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/lib/hapmapPrimateAlleles.c src/hg/lib/hapmapPrimateAlleles.c
index c3b3a31..d14778f 100644
--- src/hg/lib/hapmapPrimateAlleles.c
+++ src/hg/lib/hapmapPrimateAlleles.c
@@ -1,265 +1,265 @@
 /* hapmapPrimateAlleles.c was originally generated by the autoSql program, which also 
  * generated hapmapPrimateAlleles.h and hapmapPrimateAlleles.sql.  This module links the database and
  * the RAM representation of objects. */
 
 /* 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 "linefile.h"
 #include "dystring.h"
 #include "jksql.h"
 #include "hapmapPrimateAlleles.h"
 
 
 void hapmapPrimateAllelesStaticLoad(char **row, struct hapmapPrimateAlleles *ret)
 /* Load a row from hapmapPrimateAlleles table into ret.  The contents of ret will
  * be replaced at the next call to this function. */
 {
 
 ret->chrom = row[0];
 ret->chromStart = sqlUnsigned(row[1]);
 ret->chromEnd = sqlUnsigned(row[2]);
 ret->name = row[3];
 ret->score = sqlUnsigned(row[4]);
 ret->strand = row[5][0];
 ret->refAllele = row[6][0];
 ret->otherAllele = row[7][0];
 ret->chimpChrom = row[8];
 ret->chimpPos = sqlUnsigned(row[9]);
 ret->chimpStrand = row[10][0];
 ret->chimpAllele = row[11];
 ret->chimpQual = sqlUnsigned(row[12]);
 ret->rhesusChrom = row[13];
 ret->rhesusPos = sqlUnsigned(row[14]);
 ret->rhesusStrand = row[15][0];
 ret->rhesusAllele = row[16];
 ret->rhesusQual = sqlUnsigned(row[17]);
 }
 
 struct hapmapPrimateAlleles *hapmapPrimateAllelesLoad(char **row)
 /* Load a hapmapPrimateAlleles from row fetched with select * from hapmapPrimateAlleles
  * from database.  Dispose of this with hapmapPrimateAllelesFree(). */
 {
 struct hapmapPrimateAlleles *ret;
 
 AllocVar(ret);
 ret->chrom = cloneString(row[0]);
 ret->chromStart = sqlUnsigned(row[1]);
 ret->chromEnd = sqlUnsigned(row[2]);
 ret->name = cloneString(row[3]);
 ret->score = sqlUnsigned(row[4]);
 ret->strand = row[5][0];
 ret->refAllele = row[6][0];
 ret->otherAllele = row[7][0];
 ret->chimpChrom = cloneString(row[8]);
 ret->chimpPos = sqlUnsigned(row[9]);
 ret->chimpStrand = row[10][0];
 ret->chimpAllele = cloneString(row[11]);
 ret->chimpQual = sqlUnsigned(row[12]);
 ret->rhesusChrom = cloneString(row[13]);
 ret->rhesusPos = sqlUnsigned(row[14]);
 ret->rhesusStrand = row[15][0];
 ret->rhesusAllele = cloneString(row[16]);
 ret->rhesusQual = sqlUnsigned(row[17]);
 return ret;
 }
 
 struct hapmapPrimateAlleles *hapmapPrimateAllelesLoadAll(char *fileName) 
 /* Load all hapmapPrimateAlleles from a whitespace-separated file.
  * Dispose of this with hapmapPrimateAllelesFreeList(). */
 {
 struct hapmapPrimateAlleles *list = NULL, *el;
 struct lineFile *lf = lineFileOpen(fileName, TRUE);
 char *row[18];
 
 while (lineFileRow(lf, row))
     {
     el = hapmapPrimateAllelesLoad(row);
     slAddHead(&list, el);
     }
 lineFileClose(&lf);
 slReverse(&list);
 return list;
 }
 
 struct hapmapPrimateAlleles *hapmapPrimateAllelesLoadAllByChar(char *fileName, char chopper) 
 /* Load all hapmapPrimateAlleles from a chopper separated file.
  * Dispose of this with hapmapPrimateAllelesFreeList(). */
 {
 struct hapmapPrimateAlleles *list = NULL, *el;
 struct lineFile *lf = lineFileOpen(fileName, TRUE);
 char *row[18];
 
