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/snp/snpLoad/hapmapValidate.c src/hg/snp/snpLoad/hapmapValidate.c
index cf1e9e6..11e709c 100644
--- src/hg/snp/snpLoad/hapmapValidate.c
+++ src/hg/snp/snpLoad/hapmapValidate.c
@@ -1,364 +1,364 @@
 /* hapmapValidate -- after merging genotype files across SNPs, check: */
 /* is everything biallelic? */
 /* if valid observed, does it match? */
 
 /* 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 "hdb.h"
 #include "sqlNum.h"
 
 
 FILE *errorFileHandle = NULL;
 FILE *complexFileHandle = NULL;
 static char *db = NULL;
 struct dyString *dynamicObserved = NULL;
 
 struct snpInfo
     {
     char *chrom;
     int  chromStart;
     int  chromEnd;
     char *name;
     char *strand;
     char *observed;
 
     int  aCountCEU;       
     int  cCountCEU;       
     int  gCountCEU;       
     int  tCountCEU;       
 
     int  aCountCHB;       
     int  cCountCHB;       
     int  gCountCHB;
     int  tCountCHB;
 
     int  aCountJPT;       
     int  cCountJPT;       
     int  gCountJPT;
     int  tCountJPT;
 
     int  aCountYRI;       
     int  cCountYRI;       
     int  gCountYRI;       
     int  tCountYRI;       
     };
 
 void usage()
 /* Explain usage and exit. */
 {
 errAbort(
   "hapmapValidate - Read initial hapmap table.\n"
   "usage:\n"
   "  hapmapValidate database table\n");
 }
 
 void load(char **row, struct snpInfo *si)
 {
 si->chrom = cloneString(row[1]);
 si->chromStart = sqlUnsigned(row[2]);
 si->chromEnd = sqlUnsigned(row[3]);
 si->name = cloneString(row[4]);
 si->strand = cloneString(row[6]);
 si->observed = cloneString(row[7]);
 
 si->aCountCEU = sqlUnsigned(row[8]);       
 si->aCountCHB = sqlUnsigned(row[9]);       
 si->aCountJPT = sqlUnsigned(row[10]);       
 si->aCountYRI = sqlUnsigned(row[11]);       
 
 si->cCountCEU = sqlUnsigned(row[12]);       
 si->cCountCHB = sqlUnsigned(row[13]);       
 si->cCountJPT = sqlUnsigned(row[14]);       
 si->cCountYRI = sqlUnsigned(row[15]);       
 
 si->gCountCEU = sqlUnsigned(row[16]);       
 si->gCountCHB = sqlUnsigned(row[17]);
 si->gCountJPT = sqlUnsigned(row[18]);
 si->gCountYRI = sqlUnsigned(row[19]);       
 
 si->tCountCEU = sqlUnsigned(row[20]);       
 si->tCountCHB = sqlUnsigned(row[21]);
 si->tCountJPT = sqlUnsigned(row[22]);
 si->tCountYRI = sqlUnsigned(row[23]);       
 }
 
 
 void printOne(struct snpInfo *si)
 {
 verbose(1, "chrom = %s, name = %s, observed = %s\n", 
             si->chrom, si->name, si->observed);
 }
 
 
 char *actualObserved(struct snpInfo *si)
 {
 dyStringClear(dynamicObserved);
 if (si->aCountCEU > 0 || si->aCountCHB > 0 ||
     si->aCountJPT > 0 || si->aCountYRI)
     dyStringAppend(dynamicObserved, "A");
 
 if (si->cCountCEU > 0 || si->cCountCHB > 0 ||
     si->cCountJPT > 0 || si->cCountYRI)
     {
     if (dynamicObserved->stringSize > 0)
         dyStringAppend(dynamicObserved, "/");
     dyStringAppend(dynamicObserved, "C");
     }
 
 if (si->gCountCEU > 0 || si->gCountCHB > 0 ||
     si->gCountJPT > 0 || si->gCountYRI)
     {
     if (dynamicObserved->stringSize > 0)
         dyStringAppend(dynamicObserved, "/");
     dyStringAppend(dynamicObserved, "G");
     }
 
 if (si->tCountCEU > 0 || si->tCountCHB > 0 ||
     si->tCountJPT > 0 || si->tCountYRI)
     {
     if (dynamicObserved->stringSize > 0)
         dyStringAppend(dynamicObserved, "/");
     dyStringAppend(dynamicObserved, "T");
     }
 return dynamicObserved->string;
 
