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/protein/gadPos/gadPos.c src/hg/protein/gadPos/gadPos.c
index 8c3a62f..6bc400c 100644
--- src/hg/protein/gadPos/gadPos.c
+++ src/hg/protein/gadPos/gadPos.c
@@ -1,166 +1,167 @@
 /* gadPos - generate genomic positions for GAD entries */
 
 /* 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 "hCommon.h"
 #include "hdb.h"
 #include "options.h"
 
 // Using options just to get -verbose:
 static struct optionSpec optionSpecs[] = {
     {NULL, 0}
 };
 
 void usage()
 /* Explain usage and exit. */
 {
 errAbort(
   "gadPos -  find genomic positions for GAD entries based on gene symbol\n"
   "usage:\n"
   "   gadPos db outFile\n"
   "      db is the genome database that must contain updated gadAll table,\n"
   "      known{Gene,Canonical,Isoforms}, kg{Xref,Alias}, and ref{Gene,Link}.\n"
   "      Each geneSymbol with association=Y in gadAll is looked up first in \n"
   "      knownCanonical; if not found then refGene; if not found, then kgAlias.\n"
   "      If db contains wgEncodeGencode{Pseudogene,Comp}, they will be searched\n"
   "      if geneSymbol still has not been found.\n"
   "      outFile is the output file name for GAD positions (bed 4 format)\n"
   "example: gadPos hg17 stdout | uniq > gadPos.tab\n");
 }
 
 boolean printBed4FromQueryAndName(struct sqlConnection *conn, char *query, char *name,
 				  FILE *outF)
 /* If there are results from query, assume that they are {chrom, chromStart, chromEnd},
  * print BED4 with those coords and name, and return TRUE; */
 {
 boolean found = FALSE;
 struct sqlResult *sr = sqlGetResult(conn, query);
 char **row;
 while ((row = sqlNextRow(sr)) != NULL)
     {
     found = TRUE;
     fprintf(outF, "%s\t%s\t%s\t%s\n", row[0], row[1], row[2], name);
     }
 sqlFreeResult(&sr);
 return found;
 }
 
 boolean findInKnownCanonical(struct sqlConnection *conn, char *geneSymbol, FILE *outF)
 /* For each knownGene cluster for this geneSymbol, print output using the
  * cluster bounds as {chrom,chromStart,chromEnd} and return TRUE. */
 {
 boolean found = FALSE;
 char query[1024];
 sqlSafef(query, sizeof(query), "select distinct clusterId from kgXref x, knownIsoforms i "
 		    "where x.geneSymbol='%s' and i.transcript=x.kgId", geneSymbol);
 struct slName *id, *clusterIds = sqlQuickList(conn, query);
 for (id = clusterIds;  id != NULL;  id = id->next)
     {
     sqlSafef(query, sizeof(query), "select k.chrom, min(txStart), max(txEnd) "
 	  "from knownGene k, knownIsoforms i, knownCanonical c "
 	  "where i.clusterId=%s and i.transcript=k.name "
 	  "and c.clusterId=i.clusterId and k.chrom=c.chrom",
 	  id->name);
     found |= printBed4FromQueryAndName(conn, query, geneSymbol, outF);
     }
 slFreeList(&clusterIds);
 return found;
 }
 
 boolean findInRefGene(struct sqlConnection *conn, char *geneSymbol, FILE *outF)
 /* If there is a refGene for geneSymbol, print output using the
  * refGene coords as {chrom,chromStart,chromEnd} and return TRUE. */
 {
 char query[1024];
 sqlSafef(query, sizeof(query), "select chrom, txStart, txEnd from refGene rg, refLink rl "
       "where rl.name = '%s' and rl.mrnaAcc = rg.name", geneSymbol);
 return printBed4FromQueryAndName(conn, query, geneSymbol, outF);
 }
 
 boolean findInKgAlias(struct sqlConnection *conn, char *geneSymbol, FILE *outF)
 /* If geneSymbol can be found in kgAlias, print output using the
  * knownGene coords as {chrom,chromStart,chromEnd} and return TRUE. */
 {
 char query[1024];
 sqlSafef(query, sizeof(query), "select distinct(chrom), min(txStart), max(txEnd) "
       "from knownGene, kgAlias where alias='%s' and name=kgId "
       "group by chrom", geneSymbol);
 return printBed4FromQueryAndName(conn, query, geneSymbol, outF);
 }
 
 boolean findInGencode(struct sqlConnection *conn, char *geneSymbol, FILE *outF)
 /* If Gencode tables are present and geneSymbol can be found in them,
  * use those coords and return TRUE. */
 {
 #define PSEUDOGENE_TABLE "wgEncodeGencodePseudoGeneV14"
 #define COMP_TABLE "wgEncodeGencodeCompV14"
 boolean found = FALSE;
 char query[1024];
 if (sqlTableExists(conn, PSEUDOGENE_TABLE))
     {
     sqlSafef(query, sizeof(query), "select chrom, txStart, txEnd from %s where name2 = '%s'",
 	  PSEUDOGENE_TABLE, geneSymbol);
     found = printBed4FromQueryAndName(conn, query, geneSymbol, outF);
     }
 if (!found && sqlTableExists(conn, COMP_TABLE))
     {
     sqlSafef(query, sizeof(query), "select chrom, txStart, txEnd from %s where name2 = '%s'",
 	  COMP_TABLE, geneSymbol);
     found = printBed4FromQueryAndName(conn, query, geneSymbol, outF);
     }
 return found;
 }
 
 void gadPos(char *db, char *outFileName)
 /* Try to get genomic positions for GAD gene symbols from knownGene, refGene,
  * kgAlias and Gencode V14 in that order. */
 {
 FILE *outF = mustOpen(outFileName, "w");
 struct sqlConnection *conn = hAllocConn(db);
 
 /* loop over all gene symbols in GAD */	
-struct slName *geneSymbols = sqlQuickList(conn,
-			       NOSQLINJ "select distinct geneSymbol from gadAll where association='Y'");
+char query[1024];
+sqlSafef(query, sizeof query, "select distinct geneSymbol from gadAll where association='Y'");
+struct slName *geneSymbols = sqlQuickList(conn, query);
 struct slName *symbol;
 int kcCount = 0, rgCount = 0, kaCount = 0, gcCount = 0, missingCount = 0;
 for (symbol = geneSymbols;  symbol != NULL;  symbol = symbol->next)
     {
     if (findInKnownCanonical(conn, symbol->name, outF))
 	kcCount++;
     else if (findInRefGene(conn, symbol->name, outF))
 	rgCount++;
     else if (findInKgAlias(conn, symbol->name, outF))
 	kaCount++;
     else if (findInGencode(conn, symbol->name, outF))
 	gcCount++;
     else
 	{
 	verbose(2, "No result for gene symbol '%s'\n", symbol->name);
 	missingCount++;
 	}
     }
 verbose(1, "Found in knownCanonical: %d\n", kcCount);
 verbose(1, "Found in refGene: %d\n", rgCount);
 verbose(1, "Found in kgAlias: %d\n", kaCount);
 verbose(1, "Found in Gencode: %d\n", gcCount);
 verbose(1, "Not found: %d\n", missingCount);
 
 hFreeConn(&conn);
 carefulClose(&outF);
 }
 
 
 int main(int argc, char *argv[])
 {
 optionInit(&argc, argv, optionSpecs);
 
 if (argc != 3) usage();
 char *db   = argv[1];
 char *outFileName = argv[2];
 
 gadPos(db, outFileName);
 
 return(0);
 }