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/chainDb.c src/hg/lib/chainDb.c
index 0097cf7..701112b 100644
--- src/hg/lib/chainDb.c
+++ src/hg/lib/chainDb.c
@@ -1,166 +1,166 @@
 /* chainDb.c was originally generated by the autoSql program, which also 
  * generated chainDb.h and chainDb.sql.  This module links the database and
  * the RAM representation of objects. 
  *
  * This module was subsequently modified to blend better with the non-database
  * representation of chains.  This module really only deals with the chain
  * header in the database.  The blocks of the chain are loaded elsewhere,
  * and indeed in another table. */
 
 /* Copyright (C) 2014 The Regents of the University of California 
  * See kent/LICENSE or http://genome.ucsc.edu/license/ for licensing information. */
 
 #include "common.h"
 #include "linefile.h"
 #include "dystring.h"
 #include "jksql.h"
 #include "chain.h"
 #include "chainDb.h"
 #include "hdb.h"
 
 
 void chainHeadStaticLoad(char **row, struct chain *ret)
 /* Load a row from chain table into ret.  The contents of ret will
  * be replaced at the next call to this function. */
 {
 
 ret->score = atof(row[0]);
 ret->tName = row[1];
 ret->tSize = sqlUnsigned(row[2]);
 ret->tStart = sqlUnsigned(row[3]);
 ret->tEnd = sqlUnsigned(row[4]);
 ret->qName = row[5];
 ret->qSize = sqlUnsigned(row[6]);
 ret->qStrand = row[7][0];
 ret->qStart = sqlUnsigned(row[8]);
 ret->qEnd = sqlUnsigned(row[9]);
 ret->id = sqlUnsigned(row[10]);
 }
 
 struct chain *chainHeadLoad(char **row)
 /* Load a chain from row fetched with select * from chain
  * from database.  Dispose of this with chainFree(). */
 {
 struct chain *ret;
 
 AllocVar(ret);
 ret->score = atof(row[0]);
 ret->tName = cloneString(row[1]);
 ret->tSize = sqlUnsigned(row[2]);
 ret->tStart = sqlUnsigned(row[3]);
 ret->tEnd = sqlUnsigned(row[4]);
 ret->qName = cloneString(row[5]);
 ret->qSize = sqlUnsigned(row[6]);
 ret->qStrand = row[7][0];
 ret->qStart = sqlUnsigned(row[8]);
 ret->qEnd = sqlUnsigned(row[9]);
 ret->id = sqlUnsigned(row[10]);
 return ret;
 }
 
 struct chain *chainHeadLoadAll(char *fileName) 
 /* Load all chain from a tab-separated file.
  * Dispose of this with chainFreeList(). */
 {
 struct chain *list = NULL, *el;
 struct lineFile *lf = lineFileOpen(fileName, TRUE);
 char *row[11];
 
 while (lineFileRow(lf, row))
     {
     el = chainHeadLoad(row);
     slAddHead(&list, el);
     }
 lineFileClose(&lf);
 slReverse(&list);
 return list;
 }
 
 struct chain *chainHeadCommaIn(char **pS, struct chain *ret)
 /* Create a chain out of a comma separated string. 
  * This will fill in ret if non-null, otherwise will
  * return a new chain */
 {
 char *s = *pS;
 
 if (ret == NULL)
     AllocVar(ret);
 ret->score = sqlDoubleComma(&s);
 ret->tName = sqlStringComma(&s);
 ret->tSize = sqlUnsignedComma(&s);
 ret->tStart = sqlUnsignedComma(&s);
 ret->tEnd = sqlUnsignedComma(&s);
 ret->qName = sqlStringComma(&s);
 ret->qSize = sqlUnsignedComma(&s);
 sqlFixedStringComma(&s, &(ret->qStrand), sizeof(ret->qStrand));
 ret->qStart = sqlUnsignedComma(&s);
 ret->qEnd = sqlUnsignedComma(&s);
 ret->id = sqlUnsignedComma(&s);
 *pS = s;
 return ret;
 }
 
 void chainHeadOutput(struct chain *el, FILE *f, char sep, char lastSep) 
 /* Print out chain.  Separate fields with sep. Follow last field with lastSep. */
 {
 fprintf(f, "%f", el->score);
 fputc(sep,f);
 if (sep == ',') fputc('"',f);
 fprintf(f, "%s", el->tName);
 if (sep == ',') fputc('"',f);
 fputc(sep,f);
 fprintf(f, "%u", el->tSize);
 fputc(sep,f);
 fprintf(f, "%u", el->tStart);
 fputc(sep,f);
 fprintf(f, "%u", el->tEnd);
 fputc(sep,f);
 if (sep == ',') fputc('"',f);
 fprintf(f, "%s", el->qName);
 if (sep == ',') fputc('"',f);
 fputc(sep,f);
 fprintf(f, "%u", el->qSize);
 fputc(sep,f);
 if (sep == ',') fputc('"',f);
 fprintf(f, "%c", el->qStrand);
 if (sep == ',') fputc('"',f);
 fputc(sep,f);
 fprintf(f, "%u", el->qStart);
 fputc(sep,f);
 fprintf(f, "%u", el->qEnd);
 fputc(sep,f);
 fprintf(f, "%u", el->id);
 fputc(lastSep,f);
 }
 
 /* -------------------------------- End autoSql Generated Code -------------------------------- */
 
 void chainDbAddBlocks(struct chain *chain, char *track, struct sqlConnection *conn)
 /* Add blocks to chain header. */
 {
-struct dyString *query = newDyString(1024);
+struct dyString *query = dyStringNew(1024);
 struct sqlResult *sr = NULL;
 char **row;
 struct cBlock *b;
 char fullName[64];
 
 safef(fullName, sizeof(fullName), "%s_%s", chain->tName, track);
 if (!sqlTableExists(conn, fullName))
     strcpy(fullName, track);
 sqlDyStringPrintf(query, 
 	"select tStart,tEnd,qStart from %sLink where chainId = %d",fullName, chain->id);
 
 sr = sqlGetResult(conn, query->string);
 while ((row = sqlNextRow(sr)) != NULL)
     {
     AllocVar(b);
     b->tStart = sqlUnsigned(row[0]);
     b->tEnd = sqlUnsigned(row[1]);
     b->qStart = sqlUnsigned(row[2]);
     b->qEnd = b->qStart + (b->tEnd - b->tStart);
     slAddHead(&chain->blockList, b);
     }
 slReverse(&chain->blockList);
 sqlFreeResult(&sr);
 dyStringFree(&query);
 }