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/cgilib/chicken13kInfo.c src/hg/cgilib/chicken13kInfo.c
index 3d330d3..f09b93f 100644
--- src/hg/cgilib/chicken13kInfo.c
+++ src/hg/cgilib/chicken13kInfo.c
@@ -1,242 +1,242 @@
 /* chicken13kInfo.c was originally generated by the autoSql program, which also 
  * generated chicken13kInfo.h and chicken13kInfo.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 "chicken13kInfo.h"
 
 
 void chicken13kInfoStaticLoad(char **row, struct chicken13kInfo *ret)
 /* Load a row from chicken13kInfo table into ret.  The contents of ret will
  * be replaced at the next call to this function. */
 {
 
 ret->id = row[0];
 ret->source = row[1];
 strcpy(ret->pcr, row[2]);
 ret->library = row[3];
 ret->clone = row[4];
 ret->gbkAcc = row[5];
 ret->blat = row[6];
 ret->sourceAnnot = row[7];
 ret->tigrTc = row[8];
 ret->tigrTcAnnot = row[9];
 ret->blastAnnot = row[10];
 ret->comment = row[11];
 }
 
 struct chicken13kInfo *chicken13kInfoLoad(char **row)
 /* Load a chicken13kInfo from row fetched with select * from chicken13kInfo
  * from database.  Dispose of this with chicken13kInfoFree(). */
 {
 struct chicken13kInfo *ret;
 
 AllocVar(ret);
 ret->id = cloneString(row[0]);
 ret->source = cloneString(row[1]);
 strcpy(ret->pcr, row[2]);
 ret->library = cloneString(row[3]);
 ret->clone = cloneString(row[4]);
 ret->gbkAcc = cloneString(row[5]);
 ret->blat = cloneString(row[6]);
 ret->sourceAnnot = cloneString(row[7]);
 ret->tigrTc = cloneString(row[8]);
 ret->tigrTcAnnot = cloneString(row[9]);
 ret->blastAnnot = cloneString(row[10]);
 ret->comment = cloneString(row[11]);
 return ret;
 }
 
 struct chicken13kInfo *chicken13kInfoLoadAll(char *fileName) 
 /* Load all chicken13kInfo from a whitespace-separated file.
  * Dispose of this with chicken13kInfoFreeList(). */
 {
 struct chicken13kInfo *list = NULL, *el;
 struct lineFile *lf = lineFileOpen(fileName, TRUE);
 char *row[12];
 
 while (lineFileRow(lf, row))
     {
     el = chicken13kInfoLoad(row);
     slAddHead(&list, el);
     }
 lineFileClose(&lf);
 slReverse(&list);
 return list;
 }
 
 struct chicken13kInfo *chicken13kInfoLoadAllByChar(char *fileName, char chopper) 
 /* Load all chicken13kInfo from a chopper separated file.
  * Dispose of this with chicken13kInfoFreeList(). */
 {
 struct chicken13kInfo *list = NULL, *el;
 struct lineFile *lf = lineFileOpen(fileName, TRUE);
 char *row[12];
 
 while (lineFileNextCharRow(lf, chopper, row, ArraySize(row)))
     {
     el = chicken13kInfoLoad(row);
     slAddHead(&list, el);
     }
 lineFileClose(&lf);
 slReverse(&list);
 return list;
 }
 
 struct chicken13kInfo *chicken13kInfoLoadByQuery(struct sqlConnection *conn, char *query)
 /* Load all chicken13kInfo 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 chicken13kInfoFreeList(). */
 {
 struct chicken13kInfo *list = NULL, *el;
 struct sqlResult *sr;
 char **row;
 
 sr = sqlGetResult(conn, query);
 while ((row = sqlNextRow(sr)) != NULL)
     {
     el = chicken13kInfoLoad(row);
     slAddHead(&list, el);
     }
 slReverse(&list);
 sqlFreeResult(&sr);
 return list;
 }
 
 void chicken13kInfoSaveToDb(struct sqlConnection *conn, struct chicken13kInfo *el, char *tableName, int updateSize)
 /* Save chicken13kInfo 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','%s','%s','%s','%s','%s','%s',%s,'%s',%s,%s,%s)", 
 	tableName,  el->id,  el->source,  el->pcr,  el->library,  el->clone,  el->gbkAcc,  el->blat,  el->sourceAnnot,  el->tigrTc,  el->tigrTcAnnot,  el->blastAnnot,  el->comment);
 sqlUpdate(conn, update->string);
-freeDyString(&update);
+dyStringFree(&update);
 }
 
