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/geneBounds/lib/improbRunInfo.c src/hg/geneBounds/lib/improbRunInfo.c
index 8f91241..8afcd4b 100644
--- src/hg/geneBounds/lib/improbRunInfo.c
+++ src/hg/geneBounds/lib/improbRunInfo.c
@@ -1,253 +1,253 @@
 /* improbRunInfo.c was originally generated by the autoSql program, which also 
  * generated improbRunInfo.h and improbRunInfo.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 "improbRunInfo.h"
 
 
 struct improbRunInfo *improbRunInfoLoad(char **row)
 /* Load a improbRunInfo from row fetched with select * from improbRunInfo
  * from database.  Dispose of this with improbRunInfoFree(). */
 {
 struct improbRunInfo *ret;
 int sizeOne;
 
 AllocVar(ret);
 ret->columnCount = sqlSigned(row[9]);
 ret->controlCount = sqlSigned(row[14]);
 ret->name = cloneString(row[0]);
 ret->runScore = atof(row[1]);
 ret->bestControlScore = atof(row[2]);
 ret->meanControlScore = atof(row[3]);
 ret->sdControlScore = atof(row[4]);
 ret->seqCount = sqlSigned(row[5]);
 ret->consensus = cloneString(row[6]);
 ret->runPos = atof(row[7]);
 ret->runPosSd = atof(row[8]);
 sqlFloatDynamicArray(row[10], &ret->aProb, &sizeOne);
 assert(sizeOne == ret->columnCount);
 sqlFloatDynamicArray(row[11], &ret->cProb, &sizeOne);
 assert(sizeOne == ret->columnCount);
 sqlFloatDynamicArray(row[12], &ret->gProb, &sizeOne);
 assert(sizeOne == ret->columnCount);
 sqlFloatDynamicArray(row[13], &ret->tProb, &sizeOne);
 assert(sizeOne == ret->columnCount);
 sqlFloatDynamicArray(row[15], &ret->controlScores, &sizeOne);
 assert(sizeOne == ret->controlCount);
 return ret;
 }
 
 struct improbRunInfo *improbRunInfoLoadAll(char *fileName) 
 /* Load all improbRunInfo from a tab-separated file.
  * Dispose of this with improbRunInfoFreeList(). */
 {
 struct improbRunInfo *list = NULL, *el;
 struct lineFile *lf = lineFileOpen(fileName, TRUE);
 char *row[16];
 
 while (lineFileRow(lf, row))
     {
     el = improbRunInfoLoad(row);
     slAddHead(&list, el);
     }
 lineFileClose(&lf);
 slReverse(&list);
 return list;
 }
 
 struct improbRunInfo *improbRunInfoLoadWhere(struct sqlConnection *conn, char *table, char *where)
 /* Load all improbRunInfo from table that satisfy where clause. The
  * where clause may be NULL in which case whole table is loaded
  * Dispose of this with improbRunInfoFreeList(). */
 {
 struct improbRunInfo *list = NULL, *el;
 struct dyString *query = dyStringNew(256);
 struct sqlResult *sr;
 char **row;
 
 sqlDyStringPrintf(query, "select * from %s", table);
 if (where != NULL)
-    dyStringPrintf(query, " where %s", where);
+    sqlDyStringPrintf(query, " where %-s", where);
 sr = sqlGetResult(conn, query->string);
 while ((row = sqlNextRow(sr)) != NULL)
     {
     el = improbRunInfoLoad(row);
     slAddHead(&list, el);
     }
 slReverse(&list);
 sqlFreeResult(&sr);
 dyStringFree(&query);
 return list;
 }
 
 struct improbRunInfo *improbRunInfoCommaIn(char **pS, struct improbRunInfo *ret)
 /* Create a improbRunInfo out of a comma separated string. 
  * This will fill in ret if non-null, otherwise will
  * return a new improbRunInfo */
 {
 char *s = *pS;
 int i;
 
