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/hubPublic.c src/hg/lib/hubPublic.c
index 98fcb2e..9eb16f3 100644
--- src/hg/lib/hubPublic.c
+++ src/hg/lib/hubPublic.c
@@ -1,275 +1,275 @@
 /* hubPublic.c was originally generated by the autoSql program, which also 
  * generated hubPublic.h and hubPublic.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 "hubPublic.h"
 
 
 char *hubPublicCommaSepFieldNames = "hubUrl,shortLabel,longLabel,registrationTime,dbCount,dbList,descriptionUrl";
 
 void hubPublicStaticLoad(char **row, struct hubPublic *ret)
 /* Load a row from hubPublic table into ret.  The contents of ret will
  * be replaced at the next call to this function. */
 {
 
 ret->hubUrl = row[0];
 ret->shortLabel = row[1];
 ret->longLabel = row[2];
 ret->registrationTime = row[3];
 ret->dbCount = sqlUnsigned(row[4]);
 ret->dbList = row[5];
 ret->descriptionUrl = row[6];
 }
 
 struct hubPublic *hubPublicLoadByQuery(struct sqlConnection *conn, char *query)
 /* Load all hubPublic 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 hubPublicFreeList(). */
 {
 struct hubPublic *list = NULL, *el;
 struct sqlResult *sr;
 char **row;
 
 sr = sqlGetResult(conn, query);
 while ((row = sqlNextRow(sr)) != NULL)
     {
     el = hubPublicLoad(row);
     slAddHead(&list, el);
     }
 slReverse(&list);
 sqlFreeResult(&sr);
 return list;
 }
 
 void hubPublicSaveToDb(struct sqlConnection *conn, struct hubPublic *el, char *tableName, int updateSize)
 /* Save hubPublic 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);
 sqlDyStringPrintf(update, "insert into %s values ( '%s','%s','%s','%s',%u,'%s','%s')", 
 	tableName,  el->hubUrl,  el->shortLabel,  el->longLabel,  el->registrationTime,  el->dbCount,  el->dbList,  el->descriptionUrl);
 sqlUpdate(conn, update->string);
-freeDyString(&update);
+dyStringFree(&update);
 }
 
 struct hubPublic *hubPublicLoad(char **row)
 /* Load a hubPublic from row fetched with select * from hubPublic
  * from database.  Dispose of this with hubPublicFree(). */
 {
 struct hubPublic *ret;
 
 AllocVar(ret);
 ret->hubUrl = cloneString(row[0]);
 ret->shortLabel = cloneString(row[1]);
 ret->longLabel = cloneString(row[2]);
 ret->registrationTime = cloneString(row[3]);
 ret->dbCount = sqlUnsigned(row[4]);
 ret->dbList = cloneString(row[5]);
 ret->descriptionUrl = cloneString(row[6]);
 return ret;
 }
 
 struct hubPublic *hubPublicLoadAll(char *fileName) 
 /* Load all hubPublic from a whitespace-separated file.
  * Dispose of this with hubPublicFreeList(). */
 {
 struct hubPublic *list = NULL, *el;
 struct lineFile *lf = lineFileOpen(fileName, TRUE);
 char *row[7];
 
 while (lineFileRow(lf, row))
     {
     el = hubPublicLoad(row);
     slAddHead(&list, el);
     }
 lineFileClose(&lf);
 slReverse(&list);
 return list;
 }
 
 struct hubPublic *hubPublicLoadAllByChar(char *fileName, char chopper) 
 /* Load all hubPublic from a chopper separated file.
  * Dispose of this with hubPublicFreeList(). */
 {
 struct hubPublic *list = NULL, *el;
 struct lineFile *lf = lineFileOpen(fileName, TRUE);
 char *row[7];
 
 while (lineFileNextCharRow(lf, chopper, row, ArraySize(row)))
     {
     el = hubPublicLoad(row);
     slAddHead(&list, el);
     }
 lineFileClose(&lf);
 slReverse(&list);
 return list;
 }
 
 struct hubPublic *hubPublicCommaIn(char **pS, struct hubPublic *ret)
 /* Create a hubPublic out of a comma separated string. 
  * This will fill in ret if non-null, otherwise will
  * return a new hubPublic */
 {
 char *s = *pS;
 
 if (ret == NULL)
     AllocVar(ret);
 ret->hubUrl = sqlStringComma(&s);
 ret->shortLabel = sqlStringComma(&s);
 ret->longLabel = sqlStringComma(&s);
 ret->registrationTime = sqlStringComma(&s);
 ret->dbCount = sqlUnsignedComma(&s);
 ret->dbList = sqlStringComma(&s);
 ret->descriptionUrl = sqlStringComma(&s);
 *pS = s;
 return ret;
 }
 
