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/snpTmp.c src/hg/lib/snpTmp.c
index 0ad677e..3f029d3 100644
--- src/hg/lib/snpTmp.c
+++ src/hg/lib/snpTmp.c
@@ -1,217 +1,217 @@
 /* snpTmp.c was originally generated by the autoSql program, which also 
  * generated snpTmp.h and snpTmp.sql.  This module links the database and
  * the RAM representation of objects. */
 
 /* 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 "snpTmp.h"
 
 
 void snpTmpStaticLoad(char **row, struct snpTmp *ret)
 /* Load a row from snpTmp table into ret.  The contents of ret will
  * be replaced at the next call to this function. */
 {
 
 ret->chrom = row[0];
 ret->chromStart = sqlUnsigned(row[1]);
 ret->chromEnd = sqlUnsigned(row[2]);
 ret->name = row[3];
 strcpy(ret->strand, row[4]);
 ret->refNCBI = row[5];
 ret->locType = row[6];
 ret->func = row[7];
 ret->contigName = row[8];
 }
 
 struct snpTmp *snpTmpLoad(char **row)
 /* Load a snpTmp from row fetched with select * from snpTmp
  * from database.  Dispose of this with snpTmpFree(). */
 {
 struct snpTmp *ret;
 
 AllocVar(ret);
 ret->chrom = cloneString(row[0]);
 ret->chromStart = sqlUnsigned(row[1]);
 ret->chromEnd = sqlUnsigned(row[2]);
 ret->name = cloneString(row[3]);
 strcpy(ret->strand, row[4]);
 ret->refNCBI = cloneString(row[5]);
 ret->locType = cloneString(row[6]);
 ret->func = cloneString(row[7]);
 ret->contigName = cloneString(row[8]);
 return ret;
 }
 
 struct snpTmp *snpTmpLoadAll(char *fileName) 
 /* Load all snpTmp from a whitespace-separated file.
  * Dispose of this with snpTmpFreeList(). */
 {
 struct snpTmp *list = NULL, *el;
 struct lineFile *lf = lineFileOpen(fileName, TRUE);
 char *row[9];
 
 while (lineFileRow(lf, row))
     {
     el = snpTmpLoad(row);
     slAddHead(&list, el);
     }
 lineFileClose(&lf);
 slReverse(&list);
 return list;
 }
 
 struct snpTmp *snpTmpLoadAllByChar(char *fileName, char chopper) 
 /* Load all snpTmp from a chopper separated file.
  * Dispose of this with snpTmpFreeList(). */
 {
 struct snpTmp *list = NULL, *el;
 struct lineFile *lf = lineFileOpen(fileName, TRUE);
 char *row[9];
 
 while (lineFileNextCharRow(lf, chopper, row, ArraySize(row)))
     {
     el = snpTmpLoad(row);
     slAddHead(&list, el);
     }
 lineFileClose(&lf);
 slReverse(&list);
 return list;
 }
 
 struct snpTmp *snpTmpCommaIn(char **pS, struct snpTmp *ret)
 /* Create a snpTmp out of a comma separated string. 
  * This will fill in ret if non-null, otherwise will
  * return a new snpTmp */
 {
 char *s = *pS;
 
 if (ret == NULL)
     AllocVar(ret);
 ret->chrom = sqlStringComma(&s);
 ret->chromStart = sqlUnsignedComma(&s);
 ret->chromEnd = sqlUnsignedComma(&s);
 ret->name = sqlStringComma(&s);
 sqlFixedStringComma(&s, ret->strand, sizeof(ret->strand));
 ret->refNCBI = sqlStringComma(&s);
 ret->locType = sqlStringComma(&s);
 ret->func = sqlStringComma(&s);
 ret->contigName = sqlStringComma(&s);
 *pS = s;
 return ret;
 }
 
 void snpTmpFree(struct snpTmp **pEl)
 /* Free a single dynamically allocated snpTmp such as created
  * with snpTmpLoad(). */
 {
 struct snpTmp *el;
 