 while (lineFileNextCharRow(lf, chopper, row, ArraySize(row)))
     {
     el = hapmapPrimateAllelesLoad(row);
     slAddHead(&list, el);
     }
 lineFileClose(&lf);
 slReverse(&list);
 return list;
 }
 
 struct hapmapPrimateAlleles *hapmapPrimateAllelesLoadByQuery(struct sqlConnection *conn, char *query)
 /* Load all hapmapPrimateAlleles from table that satisfy the query given.  
  * Where query is of the form 'select * from example where something=something'
  * or 'select example.* from example, anotherTable where example.something = 
  * anotherTable.something'.
  * Dispose of this with hapmapPrimateAllelesFreeList(). */
 {
 struct hapmapPrimateAlleles *list = NULL, *el;
 struct sqlResult *sr;
 char **row;
 
 sr = sqlGetResult(conn, query);
 while ((row = sqlNextRow(sr)) != NULL)
     {
     el = hapmapPrimateAllelesLoad(row);
     slAddHead(&list, el);
     }
 slReverse(&list);
 sqlFreeResult(&sr);
 return list;
 }
 
 void hapmapPrimateAllelesSaveToDb(struct sqlConnection *conn, struct hapmapPrimateAlleles *el, char *tableName, int updateSize)
 /* Save hapmapPrimateAlleles as a row to the table specified by tableName. 
  * As blob fields may be arbitrary size updateSize specifies the approx size
  * of a string that would contain the entire query. Arrays of native types are
  * converted to comma separated strings and loaded as such, User defined types are
  * inserted as NULL. Strings are automatically escaped to allow insertion into the database. */
 {
-struct dyString *update = newDyString(updateSize);
+struct dyString *update = dyStringNew(updateSize);
 sqlDyStringPrintf(update, "insert into %s values ( '%s',%u,%u,'%s',%u,'%c','%c','%c','%s',%u,'%c','%s',%u,'%s',%u,'%c','%s',%u)", 
 	tableName,  el->chrom,  el->chromStart,  el->chromEnd,  el->name,  el->score,  el->strand,  el->refAllele,  el->otherAllele,  el->chimpChrom,  el->chimpPos,  el->chimpStrand,  el->chimpAllele,  el->chimpQual,  el->rhesusChrom,  el->rhesusPos,  el->rhesusStrand,  el->rhesusAllele,  el->rhesusQual);
 sqlUpdate(conn, update->string);
-freeDyString(&update);
+dyStringFree(&update);
 }
 
 
 struct hapmapPrimateAlleles *hapmapPrimateAllelesCommaIn(char **pS, struct hapmapPrimateAlleles *ret)
 /* Create a hapmapPrimateAlleles out of a comma separated string. 
  * This will fill in ret if non-null, otherwise will
  * return a new hapmapPrimateAlleles */
 {
 char *s = *pS;
 
 if (ret == NULL)
     AllocVar(ret);
 ret->chrom = sqlStringComma(&s);
 ret->chromStart = sqlUnsignedComma(&s);
 ret->chromEnd = sqlUnsignedComma(&s);
 ret->name = sqlStringComma(&s);
 ret->score = sqlUnsignedComma(&s);
 sqlFixedStringComma(&s, &(ret->strand), sizeof(ret->strand));
 sqlFixedStringComma(&s, &(ret->refAllele), sizeof(ret->refAllele));
 sqlFixedStringComma(&s, &(ret->otherAllele), sizeof(ret->otherAllele));
 ret->chimpChrom = sqlStringComma(&s);
 ret->chimpPos = sqlUnsignedComma(&s);
 sqlFixedStringComma(&s, &(ret->chimpStrand), sizeof(ret->chimpStrand));
 ret->chimpAllele = sqlStringComma(&s);
 ret->chimpQual = sqlUnsignedComma(&s);
 ret->rhesusChrom = sqlStringComma(&s);
 ret->rhesusPos = sqlUnsignedComma(&s);
 sqlFixedStringComma(&s, &(ret->rhesusStrand), sizeof(ret->rhesusStrand));
 ret->rhesusAllele = sqlStringComma(&s);
 ret->rhesusQual = sqlUnsignedComma(&s);
 *pS = s;
 return ret;
 }
 
