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/hgGene/alleles.c src/hg/hgGene/alleles.c
index d619d9d..f2ebc7c 100644
--- src/hg/hgGene/alleles.c
+++ src/hg/hgGene/alleles.c
@@ -1,108 +1,108 @@
 // alleles - common Gene haplotype alleles. */
 
 /* Copyright (C) 2014 The Regents of the University of California 
  * See kent/LICENSE or http://genome.ucsc.edu/license/ for licensing information. */
 
 #include "common.h"
 #include "web.h"
 #include "genePredReader.h"
 #include "vcf.h"
 #include "haplotypes.h"
 #include "hgGene.h"
 
 static struct allelesInfo {
     struct genePred *gp;
     struct vcfFile *vcf;
     struct haploExtras *he;
     } allelesInfo;
 
 static boolean allelesExists(struct section *section,
         struct sqlConnection *conn, char *geneId)
 // Return TRUE if common haplotype alleles exist.
 {
 // If there was a reset then clear out settings
 if (cartUsualBoolean(cart, HAPLO_RESET_ALL, FALSE))
     cartRemovePrefix(cart,HAPLO_TABLE "_" );
 
 // Start with the default variables for haplotype retrieval
 struct haploExtras *he = haplotypeExtrasDefault(database, 0);
 
 // Need to get genePred struct from geneId
 char where[128];
-sqlSafefFrag(where, sizeof(where),"name = '%s'",geneId);
+sqlSafef(where, sizeof(where),"name = '%s'",geneId);
 struct genePred *gp = genePredReaderLoadQuery(conn,he->geneTable, where);
 if (gp == NULL || gp->cdsStart == gp->cdsEnd)  // Ain't interested in non-protein coding genes
     {
     haplotypeExtrasFree(&he);
     return FALSE;
     }
 
 he->chrom = gp->chrom; // Probably not needed
 he->justModel = lmCloneString(he->lm, geneId);
 //he->growTree = FALSE; // Tree growing not needed here
 
 // Need to determine the correct vcf file and open it
 if (haplotypesDiscoverVcfFile(he, gp->chrom) == NULL)
     {
     haplotypeExtrasFree(&he);
     return FALSE;
     }
 struct vcfFile *vcf = vcfTabixFileMayOpen(he->inFile, NULL, 0, 0,VCF_IGNORE_ERRS, 0);
 if (vcf == NULL)
     {
     haplotypeExtrasFree(&he);
     return FALSE;
     }
 allelesInfo.gp = gp;
 allelesInfo.he = he;
 allelesInfo.vcf = vcf;
 section->items = &allelesInfo;
 return TRUE;
 }
 
 static void allelesPrint(struct section *section, struct sqlConnection *conn, char *geneId)
 // Print out common gene haplotype alleles.
 {
 struct allelesInfo *info = section->items;
 struct vcfFile *vcf = info->vcf;
 struct haploExtras *he = info->he;
 struct genePred *gp = info->gp;
 
 vcfFileMakeReusePool(vcf,1024 * 1024);
 
 // All or Limit to the 99%
 boolean rareVars =  cartUsualBoolean(cart, HAPLO_RARE_VAR, FALSE);
 if (rareVars)
     he->synonymous = TRUE;
 else
     he->variantMinPct = HAPLO_COMMON_VARIANT_MIN_PCT;
 
 // Lets show the population distribution
 he->populationsToo   = cartUsualBoolean(cart, HAPLO_MAJOR_DIST, FALSE);
 he->populationsMinor = cartUsualBoolean(cart, HAPLO_MINOR_DIST, FALSE);
 if (he->populationsToo)
     he->populationMinPct = 5;
 else if (he->populationsMinor)
     {
     he->populationsMinor = FALSE;
     cartRemove(cart, HAPLO_MINOR_DIST );
     }
 
 // Need to generate haplotypes
 struct haplotypeSet *hapSet = geneHapSetForOneModel(he, vcf, gp, TRUE);
 geneAllelesTableAndControls(cart, geneId, he, hapSet);
 haplotypeExtrasFree(&he);
 }
 
 struct section *allelesSection(struct sqlConnection *conn, struct hash *sectionRa)
 // Create UCSC KG Method section.
 {
 struct section *section = sectionNew(sectionRa, HGG_GENE_ALLELES);
 if (section != NULL)
     {
     section->exists = allelesExists;
     section->print = allelesPrint;
     }
 return section;
 }