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/gtexTissueData.c src/hg/lib/gtexTissueData.c
index 53caaa3..0ec55fb 100644
--- src/hg/lib/gtexTissueData.c
+++ src/hg/lib/gtexTissueData.c
@@ -1,187 +1,187 @@
 /* gtexTissueData.c was originally generated by the autoSql program, which also 
  * generated gtexTissueData.h and gtexTissueData.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 "gtexTissueData.h"
 
 
 
 char *gtexTissueDataCommaSepFieldNames = "geneId,tissue,min,q1,median,q3,max";
 
 void gtexTissueDataStaticLoad(char **row, struct gtexTissueData *ret)
 /* Load a row from gtexTissueData table into ret.  The contents of ret will
  * be replaced at the next call to this function. */
 {
 
 ret->geneId = row[0];
 ret->tissue = row[1];
 ret->min = sqlDouble(row[2]);
 ret->q1 = sqlDouble(row[3]);
 ret->median = sqlDouble(row[4]);
 ret->q3 = sqlDouble(row[5]);
 ret->max = sqlDouble(row[6]);
 }
 
 struct gtexTissueData *gtexTissueDataLoadByQuery(struct sqlConnection *conn, char *query)
 /* Load all gtexTissueData 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 gtexTissueDataFreeList(). */
 {
 struct gtexTissueData *list = NULL, *el;
 struct sqlResult *sr;
 char **row;
 
 sr = sqlGetResult(conn, query);
 while ((row = sqlNextRow(sr)) != NULL)
     {
     el = gtexTissueDataLoad(row);
     slAddHead(&list, el);
     }
 slReverse(&list);
 sqlFreeResult(&sr);
 return list;
 }
 
 void gtexTissueDataSaveToDb(struct sqlConnection *conn, struct gtexTissueData *el, char *tableName, int updateSize)
 /* Save gtexTissueData 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',%g,%g,%g,%g,%g)", 
 	tableName,  el->geneId,  el->tissue,  el->min,  el->q1,  el->median,  el->q3,  el->max);
 sqlUpdate(conn, update->string);
-freeDyString(&update);
+dyStringFree(&update);
 }
 
 struct gtexTissueData *gtexTissueDataLoad(char **row)
 /* Load a gtexTissueData from row fetched with select * from gtexTissueData
  * from database.  Dispose of this with gtexTissueDataFree(). */
 {
 struct gtexTissueData *ret;
 
 AllocVar(ret);
 ret->geneId = cloneString(row[0]);
 ret->tissue = cloneString(row[1]);
 ret->min = sqlDouble(row[2]);
 ret->q1 = sqlDouble(row[3]);
 ret->median = sqlDouble(row[4]);
 ret->q3 = sqlDouble(row[5]);
 ret->max = sqlDouble(row[6]);
 return ret;
 }
 
 struct gtexTissueData *gtexTissueDataLoadAll(char *fileName) 
 /* Load all gtexTissueData from a whitespace-separated file.
  * Dispose of this with gtexTissueDataFreeList(). */
 {
 struct gtexTissueData *list = NULL, *el;
 struct lineFile *lf = lineFileOpen(fileName, TRUE);
 char *row[7];
 
 while (lineFileRow(lf, row))
     {
     el = gtexTissueDataLoad(row);
     slAddHead(&list, el);
     }
 lineFileClose(&lf);
 slReverse(&list);
 return list;
 }
 
 struct gtexTissueData *gtexTissueDataLoadAllByChar(char *fileName, char chopper) 
 /* Load all gtexTissueData from a chopper separated file.
  * Dispose of this with gtexTissueDataFreeList(). */
 {
 struct gtexTissueData *list = NULL, *el;
 struct lineFile *lf = lineFileOpen(fileName, TRUE);
 char *row[7];
 
 while (lineFileNextCharRow(lf, chopper, row, ArraySize(row)))
     {
     el = gtexTissueDataLoad(row);
     slAddHead(&list, el);
     }
 lineFileClose(&lf);
 slReverse(&list);
 return list;
 }
 
 struct gtexTissueData *gtexTissueDataCommaIn(char **pS, struct gtexTissueData *ret)
 /* Create a gtexTissueData out of a comma separated string. 
  * This will fill in ret if non-null, otherwise will
  * return a new gtexTissueData */
 {
 char *s = *pS;
 
 if (ret == NULL)
     AllocVar(ret);
 ret->geneId = sqlStringComma(&s);
 ret->tissue = sqlStringComma(&s);
 ret->min = sqlDoubleComma(&s);
 ret->q1 = sqlDoubleComma(&s);
 ret->median = sqlDoubleComma(&s);
 ret->q3 = sqlDoubleComma(&s);
 ret->max = sqlDoubleComma(&s);
 *pS = s;
 return ret;
 }
 
 void gtexTissueDataFree(struct gtexTissueData **pEl)
 /* Free a single dynamically allocated gtexTissueData such as created
  * with gtexTissueDataLoad(). */
 {
 struct gtexTissueData *el;
 
 if ((el = *pEl) == NULL) return;
 freeMem(el->geneId);
 freeMem(el->tissue);
 freez(pEl);
 }
 
 void gtexTissueDataFreeList(struct gtexTissueData **pList)
 /* Free a list of dynamically allocated gtexTissueData's */
 {
 struct gtexTissueData *el, *next;
 
 for (el = *pList; el != NULL; el = next)
     {
     next = el->next;
     gtexTissueDataFree(&el);
     }
 *pList = NULL;
 }
 
 void gtexTissueDataOutput(struct gtexTissueData *el, FILE *f, char sep, char lastSep) 
 /* Print out gtexTissueData.  Separate fields with sep. Follow last field with lastSep. */
 {
 if (sep == ',') fputc('"',f);
 fprintf(f, "%s", el->geneId);
 if (sep == ',') fputc('"',f);
 fputc(sep,f);
 if (sep == ',') fputc('"',f);
 fprintf(f, "%s", el->tissue);
 if (sep == ',') fputc('"',f);
 fputc(sep,f);
 fprintf(f, "%g", el->min);
 fputc(sep,f);
 fprintf(f, "%g", el->q1);
 fputc(sep,f);
 fprintf(f, "%g", el->median);
 fputc(sep,f);
 fprintf(f, "%g", el->q3);
 fputc(sep,f);
 fprintf(f, "%g", el->max);
 fputc(lastSep,f);
 }
 
 /* -------------------------------- End autoSql Generated Code -------------------------------- */