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/altSplice/lib/mouseAPSetEventMap.c src/hg/altSplice/lib/mouseAPSetEventMap.c
index a5bef59..16f738f 100644
--- src/hg/altSplice/lib/mouseAPSetEventMap.c
+++ src/hg/altSplice/lib/mouseAPSetEventMap.c
@@ -1,230 +1,230 @@
 /* mouseAPSetEventMap.c was originally generated by the autoSql program, which also 
  * generated mouseAPSetEventMap.h and mouseAPSetEventMap.sql.  This module links the database and
  * the RAM representation of objects. */
 
 #include "common.h"
 #include "linefile.h"
 #include "dystring.h"
 #include "jksql.h"
 #include "mouseAPSetEventMap.h"
 
 
 struct mouseAPSetEventMap *mouseAPSetEventMapLoad(char **row)
 /* Load a mouseAPSetEventMap from row fetched with select * from mouseAPSetEventMap
  * from database.  Dispose of this with mouseAPSetEventMapFree(). */
 {
 struct mouseAPSetEventMap *ret;
 
 AllocVar(ret);
 ret->incCount = sqlUnsigned(row[2]);
 ret->geneCount = sqlUnsigned(row[4]);
 ret->geneName = cloneString(row[0]);
 ret->skipPSet = cloneString(row[1]);
 {
 int sizeOne;
 sqlStringDynamicArray(row[3], &ret->incPSets, &sizeOne);
 assert(sizeOne == ret->incCount);
 }
 {
 int sizeOne;
 sqlStringDynamicArray(row[5], &ret->genePSets, &sizeOne);
 assert(sizeOne == ret->geneCount);
 }
 return ret;
 }
 
 struct mouseAPSetEventMap *mouseAPSetEventMapLoadAll(char *fileName) 
 /* Load all mouseAPSetEventMap from a whitespace-separated file.
  * Dispose of this with mouseAPSetEventMapFreeList(). */
 {
 struct mouseAPSetEventMap *list = NULL, *el;
 struct lineFile *lf = lineFileOpen(fileName, TRUE);
 char *row[6];
 
 while (lineFileRow(lf, row))
     {
     el = mouseAPSetEventMapLoad(row);
     slAddHead(&list, el);
     }
 lineFileClose(&lf);
 slReverse(&list);
 return list;
 }
 
 struct mouseAPSetEventMap *mouseAPSetEventMapLoadAllByChar(char *fileName, char chopper) 
 /* Load all mouseAPSetEventMap from a chopper separated file.
  * Dispose of this with mouseAPSetEventMapFreeList(). */
 {
 struct mouseAPSetEventMap *list = NULL, *el;
 struct lineFile *lf = lineFileOpen(fileName, TRUE);
 char *row[6];
 
 while (lineFileNextCharRow(lf, chopper, row, ArraySize(row)))
     {
     el = mouseAPSetEventMapLoad(row);
     slAddHead(&list, el);
     }
 lineFileClose(&lf);
 slReverse(&list);
 return list;
 }
 
 struct mouseAPSetEventMap *mouseAPSetEventMapLoadByQuery(struct sqlConnection *conn, char *query)
 /* Load all mouseAPSetEventMap 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 mouseAPSetEventMapFreeList(). */
 {
 struct mouseAPSetEventMap *list = NULL, *el;
 struct sqlResult *sr;
 char **row;
 
 sr = sqlGetResult(conn, query);
 while ((row = sqlNextRow(sr)) != NULL)
     {
     el = mouseAPSetEventMapLoad(row);
     slAddHead(&list, el);
     }
 slReverse(&list);
 sqlFreeResult(&sr);
 return list;
 }
 
 void mouseAPSetEventMapSaveToDb(struct sqlConnection *conn, struct mouseAPSetEventMap *el, char *tableName, int updateSize)
 /* Save mouseAPSetEventMap 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);
 char  *incPSetsArray, *genePSetsArray;
 incPSetsArray = sqlStringArrayToString(el->incPSets, el->incCount);
 genePSetsArray = sqlStringArrayToString(el->genePSets, el->geneCount);
 sqlDyStringPrintf(update, "insert into %s values ( '%s','%s',%u,'%s',%u,'%s')", 
 	tableName,  el->geneName,  el->skipPSet,  el->incCount,  incPSetsArray ,  el->geneCount,  genePSetsArray );
 sqlUpdate(conn, update->string);
-freeDyString(&update);
+dyStringFree(&update);
 freez(&incPSetsArray);
 freez(&genePSetsArray);
 }
 