 void hapmapPrimateAllelesFree(struct hapmapPrimateAlleles **pEl)
 /* Free a single dynamically allocated hapmapPrimateAlleles such as created
  * with hapmapPrimateAllelesLoad(). */
 {
 struct hapmapPrimateAlleles *el;
 
 if ((el = *pEl) == NULL) return;
 freeMem(el->chrom);
 freeMem(el->name);
 freeMem(el->chimpChrom);
 freeMem(el->chimpAllele);
 freeMem(el->rhesusChrom);
 freeMem(el->rhesusAllele);
 freez(pEl);
 }
 
 void hapmapPrimateAllelesFreeList(struct hapmapPrimateAlleles **pList)
 /* Free a list of dynamically allocated hapmapPrimateAlleles's */
 {
 struct hapmapPrimateAlleles *el, *next;
 
 for (el = *pList; el != NULL; el = next)
     {
     next = el->next;
     hapmapPrimateAllelesFree(&el);
     }
 *pList = NULL;
 }
 
 void hapmapPrimateAllelesOutput(struct hapmapPrimateAlleles *el, FILE *f, char sep, char lastSep) 
 /* Print out hapmapPrimateAlleles.  Separate fields with sep. Follow last field with lastSep. */
 {
 if (sep == ',') fputc('"',f);
 fprintf(f, "%s", el->chrom);
 if (sep == ',') fputc('"',f);
 fputc(sep,f);
 fprintf(f, "%u", el->chromStart);
 fputc(sep,f);
 fprintf(f, "%u", el->chromEnd);
 fputc(sep,f);
 if (sep == ',') fputc('"',f);
 fprintf(f, "%s", el->name);
 if (sep == ',') fputc('"',f);
 fputc(sep,f);
 fprintf(f, "%u", el->score);
 fputc(sep,f);
 if (sep == ',') fputc('"',f);
 fprintf(f, "%c", el->strand);
 if (sep == ',') fputc('"',f);
 fputc(sep,f);
 if (sep == ',') fputc('"',f);
 fprintf(f, "%c", el->refAllele);
 if (sep == ',') fputc('"',f);
 fputc(sep,f);
 if (sep == ',') fputc('"',f);
 fprintf(f, "%c", el->otherAllele);
 if (sep == ',') fputc('"',f);
 fputc(sep,f);
 if (sep == ',') fputc('"',f);
 fprintf(f, "%s", el->chimpChrom);
 if (sep == ',') fputc('"',f);
 fputc(sep,f);
 fprintf(f, "%u", el->chimpPos);
 fputc(sep,f);
 if (sep == ',') fputc('"',f);
 fprintf(f, "%c", el->chimpStrand);
 if (sep == ',') fputc('"',f);
 fputc(sep,f);
 if (sep == ',') fputc('"',f);
 fprintf(f, "%s", el->chimpAllele);
 if (sep == ',') fputc('"',f);
 fputc(sep,f);
 fprintf(f, "%u", el->chimpQual);
 fputc(sep,f);
 if (sep == ',') fputc('"',f);
 fprintf(f, "%s", el->rhesusChrom);
 if (sep == ',') fputc('"',f);
 fputc(sep,f);
 fprintf(f, "%u", el->rhesusPos);
 fputc(sep,f);
 if (sep == ',') fputc('"',f);
 fprintf(f, "%c", el->rhesusStrand);
 if (sep == ',') fputc('"',f);
 fputc(sep,f);
 if (sep == ',') fputc('"',f);
 fprintf(f, "%s", el->rhesusAllele);
 if (sep == ',') fputc('"',f);
 fputc(sep,f);
 fprintf(f, "%u", el->rhesusQual);
 fputc(lastSep,f);
 }
 
 /* -------------------------------- End autoSql Generated Code -------------------------------- */