 }
 
 boolean isComplexType(struct snpInfo *si)
 {
 if (sameString(si->observed, "A/C")) return FALSE;
 if (sameString(si->observed, "A/G")) return FALSE;
 if (sameString(si->observed, "A/T")) return FALSE;
 if (sameString(si->observed, "C/G")) return FALSE;
 if (sameString(si->observed, "C/T")) return FALSE;
 if (sameString(si->observed, "G/T")) return FALSE;
 return TRUE;
 }
 
 boolean isMonomorphic(struct snpInfo *si)
 {
 boolean gotA = FALSE;
 boolean gotC = FALSE;
 boolean gotG = FALSE;
 boolean gotT = FALSE;
 int alleleCount = 0;
 
 if (si->aCountCEU > 0) gotA = TRUE;
 if (si->aCountCHB > 0) gotA = TRUE;
 if (si->aCountJPT > 0) gotA = TRUE;
 if (si->aCountYRI > 0) gotA = TRUE;
 if (gotA) alleleCount++;
 
 if (si->cCountCEU > 0) gotC = TRUE;
 if (si->cCountCHB > 0) gotC = TRUE;
 if (si->cCountJPT > 0) gotC = TRUE;
 if (si->cCountYRI > 0) gotC = TRUE;
 if (gotC) alleleCount++;
 
 if (si->gCountCEU > 0) gotG = TRUE;
 if (si->gCountCHB > 0) gotG = TRUE;
 if (si->gCountJPT > 0) gotG = TRUE;
 if (si->gCountYRI > 0) gotG = TRUE;
 if (gotG) alleleCount++;
 
 if (si->tCountCEU > 0) gotT = TRUE;
 if (si->tCountCHB > 0) gotT = TRUE;
 if (si->tCountJPT > 0) gotT = TRUE;
 if (si->tCountYRI > 0) gotT = TRUE;
 if (gotT) alleleCount++;
 
 if (alleleCount == 1) return TRUE;
 return FALSE;
 
 }
 
 boolean allPopulations(struct snpInfo *si)
 {
 boolean gotCEU = FALSE;
 boolean gotCHB = FALSE;
 boolean gotJPT = FALSE;
 boolean gotYRI = FALSE;
 int popCount = 0;
 
 if (si->aCountCEU > 0) gotCEU = TRUE;
 if (si->cCountCEU > 0) gotCEU = TRUE;
 if (si->gCountCEU > 0) gotCEU = TRUE;
 if (si->tCountCEU > 0) gotCEU = TRUE;
 if (gotCEU) popCount++;
 
 if (si->aCountCHB > 0) gotCHB = TRUE;
 if (si->cCountCHB > 0) gotCHB = TRUE;
 if (si->gCountCHB > 0) gotCHB = TRUE;
 if (si->tCountCHB > 0) gotCHB = TRUE;
 if (gotCHB) popCount++;
 
 if (si->aCountJPT > 0) gotJPT = TRUE;
 if (si->cCountJPT > 0) gotJPT = TRUE;
 if (si->gCountJPT > 0) gotJPT = TRUE;
 if (si->tCountJPT > 0) gotJPT = TRUE;
 if (gotJPT) popCount++;
 
 if (si->aCountYRI > 0) gotYRI = TRUE;
 if (si->cCountYRI > 0) gotYRI = TRUE;
 if (si->gCountYRI > 0) gotYRI = TRUE;
 if (si->tCountYRI > 0) gotYRI = TRUE;
 if (gotYRI) popCount++;
 
