
 /* Given a connection to a genome database (e.g., hg19), the name of that database, and
  * a list of identifiers, search for any EMBL mRNA names that we have positions for.
  * Return a list of matching positions. */
 {
 struct linkInResult *results = NULL;
 bool hasMRna = sqlTableExists(conn, "all_mrna");
 if (!hasMRna)
     return NULL;
 struct dyString *query = dyStringNew(0);
 sqlDyStringPrintf(query, "select tName, tStart, tEnd from all_mrna where qName in (");
 struct slName *thisName = emblNames;
 bool firstName = TRUE;
 while (thisName != NULL)
     {
     if (firstName)
         {
-        sqlDyStringPrintfFrag(query, "'%s'", thisName->name);
+        sqlDyStringPrintf(query, "'%s'", thisName->name);
         firstName = FALSE;
         }
     else
-        sqlDyStringPrintfFrag(query, ",'%s'", thisName->name);
+        sqlDyStringPrintf(query, ",'%s'", thisName->name);
     thisName = thisName->next;
     }
-sqlDyStringPrintfFrag(query, ")");
+sqlDyStringPrintf(query, ")");
 struct sqlResult *sr = sqlGetResult(conn, dyStringContents(query));
 char **row = NULL;
 while ((row = sqlNextRow(sr)) != NULL)
     {
     struct linkInResult *newResult = NULL;
     AllocVar(newResult);
     newResult->db = cloneString(db);
     char position[4096];
     safef(position, sizeof(position), "%s:%s-%s", row[0], row[1], row[2]);
     newResult->position = cloneString(position);
     newResult->trackToView = cloneString("all_mrna");
     slAddHead(&results, newResult);
     }
 slReverse(&results);
 sqlFreeResult(&sr);
 return results;
 }
 
 
 struct linkInResult *getRefGeneList(char *db, struct slName *refNames, struct sqlConnection *conn)
 /* Given a connection to a genome database (e.g., hg19), the name of that database, and
  * a list of identifiers, search for any RefSeq gene names that we have positions for.
  * Return a list of matching positions. */
 {
 struct linkInResult *results = NULL;
 bool hasNcbiRefGene = sqlTableExists(conn, "ncbiRefGene");
 bool hasRefGene = sqlTableExists(conn, "refGene");
 if (!hasNcbiRefGene && !hasRefGene)
     return NULL;
 struct dyString *query = dyStringNew(0);
 sqlDyStringPrintf(query, "select chrom, txStart, txEnd from %s where name in (",
         hasNcbiRefGene?"ncbiRefGene":"refGene");
 struct slName *thisName = refNames;
 bool firstName = TRUE;
 while (thisName != NULL)
     {
     if (firstName)
         {
-        sqlDyStringPrintfFrag(query, "'%s'", thisName->name);
+        sqlDyStringPrintf(query, "'%s'", thisName->name);
         firstName = FALSE;
         }
     else
-        sqlDyStringPrintfFrag(query, ",'%s'", thisName->name);
+        sqlDyStringPrintf(query, ",'%s'", thisName->name);
     thisName = thisName->next;
     }
-sqlDyStringPrintfFrag(query, ")");
+sqlDyStringPrintf(query, ")");
 struct sqlResult *sr = sqlGetResult(conn, dyStringContents(query));
 char **row = NULL;
 while ((row = sqlNextRow(sr)) != NULL)
     {
     struct linkInResult *newResult = NULL;
     AllocVar(newResult);
     newResult->db = cloneString(db);
     char position[4096];
     safef(position, sizeof(position), "%s:%s-%s", row[0], row[1], row[2]);
     newResult->position = cloneString(position);
     newResult->trackToView = cloneString(hasNcbiRefGene?"ncbiRefGene":"refGene");
     slAddHead(&results, newResult);
     }
 slReverse(&results);
 sqlFreeResult(&sr);
 return results;
 }
 
 
 struct linkInResult *uniProtHandler(struct sqlConnection *conn, char *id)
 /* Handler for translating a UniProtKB identifier to a genome assembly and
  * positions within that assembly.  Changes the database that conn
  * points to - first to uniProt, then to the relevant assembly.
  * Looks first for related RefSeq gene positions.  If none are found, will
  * then search for related mRNA positions. */
 {
 char query[8092], **row = NULL;
 struct slName *emblIdList = NULL, *refSeqIdList = NULL;
 
 sqlSafef(query, sizeof(query), "use uniProt");
 sqlUpdate(conn, query);
 char *db = uniProtAccToDb(id, conn);
 if (isEmpty(db))
     return NULL;
 
 sqlSafef(query, sizeof(query),
         "select extDb, extAcc1, extAcc2, extAcc3 from extDbRef where "
         "acc = '%s' and extDb in (%d, %d)", id, UniProtExtRefSeqId, UniProtExtEMBLId);
 /* Assemble resulting IDs into two lists; one for refSeq, and one for EMBL */
 struct sqlResult *sr = sqlGetResult(conn, query);
 while ((row = sqlNextRow(sr)) != NULL)
     {
     int extDbId = atoi(row[0]);
     switch(extDbId)
         {
         case UniProtExtEMBLId:
             addIdsToList(&emblIdList, &row[1], 3);
             break;
         case UniProtExtRefSeqId:
             addIdsToList(&refSeqIdList, &row[1], 3);
             break;
         default:
             errAbort("Got unexpected external database ID %d", extDbId);
         }
     }
 sqlFreeResult(&sr);
 
 sqlSafef(query, sizeof(query), "use %s", db);
 sqlUpdate(conn, query);
 struct linkInResult *searchResults = NULL;
 /* If there are any RefSeq IDs, and if they're in our database, use that */
 if (refSeqIdList != NULL)
     searchResults = getRefGeneList(db, refSeqIdList, conn);
 
 /* otherwise, hunt for any EMBL hits */
 if ((searchResults == NULL) && (emblIdList != NULL))
     searchResults = getEmblList(db, emblIdList, conn);
 
 return searchResults;
 }
 
 /***************************************
  *      End of UniProtKB handler
  **************************************/