 
 struct mouseAPSetEventMap *mouseAPSetEventMapCommaIn(char **pS, struct mouseAPSetEventMap *ret)
 /* Create a mouseAPSetEventMap out of a comma separated string. 
  * This will fill in ret if non-null, otherwise will
  * return a new mouseAPSetEventMap */
 {
 char *s = *pS;
 
 if (ret == NULL)
     AllocVar(ret);
 ret->geneName = sqlStringComma(&s);
 ret->skipPSet = sqlStringComma(&s);
 ret->incCount = sqlUnsignedComma(&s);
 {
 int i;
 s = sqlEatChar(s, '{');
 AllocArray(ret->incPSets, ret->incCount);
 for (i=0; i<ret->incCount; ++i)
     {
     ret->incPSets[i] = sqlStringComma(&s);
     }
 s = sqlEatChar(s, '}');
 s = sqlEatChar(s, ',');
 }
 ret->geneCount = sqlUnsignedComma(&s);
 {
 int i;
 s = sqlEatChar(s, '{');
 AllocArray(ret->genePSets, ret->geneCount);
 for (i=0; i<ret->geneCount; ++i)
     {
     ret->genePSets[i] = sqlStringComma(&s);
     }
 s = sqlEatChar(s, '}');
 s = sqlEatChar(s, ',');
 }
 *pS = s;
 return ret;
 }
 
 void mouseAPSetEventMapFree(struct mouseAPSetEventMap **pEl)
 /* Free a single dynamically allocated mouseAPSetEventMap such as created
  * with mouseAPSetEventMapLoad(). */
 {
 struct mouseAPSetEventMap *el;
 
 if ((el = *pEl) == NULL) return;
 freeMem(el->geneName);
 freeMem(el->skipPSet);
 /* All strings in incPSets are allocated at once, so only need to free first. */
 if (el->incPSets != NULL)
     freeMem(el->incPSets[0]);
 freeMem(el->incPSets);
 /* All strings in genePSets are allocated at once, so only need to free first. */
 if (el->genePSets != NULL)
     freeMem(el->genePSets[0]);
 freeMem(el->genePSets);
 freez(pEl);
 }
 
 void mouseAPSetEventMapFreeList(struct mouseAPSetEventMap **pList)
 /* Free a list of dynamically allocated mouseAPSetEventMap's */
 {
 struct mouseAPSetEventMap *el, *next;
 
 for (el = *pList; el != NULL; el = next)
     {
     next = el->next;
     mouseAPSetEventMapFree(&el);
     }
 *pList = NULL;
 }
 
 void mouseAPSetEventMapOutput(struct mouseAPSetEventMap *el, FILE *f, char sep, char lastSep) 
 /* Print out mouseAPSetEventMap.  Separate fields with sep. Follow last field with lastSep. */
 {
 if (sep == ',') fputc('"',f);
 fprintf(f, "%s", el->geneName);
 if (sep == ',') fputc('"',f);
 fputc(sep,f);
 if (sep == ',') fputc('"',f);
 fprintf(f, "%s", el->skipPSet);
 if (sep == ',') fputc('"',f);
 fputc(sep,f);
 fprintf(f, "%u", el->incCount);
 fputc(sep,f);
 {
 int i;
 if (sep == ',') fputc('{',f);
 for (i=0; i<el->incCount; ++i)
     {
     if (sep == ',') fputc('"',f);
     fprintf(f, "%s", el->incPSets[i]);
     if (sep == ',') fputc('"',f);
     fputc(',', f);
     }
 if (sep == ',') fputc('}',f);
 }
 fputc(sep,f);
 fprintf(f, "%u", el->geneCount);
 fputc(sep,f);
 {
 int i;
 if (sep == ',') fputc('{',f);
 for (i=0; i<el->geneCount; ++i)
     {
     if (sep == ',') fputc('"',f);
     fprintf(f, "%s", el->genePSets[i]);
     if (sep == ',') fputc('"',f);
     fputc(',', f);
     }
 if (sep == ',') fputc('}',f);
 }
 fputc(lastSep,f);
 }
 
 /* -------------------------------- End autoSql Generated Code -------------------------------- */