 if (popCount == 4) return TRUE;
 return FALSE;
 }
 
 boolean isBiallelic(struct snpInfo *si)
 {
 if (sameString(si->observed,"A/C")) 
     {
     if (si->gCountCEU > 0) return FALSE;
     if (si->gCountCHB > 0) return FALSE;
     if (si->gCountJPT > 0) return FALSE;
     if (si->gCountYRI > 0) return FALSE;
     if (si->tCountCEU > 0) return FALSE;
     if (si->tCountCHB > 0) return FALSE;
     if (si->tCountJPT > 0) return FALSE;
     if (si->tCountYRI > 0) return FALSE;
     return TRUE;
     }
 if (sameString(si->observed,"A/G")) 
     {
     if (si->cCountCEU > 0) return FALSE;
     if (si->cCountCHB > 0) return FALSE;
     if (si->cCountJPT > 0) return FALSE;
     if (si->cCountYRI > 0) return FALSE;
     if (si->tCountCEU > 0) return FALSE;
     if (si->tCountCHB > 0) return FALSE;
     if (si->tCountJPT > 0) return FALSE;
     if (si->tCountYRI > 0) return FALSE;
     return TRUE;
     }
 if (sameString(si->observed,"A/T")) 
     {
     if (si->cCountCEU > 0) return FALSE;
     if (si->cCountCHB > 0) return FALSE;
     if (si->cCountJPT > 0) return FALSE;
     if (si->cCountYRI > 0) return FALSE;
     if (si->gCountCEU > 0) return FALSE;
     if (si->gCountCHB > 0) return FALSE;
     if (si->gCountJPT > 0) return FALSE;
     if (si->gCountYRI > 0) return FALSE;
     return TRUE;
     }
 if (sameString(si->observed,"C/G")) 
     {
     if (si->aCountCEU > 0) return FALSE;
     if (si->aCountCHB > 0) return FALSE;
     if (si->aCountJPT > 0) return FALSE;
     if (si->aCountYRI > 0) return FALSE;
     if (si->tCountCEU > 0) return FALSE;
     if (si->tCountCHB > 0) return FALSE;
     if (si->tCountJPT > 0) return FALSE;
     if (si->tCountYRI > 0) return FALSE;
     return TRUE;
     }
 if (sameString(si->observed,"C/T")) 
     {
     if (si->aCountCEU > 0) return FALSE;
     if (si->aCountCHB > 0) return FALSE;
     if (si->aCountJPT > 0) return FALSE;
     if (si->aCountYRI > 0) return FALSE;
     if (si->gCountCEU > 0) return FALSE;
     if (si->gCountCHB > 0) return FALSE;
     if (si->gCountJPT > 0) return FALSE;
     if (si->gCountYRI > 0) return FALSE;
     return TRUE;
     }
 if (sameString(si->observed,"G/T")) 
     {
     if (si->aCountCEU > 0) return FALSE;
     if (si->aCountCHB > 0) return FALSE;
     if (si->aCountJPT > 0) return FALSE;
     if (si->aCountYRI > 0) return FALSE;
     if (si->cCountCEU > 0) return FALSE;
     if (si->cCountCHB > 0) return FALSE;
     if (si->cCountJPT > 0) return FALSE;
     if (si->cCountYRI > 0) return FALSE;
     return TRUE;
     }
 return FALSE;
 }
 
 char *characterizeObserved(char *observed)
 {
 if (sameString(observed, "A")) return "monomorphic";
 if (sameString(observed, "C")) return "monomorphic";
 if (sameString(observed, "G")) return "monomorphic";
 if (sameString(observed, "T")) return "monomorphic";
 if (sameString(observed, "A/C")) return "bi-allelic";
 if (sameString(observed, "A/G")) return "bi-allelic";
 if (sameString(observed, "A/T")) return "bi-allelic";
 if (sameString(observed, "C/G")) return "bi-allelic";
 if (sameString(observed, "C/T")) return "bi-allelic";
 if (sameString(observed, "G/T")) return "bi-allelic";
 return "complex";
 }
 
 
 void hapmapValidate(char *tableName)
 {
 struct snpInfo *si = NULL;
 char query[512];
 struct sqlConnection *conn = hAllocConn();
 struct sqlResult *sr;
 char **row;
 char *observedActual;
 
 AllocVar(si);
 sqlSafef(query, sizeof(query), "select * from %s", tableName);
 
 sr = sqlGetResult(conn, query);
 while ((row = sqlNextRow(sr)) != NULL)
     {
     load(row, si);
     // skip these for now
     if (isComplexType(si)) 
         {
 	observedActual = actualObserved(si);
 	fprintf(complexFileHandle, "%s %s %s\n", 
 	    row[4], observedActual, characterizeObserved(observedActual));
         continue;
         }
     // if (!isBiallelic(si))
         // fprintf(errorFileHandle, "%s is not biallelic\n", si->name);
     // if (isMonomorphic(si))
         // fprintf(errorFileHandle, "%s is monomorphic\n", si->name);
     if (!allPopulations(si))
         fprintf(errorFileHandle, "%s not available for all populations\n", si->name);
     }
 }
 
 
 int main(int argc, char *argv[])
 {
 if (argc != 3)
     usage();
 
 db = argv[1];
 hSetDb(db);
 
 if (!hTableExists(argv[2])) 
     {
     verbose(1, "can't find table %s\n", argv[2]);
     return 1;
     }
 
 errorFileHandle = mustOpen("hapmapValidate.error", "w");
 complexFileHandle = mustOpen("hapmapValidate.complex", "w");
-dynamicObserved = newDyString(32);
+dynamicObserved = dyStringNew(32);
 hapmapValidate(argv[2]);
 carefulClose(&errorFileHandle);
 carefulClose(&complexFileHandle);
 
 return 0;
 }