 void hubPublicFree(struct hubPublic **pEl)
 /* Free a single dynamically allocated hubPublic such as created
  * with hubPublicLoad(). */
 {
 struct hubPublic *el;
 
 if ((el = *pEl) == NULL) return;
 freeMem(el->hubUrl);
 freeMem(el->shortLabel);
 freeMem(el->longLabel);
 freeMem(el->registrationTime);
 freeMem(el->dbList);
 freeMem(el->descriptionUrl);
 freez(pEl);
 }
 
 void hubPublicFreeList(struct hubPublic **pList)
 /* Free a list of dynamically allocated hubPublic's */
 {
 struct hubPublic *el, *next;
 
 for (el = *pList; el != NULL; el = next)
     {
     next = el->next;
     hubPublicFree(&el);
     }
 *pList = NULL;
 }
 
 void hubPublicOutput(struct hubPublic *el, FILE *f, char sep, char lastSep) 
 /* Print out hubPublic.  Separate fields with sep. Follow last field with lastSep. */
 {
 if (sep == ',') fputc('"',f);
 fprintf(f, "%s", el->hubUrl);
 if (sep == ',') fputc('"',f);
 fputc(sep,f);
 if (sep == ',') fputc('"',f);
 fprintf(f, "%s", el->shortLabel);
 if (sep == ',') fputc('"',f);
 fputc(sep,f);
 if (sep == ',') fputc('"',f);
 fprintf(f, "%s", el->longLabel);
 if (sep == ',') fputc('"',f);
 fputc(sep,f);
 if (sep == ',') fputc('"',f);
 fprintf(f, "%s", el->registrationTime);
 if (sep == ',') fputc('"',f);
 fputc(sep,f);
 fprintf(f, "%u", el->dbCount);
 fputc(sep,f);
 if (sep == ',') fputc('"',f);
 fprintf(f, "%s", el->dbList);
 if (sep == ',') fputc('"',f);
 fputc(sep,f);
 if (sep == ',') fputc('"',f);
 fprintf(f, "%s", el->descriptionUrl);
 if (sep == ',') fputc('"',f);
 fputc(lastSep,f);
 }
 
 void hubPublicJsonOutput(struct hubPublic *el, FILE *f) 
 /* Print out hubPublic in JSON format. */
 {
 fputc('{',f);
 fputc('"',f);
 fprintf(f,"hubUrl");
 fputc('"',f);
 fputc(':',f);
 fputc('"',f);
 fprintf(f, "%s", el->hubUrl);
 fputc('"',f);
 fputc(',',f);
 fputc('"',f);
 fprintf(f,"shortLabel");
 fputc('"',f);
 fputc(':',f);
 fputc('"',f);
 fprintf(f, "%s", el->shortLabel);
 fputc('"',f);
 fputc(',',f);
 fputc('"',f);
 fprintf(f,"longLabel");
 fputc('"',f);
 fputc(':',f);
 fputc('"',f);
 fprintf(f, "%s", el->longLabel);
 fputc('"',f);
 fputc(',',f);
 fputc('"',f);
 fprintf(f,"registrationTime");
 fputc('"',f);
 fputc(':',f);
 fputc('"',f);
 fprintf(f, "%s", el->registrationTime);
 fputc('"',f);
 fputc(',',f);
 fputc('"',f);
 fprintf(f,"dbCount");
 fputc('"',f);
 fputc(':',f);
 fprintf(f, "%u", el->dbCount);
 fputc(',',f);
 fputc('"',f);
 fprintf(f,"dbList");
 fputc('"',f);
 fputc(':',f);
 fputc('"',f);
 fprintf(f, "%s", el->dbList);
 fputc('"',f);
 fputc(',',f);
 fputc('"',f);
 fprintf(f,"descriptionUrl");
 fputc('"',f);
 fputc(':',f);
 fputc('"',f);
 fprintf(f, "%s", el->descriptionUrl);
 fputc('"',f);
 fputc('}',f);
 }
 
 /* -------------------------------- End autoSql Generated Code -------------------------------- */
 
 
 struct hubEntry *hubEntryTextLoad(char **row, bool hasDescription)
 {
 struct hubEntry *ret;
 AllocVar(ret);
 ret->hubUrl = cloneString(row[0]);
 ret->shortLabel = cloneString(row[1]);
 ret->longLabel = cloneString(row[2]);
 ret->dbList = cloneString(row[3]);
 ret->errorMessage = cloneString(row[4]);
 ret->id = sqlUnsigned(row[5]);
 if (hasDescription)
     ret->descriptionUrl = cloneString(row[6]);
 else
     ret->descriptionUrl = NULL;
 return ret;
 }