 if (ret == NULL)
     AllocVar(ret);
 ret->name = sqlStringComma(&s);
 ret->runScore = sqlFloatComma(&s);
 ret->bestControlScore = sqlFloatComma(&s);
 ret->meanControlScore = sqlFloatComma(&s);
 ret->sdControlScore = sqlFloatComma(&s);
 ret->seqCount = sqlSignedComma(&s);
 ret->consensus = sqlStringComma(&s);
 ret->runPos = sqlFloatComma(&s);
 ret->runPosSd = sqlFloatComma(&s);
 ret->columnCount = sqlSignedComma(&s);
 s = sqlEatChar(s, '{');
 AllocArray(ret->aProb, ret->columnCount);
 for (i=0; i<ret->columnCount; ++i)
     {
     ret->aProb[i] = sqlFloatComma(&s);
     }
 s = sqlEatChar(s, '}');
 s = sqlEatChar(s, ',');
 s = sqlEatChar(s, '{');
 AllocArray(ret->cProb, ret->columnCount);
 for (i=0; i<ret->columnCount; ++i)
     {
     ret->cProb[i] = sqlFloatComma(&s);
     }
 s = sqlEatChar(s, '}');
 s = sqlEatChar(s, ',');
 s = sqlEatChar(s, '{');
 AllocArray(ret->gProb, ret->columnCount);
 for (i=0; i<ret->columnCount; ++i)
     {
     ret->gProb[i] = sqlFloatComma(&s);
     }
 s = sqlEatChar(s, '}');
 s = sqlEatChar(s, ',');
 s = sqlEatChar(s, '{');
 AllocArray(ret->tProb, ret->columnCount);
 for (i=0; i<ret->columnCount; ++i)
     {
     ret->tProb[i] = sqlFloatComma(&s);
     }
 s = sqlEatChar(s, '}');
 s = sqlEatChar(s, ',');
 ret->controlCount = sqlSignedComma(&s);
 s = sqlEatChar(s, '{');
 AllocArray(ret->controlScores, ret->controlCount);
 for (i=0; i<ret->controlCount; ++i)
     {
     ret->controlScores[i] = sqlFloatComma(&s);
     }
 s = sqlEatChar(s, '}');
 s = sqlEatChar(s, ',');
 *pS = s;
 return ret;
 }
 
 void improbRunInfoFree(struct improbRunInfo **pEl)
 /* Free a single dynamically allocated improbRunInfo such as created
  * with improbRunInfoLoad(). */
 {
 struct improbRunInfo *el;
 
 if ((el = *pEl) == NULL) return;
 freeMem(el->name);
 freeMem(el->consensus);
 freeMem(el->aProb);
 freeMem(el->cProb);
 freeMem(el->gProb);
 freeMem(el->tProb);
 freeMem(el->controlScores);
 freez(pEl);
 }
 
 void improbRunInfoFreeList(struct improbRunInfo **pList)
 /* Free a list of dynamically allocated improbRunInfo's */
 {
 struct improbRunInfo *el, *next;
 
 for (el = *pList; el != NULL; el = next)
     {
     next = el->next;
     improbRunInfoFree(&el);
     }
 *pList = NULL;
 }
 
 void improbRunInfoOutput(struct improbRunInfo *el, FILE *f, char sep, char lastSep) 
 /* Print out improbRunInfo.  Separate fields with sep. Follow last field with lastSep. */
 {
 int i;
 if (sep == ',') fputc('"',f);
 fprintf(f, "%s", el->name);
 if (sep == ',') fputc('"',f);
 fputc(sep,f);
 fprintf(f, "%f", el->runScore);
 fputc(sep,f);
 fprintf(f, "%f", el->bestControlScore);
 fputc(sep,f);
 fprintf(f, "%f", el->meanControlScore);
 fputc(sep,f);
 fprintf(f, "%f", el->sdControlScore);
 fputc(sep,f);
 fprintf(f, "%d", el->seqCount);
 fputc(sep,f);
 if (sep == ',') fputc('"',f);
 fprintf(f, "%s", el->consensus);
 if (sep == ',') fputc('"',f);
 fputc(sep,f);
 fprintf(f, "%f", el->runPos);
 fputc(sep,f);
 fprintf(f, "%f", el->runPosSd);
 fputc(sep,f);
 fprintf(f, "%d", el->columnCount);
 fputc(sep,f);
 if (sep == ',') fputc('{',f);
 for (i=0; i<el->columnCount; ++i)
     {
     fprintf(f, "%f", el->aProb[i]);
     fputc(',', f);
     }
 if (sep == ',') fputc('}',f);
 fputc(sep,f);
 if (sep == ',') fputc('{',f);
 for (i=0; i<el->columnCount; ++i)
     {
     fprintf(f, "%f", el->cProb[i]);
     fputc(',', f);
     }
 if (sep == ',') fputc('}',f);
 fputc(sep,f);
 if (sep == ',') fputc('{',f);
 for (i=0; i<el->columnCount; ++i)
     {
     fprintf(f, "%f", el->gProb[i]);
     fputc(',', f);
     }
 if (sep == ',') fputc('}',f);
 fputc(sep,f);
 if (sep == ',') fputc('{',f);
 for (i=0; i<el->columnCount; ++i)
     {
     fprintf(f, "%f", el->tProb[i]);
     fputc(',', f);
     }
 if (sep == ',') fputc('}',f);
 fputc(sep,f);
 fprintf(f, "%d", el->controlCount);
 fputc(sep,f);
 if (sep == ',') fputc('{',f);
 for (i=0; i<el->controlCount; ++i)
     {
     fprintf(f, "%f", el->controlScores[i]);
     fputc(',', f);
     }
 if (sep == ',') fputc('}',f);
 fputc(lastSep,f);
 }