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/autoSql/tests/expected/newTest.c src/hg/autoSql/tests/expected/newTest.c
index ba4502e..adba7d6 100644
--- src/hg/autoSql/tests/expected/newTest.c
+++ src/hg/autoSql/tests/expected/newTest.c
@@ -1,408 +1,408 @@
 /* newTest.c was originally generated by the autoSql program, which also 
  * generated newTest.h and newTest.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 "output/newTest.h"
 
 
 
 char *pointCommaSepFieldNames = "x,y";
 
 struct point *pointLoad(char **row)
 /* Load a point from row fetched with select * from point
  * from database.  Dispose of this with pointFree(). */
 {
 struct point *ret;
 
 AllocVar(ret);
 ret->x = sqlSigned(row[0]);
 ret->y = sqlSigned(row[1]);
 return ret;
 }
 
 struct point *pointLoadAll(char *fileName) 
 /* Load all point from a whitespace-separated file.
  * Dispose of this with pointFreeList(). */
 {
 struct point *list = NULL, *el;
 struct lineFile *lf = lineFileOpen(fileName, TRUE);
 char *row[2];
 
 while (lineFileRow(lf, row))
     {
     el = pointLoad(row);
     slAddHead(&list, el);
     }
 lineFileClose(&lf);
 slReverse(&list);
 return list;
 }
 
 struct point *pointLoadAllByChar(char *fileName, char chopper) 
 /* Load all point from a chopper separated file.
  * Dispose of this with pointFreeList(). */
 {
 struct point *list = NULL, *el;
 struct lineFile *lf = lineFileOpen(fileName, TRUE);
 char *row[2];
 
 while (lineFileNextCharRow(lf, chopper, row, ArraySize(row)))
     {
     el = pointLoad(row);
     slAddHead(&list, el);
     }
 lineFileClose(&lf);
 slReverse(&list);
 return list;
 }
 
 struct point *pointCommaIn(char **pS, struct point *ret)
 /* Create a point out of a comma separated string. 
  * This will fill in ret if non-null, otherwise will
  * return a new point */
 {
 char *s = *pS;
 
 if (ret == NULL)
     AllocVar(ret);
 ret->x = sqlSignedComma(&s);
 ret->y = sqlSignedComma(&s);
 *pS = s;
 return ret;
 }
 
 void pointFree(struct point **pEl)
 /* Free a single dynamically allocated point such as created
  * with pointLoad(). */
 {
 struct point *el;
 
 if ((el = *pEl) == NULL) return;
 freez(pEl);
 }
 
 void pointFreeList(struct point **pList)
 /* Free a list of dynamically allocated point's */
 {
 struct point *el, *next;
 
 for (el = *pList; el != NULL; el = next)
     {
     next = el->next;
     pointFree(&el);
     }
 *pList = NULL;
 }
 
 void pointOutput(struct point *el, FILE *f, char sep, char lastSep) 
 /* Print out point.  Separate fields with sep. Follow last field with lastSep. */
 {
 fprintf(f, "%d", el->x);
 fputc(sep,f);
 fprintf(f, "%d", el->y);
 fputc(lastSep,f);
 }
 
 
 char *autoTestCommaSepFieldNames = "id,shortName,longName,aliases,ptCount,pts,difCount,difs,xy,valCount,vals";
 
 struct autoTest *autoTestLoadByQuery(struct sqlConnection *conn, char *query)
 /* Load all autoTest 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 autoTestFreeList(). */
 {
 struct autoTest *list = NULL, *el;
 struct sqlResult *sr;
 char **row;
 
 sr = sqlGetResult(conn, query);
 while ((row = sqlNextRow(sr)) != NULL)
     {
     el = autoTestLoad(row);
     slAddHead(&list, el);
     }
 slReverse(&list);
 sqlFreeResult(&sr);
 return list;
 }
 