 
 struct chicken13kInfo *chicken13kInfoCommaIn(char **pS, struct chicken13kInfo *ret)
 /* Create a chicken13kInfo out of a comma separated string. 
  * This will fill in ret if non-null, otherwise will
  * return a new chicken13kInfo */
 {
 char *s = *pS;
 
 if (ret == NULL)
     AllocVar(ret);
 ret->id = sqlStringComma(&s);
 ret->source = sqlStringComma(&s);
 sqlFixedStringComma(&s, ret->pcr, sizeof(ret->pcr));
 ret->library = sqlStringComma(&s);
 ret->clone = sqlStringComma(&s);
 ret->gbkAcc = sqlStringComma(&s);
 ret->blat = sqlStringComma(&s);
 ret->sourceAnnot = sqlStringComma(&s);
 ret->tigrTc = sqlStringComma(&s);
 ret->tigrTcAnnot = sqlStringComma(&s);
 ret->blastAnnot = sqlStringComma(&s);
 ret->comment = sqlStringComma(&s);
 *pS = s;
 return ret;
 }
 
 void chicken13kInfoFree(struct chicken13kInfo **pEl)
 /* Free a single dynamically allocated chicken13kInfo such as created
  * with chicken13kInfoLoad(). */
 {
 struct chicken13kInfo *el;
 
 if ((el = *pEl) == NULL) return;
 freeMem(el->id);
 freeMem(el->source);
 freeMem(el->library);
 freeMem(el->clone);
 freeMem(el->gbkAcc);
 freeMem(el->blat);
 freeMem(el->sourceAnnot);
 freeMem(el->tigrTc);
 freeMem(el->tigrTcAnnot);
 freeMem(el->blastAnnot);
 freeMem(el->comment);
 freez(pEl);
 }
 
 void chicken13kInfoFreeList(struct chicken13kInfo **pList)
 /* Free a list of dynamically allocated chicken13kInfo's */
 {
 struct chicken13kInfo *el, *next;
 
 for (el = *pList; el != NULL; el = next)
     {
     next = el->next;
     chicken13kInfoFree(&el);
     }
 *pList = NULL;
 }
 
 void chicken13kInfoOutput(struct chicken13kInfo *el, FILE *f, char sep, char lastSep) 
 /* Print out chicken13kInfo.  Separate fields with sep. Follow last field with lastSep. */
 {
 if (sep == ',') fputc('"',f);
 fprintf(f, "%s", el->id);
 if (sep == ',') fputc('"',f);
 fputc(sep,f);
 if (sep == ',') fputc('"',f);
 fprintf(f, "%s", el->source);
 if (sep == ',') fputc('"',f);
 fputc(sep,f);
 if (sep == ',') fputc('"',f);
 fprintf(f, "%s", el->pcr);
 if (sep == ',') fputc('"',f);
 fputc(sep,f);
 if (sep == ',') fputc('"',f);
 fprintf(f, "%s", el->library);
 if (sep == ',') fputc('"',f);
 fputc(sep,f);
 if (sep == ',') fputc('"',f);
 fprintf(f, "%s", el->clone);
 if (sep == ',') fputc('"',f);
 fputc(sep,f);
 if (sep == ',') fputc('"',f);
 fprintf(f, "%s", el->gbkAcc);
 if (sep == ',') fputc('"',f);
 fputc(sep,f);
 if (sep == ',') fputc('"',f);
 fprintf(f, "%s", el->blat);
 if (sep == ',') fputc('"',f);
 fputc(sep,f);
 if (sep == ',') fputc('"',f);
 fprintf(f, "%s", el->sourceAnnot);
 if (sep == ',') fputc('"',f);
 fputc(sep,f);
 if (sep == ',') fputc('"',f);
 fprintf(f, "%s", el->tigrTc);
 if (sep == ',') fputc('"',f);
 fputc(sep,f);
 if (sep == ',') fputc('"',f);
 fprintf(f, "%s", el->tigrTcAnnot);
 if (sep == ',') fputc('"',f);
 fputc(sep,f);
 if (sep == ',') fputc('"',f);
 fprintf(f, "%s", el->blastAnnot);
 if (sep == ',') fputc('"',f);
 fputc(sep,f);
 if (sep == ',') fputc('"',f);
 fprintf(f, "%s", el->comment);
 if (sep == ',') fputc('"',f);
 fputc(lastSep,f);
 }
 
 /* -------------------------------- End autoSql Generated Code -------------------------------- */