 if ((el = *pEl) == NULL) return;
 freeMem(el->chrom);
 freeMem(el->name);
 freeMem(el->refNCBI);
 freeMem(el->locType);
 freeMem(el->func);
 freeMem(el->contigName);
 freez(pEl);
 }
 
 void snpTmpFreeList(struct snpTmp **pList)
 /* Free a list of dynamically allocated snpTmp's */
 {
 struct snpTmp *el, *next;
 
 for (el = *pList; el != NULL; el = next)
     {
     next = el->next;
     snpTmpFree(&el);
     }
 *pList = NULL;
 }
 
 void snpTmpOutput(struct snpTmp *el, FILE *f, char sep, char lastSep) 
 /* Print out snpTmp.  Separate fields with sep. Follow last field with lastSep. */
 {
 if (sep == ',') fputc('"',f);
 fprintf(f, "%s", el->chrom);
 if (sep == ',') fputc('"',f);
 fputc(sep,f);
 fprintf(f, "%u", el->chromStart);
 fputc(sep,f);
 fprintf(f, "%u", el->chromEnd);
 fputc(sep,f);
 if (sep == ',') fputc('"',f);
 fprintf(f, "%s", el->name);
 if (sep == ',') fputc('"',f);
 fputc(sep,f);
 if (sep == ',') fputc('"',f);
 fprintf(f, "%s", el->strand);
 if (sep == ',') fputc('"',f);
 fputc(sep,f);
 if (sep == ',') fputc('"',f);
 fprintf(f, "%s", el->refNCBI);
 if (sep == ',') fputc('"',f);
 fputc(sep,f);
 if (sep == ',') fputc('"',f);
 fprintf(f, "%s", el->locType);
 if (sep == ',') fputc('"',f);
 fputc(sep,f);
 if (sep == ',') fputc('"',f);
 fprintf(f, "%s", el->func);
 if (sep == ',') fputc('"',f);
 fputc(sep,f);
 if (sep == ',') fputc('"',f);
 fprintf(f, "%s", el->contigName);
 if (sep == ',') fputc('"',f);
 fputc(lastSep,f);
 }
 
 /* -------------------------------- End autoSql Generated Code -------------------------------- */
 
 
 
 void snpTmpTableCreate(struct sqlConnection *conn, char *tableName)
 /* create a chrN_snpTmp table */
 {
 char *createString =
 "CREATE TABLE %s (\n"
 "    chrom         varchar(255) not null,\n"
 "    chromStart    int unsigned not null,\n"
 "    chromEnd      int unsigned not null,\n"
 "    name          varchar(255) not null,\n"
 "    strand        char(1) not null,\n"
 "    refNCBI       longblob not null,\n"
 "    locType       enum('unknown', 'range', 'exact', 'between',\n"
 "                  'rangeInsertion', 'rangeSubstitution', 'rangeDeletion') \n"
 "                  DEFAULT 'unknown' NOT NULL,\n"
 "    func       set( 'unknown', 'locus', 'coding', 'coding-synon', 'coding-nonsynon', \n"
 "    		     'untranslated', 'intron', 'splice-site', 'cds-reference') \n"
 "		     DEFAULT 'unknown' NOT NULL,\n"
 "    			# The functional category of the SNP\n"
 "    contigName    varchar(255) not null,\n"
 "    INDEX         name(name)\n"
 ")\n";
 
-struct dyString *dy = newDyString(512);
+struct dyString *dy = dyStringNew(512);
 
 sqlDyStringPrintf(dy, createString, tableName);
 sqlRemakeTable(conn, tableName, dy->string);
 dyStringFree(&dy);
 }
 
 int snpTmpCmp(const void *va, const void *vb)
 {
 const struct snpTmp *a = *((struct snpTmp **)va);
 const struct snpTmp *b = *((struct snpTmp **)vb);
 int dif;
 dif = strcmp(a->chrom, b->chrom);
 if (dif == 0)
     dif = a->chromStart - b->chromStart;
 return dif;
 }