 void autoTestSaveToDb(struct sqlConnection *conn, struct autoTest *el, char *tableName, int updateSize)
 /* Save autoTest 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. This function automatically escapes quoted strings for mysql. */
 {
-struct dyString *update = newDyString(updateSize);
+struct dyString *update = dyStringNew(updateSize);
 char  *aliasesArray, *ptsArray, *difsArray, *valsArray;
 aliasesArray = sqlStringArrayToString(el->aliases, 3);
 ptsArray = sqlShortArrayToString(el->pts, el->ptCount);
 difsArray = sqlUbyteArrayToString(el->difs, el->difCount);
 valsArray = sqlStringArrayToString(el->vals, el->valCount);
 sqlDyStringPrintf(update, "insert into %s values ( %u,'%s','%s','%s',%d,'%s',%d,'%s', NULL ,%d,'%s')", 
 	tableName,  el->id,  el->shortName,  el->longName,  aliasesArray ,  el->ptCount,  ptsArray ,  el->difCount,  difsArray ,  el->valCount,  valsArray );
 sqlUpdate(conn, update->string);
-freeDyString(&update);
+dyStringFree(&update);
 freez(&aliasesArray);
 freez(&ptsArray);
 freez(&difsArray);
 freez(&valsArray);
 }
 
 struct autoTest *autoTestLoad(char **row)
 /* Load a autoTest from row fetched with select * from autoTest
  * from database.  Dispose of this with autoTestFree(). */
 {
 struct autoTest *ret;
 
 AllocVar(ret);
 ret->ptCount = sqlSigned(row[4]);
 ret->difCount = sqlSigned(row[6]);
 ret->valCount = sqlSigned(row[9]);
 ret->id = sqlUnsigned(row[0]);
 safecpy(ret->shortName, sizeof(ret->shortName), row[1]);
 ret->longName = cloneString(row[2]);
 {
 char *s = cloneString(row[3]);
 sqlStringArray(s, ret->aliases, 3);
 }
 {
 int sizeOne;
 sqlShortDynamicArray(row[5], &ret->pts, &sizeOne);
 assert(sizeOne == ret->ptCount);
 }
 {
 int sizeOne;
 sqlUbyteDynamicArray(row[7], &ret->difs, &sizeOne);
 assert(sizeOne == ret->difCount);
 }
 {
 char *s = row[8];
 if(s != NULL && differentString(s, ""))
    ret->xy = pointCommaIn(&s, NULL);
 }
 {
 int sizeOne;
 sqlStringDynamicArray(row[10], &ret->vals, &sizeOne);
 assert(sizeOne == ret->valCount);
 }
 return ret;
 }
 
 struct autoTest *autoTestLoadAll(char *fileName) 
 /* Load all autoTest from a whitespace-separated file.
  * Dispose of this with autoTestFreeList(). */
 {
 struct autoTest *list = NULL, *el;
 struct lineFile *lf = lineFileOpen(fileName, TRUE);
 char *row[11];
 
 while (lineFileRow(lf, row))
     {
     el = autoTestLoad(row);
     slAddHead(&list, el);
     }
 lineFileClose(&lf);
 slReverse(&list);
 return list;
 }
 
 struct autoTest *autoTestLoadAllByChar(char *fileName, char chopper) 
 /* Load all autoTest from a chopper separated file.
  * Dispose of this with autoTestFreeList(). */
 {
 struct autoTest *list = NULL, *el;
 struct lineFile *lf = lineFileOpen(fileName, TRUE);
 char *row[11];
 
 while (lineFileNextCharRow(lf, chopper, row, ArraySize(row)))
     {
     el = autoTestLoad(row);
     slAddHead(&list, el);
     }
 lineFileClose(&lf);
 slReverse(&list);
 return list;
 }
 
 struct autoTest *autoTestCommaIn(char **pS, struct autoTest *ret)
 /* Create a autoTest out of a comma separated string. 
  * This will fill in ret if non-null, otherwise will
  * return a new autoTest */
 {
 char *s = *pS;
 
 if (ret == NULL)
     AllocVar(ret);
 ret->id = sqlUnsignedComma(&s);
 sqlFixedStringComma(&s, ret->shortName, sizeof(ret->shortName));
 ret->longName = sqlStringComma(&s);
 {
 int i;
 s = sqlEatChar(s, '{');
 for (i=0; i<3; ++i)
     {
     ret->aliases[i] = sqlStringComma(&s);
     }
 s = sqlEatChar(s, '}');
 s = sqlEatChar(s, ',');
 }
 ret->ptCount = sqlSignedComma(&s);
 {
 int i;
 s = sqlEatChar(s, '{');
 AllocArray(ret->pts, ret->ptCount);
 for (i=0; i<ret->ptCount; ++i)
     {
     ret->pts[i] = sqlSignedComma(&s);
     }
 s = sqlEatChar(s, '}');
 s = sqlEatChar(s, ',');
 }
 ret->difCount = sqlSignedComma(&s);
 {
 int i;
 s = sqlEatChar(s, '{');
 AllocArray(ret->difs, ret->difCount);
 for (i=0; i<ret->difCount; ++i)
     {
     ret->difs[i] = sqlUnsignedComma(&s);
     }
 s = sqlEatChar(s, '}');
 s = sqlEatChar(s, ',');
 }
 s = sqlEatChar(s, '{');
 if(s[0] != '}')    slSafeAddHead(&ret->xy, pointCommaIn(&s,NULL));
 s = sqlEatChar(s, '}');
 s = sqlEatChar(s, ',');
 ret->valCount = sqlSignedComma(&s);
 {
 int i;
 s = sqlEatChar(s, '{');
 AllocArray(ret->vals, ret->valCount);
 for (i=0; i<ret->valCount; ++i)
     {
     ret->vals[i] = sqlStringComma(&s);
     }
 s = sqlEatChar(s, '}');
 s = sqlEatChar(s, ',');
 }
 *pS = s;
 return ret;
 }
 
 void autoTestFree(struct autoTest **pEl)
 /* Free a single dynamically allocated autoTest such as created
  * with autoTestLoad(). */
 {
 struct autoTest *el;
 
 if ((el = *pEl) == NULL) return;
 freeMem(el->longName);
 /* All strings in aliases are allocated at once, so only need to free first. */
 if (el->aliases != NULL)
     freeMem(el->aliases[0]);
 freeMem(el->pts);
 freeMem(el->difs);
 pointFreeList(&el->xy);
 /* All strings in vals are allocated at once, so only need to free first. */
 if (el->vals != NULL)
     freeMem(el->vals[0]);
 freeMem(el->vals);
 freez(pEl);
 }
 
 void autoTestFreeList(struct autoTest **pList)
 /* Free a list of dynamically allocated autoTest's */
 {
 struct autoTest *el, *next;
 
 for (el = *pList; el != NULL; el = next)
     {
     next = el->next;
     autoTestFree(&el);
     }
 *pList = NULL;
 }
 
 void autoTestOutput(struct autoTest *el, FILE *f, char sep, char lastSep) 
 /* Print out autoTest.  Separate fields with sep. Follow last field with lastSep. */
 {
 fprintf(f, "%u", el->id);
 fputc(sep,f);
 if (sep == ',') fputc('"',f);
 fprintf(f, "%s", el->shortName);
 if (sep == ',') fputc('"',f);
 fputc(sep,f);
 if (sep == ',') fputc('"',f);
 fprintf(f, "%s", el->longName);
 if (sep == ',') fputc('"',f);
 fputc(sep,f);
 {
 int i;
 if (sep == ',') fputc('{',f);
 for (i=0; i<3; ++i)
     {
     if (sep == ',') fputc('"',f);
     fprintf(f, "%s", el->aliases[i]);
     if (sep == ',') fputc('"',f);
     fputc(',', f);
     }
 if (sep == ',') fputc('}',f);
 }
 fputc(sep,f);
 fprintf(f, "%d", el->ptCount);
 fputc(sep,f);
 {
 int i;
 if (sep == ',') fputc('{',f);
 for (i=0; i<el->ptCount; ++i)
     {
     fprintf(f, "%d", el->pts[i]);
     fputc(',', f);
     }
 if (sep == ',') fputc('}',f);
 }
 fputc(sep,f);
 fprintf(f, "%d", el->difCount);
 fputc(sep,f);
 {
 int i;
 if (sep == ',') fputc('{',f);
 for (i=0; i<el->difCount; ++i)
     {
     fprintf(f, "%u", el->difs[i]);
     fputc(',', f);
     }
 if (sep == ',') fputc('}',f);
 }
 fputc(sep,f);
 if (sep == ',') fputc('{',f);
 if(el->xy != NULL)    pointCommaOut(el->xy,f);
 if (sep == ',') fputc('}',f);
 fputc(sep,f);
 fprintf(f, "%d", el->valCount);
 fputc(sep,f);
 {
 int i;
 if (sep == ',') fputc('{',f);
 for (i=0; i<el->valCount; ++i)
     {
     if (sep == ',') fputc('"',f);
     fprintf(f, "%s", el->vals[i]);
     if (sep == ',') fputc('"',f);
     fputc(',', f);
     }
 if (sep == ',') fputc('}',f);
 }
 fputc(lastSep,f);
 }
 
 /* -------------------------------- End autoSql Generated Code -------------------------------- */