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/cgilib/gencodeIntron.c src/hg/cgilib/gencodeIntron.c
index dc1a5dd..b0d0ec3 100644
--- src/hg/cgilib/gencodeIntron.c
+++ src/hg/cgilib/gencodeIntron.c
@@ -1,226 +1,226 @@
 /* gencodeIntron.c was originally generated by the autoSql program, which also 
  * generated gencodeIntron.h and gencodeIntron.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 "gencodeIntron.h"
 
 
 void gencodeIntronStaticLoad(char **row, struct gencodeIntron *ret)
 /* Load a row from gencodeIntron 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];
 ret->status = row[4];
 strcpy(ret->strand, row[5]);
 ret->transcript = row[6];
 ret->geneId = row[7];
 }
 
 struct gencodeIntron *gencodeIntronLoad(char **row)
 /* Load a gencodeIntron from row fetched with select * from gencodeIntron
  * from database.  Dispose of this with gencodeIntronFree(). */
 {
 struct gencodeIntron *ret;
 
 AllocVar(ret);
 ret->chrom = cloneString(row[0]);
 ret->chromStart = sqlUnsigned(row[1]);
 ret->chromEnd = sqlUnsigned(row[2]);
 ret->name = cloneString(row[3]);
 ret->status = cloneString(row[4]);
 strcpy(ret->strand, row[5]);
 ret->transcript = cloneString(row[6]);
 ret->geneId = cloneString(row[7]);
 return ret;
 }
 
 struct gencodeIntron *gencodeIntronLoadAll(char *fileName) 
 /* Load all gencodeIntron from a whitespace-separated file.
  * Dispose of this with gencodeIntronFreeList(). */
 {
 struct gencodeIntron *list = NULL, *el;
 struct lineFile *lf = lineFileOpen(fileName, TRUE);
 char *row[8];
 
 while (lineFileRow(lf, row))
     {
     el = gencodeIntronLoad(row);
     slAddHead(&list, el);
     }
 lineFileClose(&lf);
 slReverse(&list);
 return list;
 }
 
 struct gencodeIntron *gencodeIntronLoadAllByChar(char *fileName, char chopper) 
 /* Load all gencodeIntron from a chopper separated file.
  * Dispose of this with gencodeIntronFreeList(). */
 {
 struct gencodeIntron *list = NULL, *el;
 struct lineFile *lf = lineFileOpen(fileName, TRUE);
 char *row[8];
 
 while (lineFileNextCharRow(lf, chopper, row, ArraySize(row)))
     {
     el = gencodeIntronLoad(row);
     slAddHead(&list, el);
     }
 lineFileClose(&lf);
 slReverse(&list);
 return list;
 }
 
 struct gencodeIntron *gencodeIntronLoadByQuery(struct sqlConnection *conn, char *query, int rowOffset)
 /* Load all gencodeIntron 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 gencodeIntronFreeList(). */
 {
 struct gencodeIntron *list = NULL, *el;
 struct sqlResult *sr;
 char **row;
 
 sr = sqlGetResult(conn, query);
 while ((row = sqlNextRow(sr)) != NULL)
     {
     el = gencodeIntronLoad(row+rowOffset);
     slAddHead(&list, el);
     }
 slReverse(&list);
 sqlFreeResult(&sr);
 return list;
 }
 
 void gencodeIntronSaveToDb(struct sqlConnection *conn, struct gencodeIntron *el, char *tableName, int updateSize)
 /* Save gencodeIntron 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. Strings are automatically escaped to allow insertion into the database. */
 {
-struct dyString *update = newDyString(updateSize);
+struct dyString *update = dyStringNew(updateSize);
 sqlDyStringPrintf(update, "insert into %s values ( '%s',%u,%u,'%s','%s','%s','%s','%s')", 
 	tableName,  el->chrom,  el->chromStart,  el->chromEnd,  el->name,  el->status,  el->strand,  el->transcript,  el->geneId);
 sqlUpdate(conn, update->string);
-freeDyString(&update);
+dyStringFree(&update);
 }
 
 
 struct gencodeIntron *gencodeIntronCommaIn(char **pS, struct gencodeIntron *ret)
 /* Create a gencodeIntron out of a comma separated string. 
  * This will fill in ret if non-null, otherwise will
  * return a new gencodeIntron */
 {
 char *s = *pS;
 
 if (ret == NULL)
     AllocVar(ret);
 ret->chrom = sqlStringComma(&s);
 ret->chromStart = sqlUnsignedComma(&s);
 ret->chromEnd = sqlUnsignedComma(&s);
 ret->name = sqlStringComma(&s);
 ret->status = sqlStringComma(&s);
 sqlFixedStringComma(&s, ret->strand, sizeof(ret->strand));
 ret->transcript = sqlStringComma(&s);
 ret->geneId = sqlStringComma(&s);
 *pS = s;
 return ret;
 }
 
 void gencodeIntronFree(struct gencodeIntron **pEl)
 /* Free a single dynamically allocated gencodeIntron such as created
  * with gencodeIntronLoad(). */
 {
 struct gencodeIntron *el;
 
 if ((el = *pEl) == NULL) return;
 freeMem(el->chrom);
 freeMem(el->name);
 freeMem(el->status);
 freeMem(el->transcript);
 freeMem(el->geneId);
 freez(pEl);
 }
 
 void gencodeIntronFreeList(struct gencodeIntron **pList)
 /* Free a list of dynamically allocated gencodeIntron's */
 {
 struct gencodeIntron *el, *next;
 
 for (el = *pList; el != NULL; el = next)
     {
     next = el->next;
     gencodeIntronFree(&el);
     }
 *pList = NULL;
 }
 
 void gencodeIntronOutput(struct gencodeIntron *el, FILE *f, char sep, char lastSep) 
 /* Print out gencodeIntron.  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->status);
 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->transcript);
 if (sep == ',') fputc('"',f);
 fputc(sep,f);
 if (sep == ',') fputc('"',f);
 fprintf(f, "%s", el->geneId);
 if (sep == ',') fputc('"',f);
 fputc(lastSep,f);
 }
 
 /* -------------------------------- End autoSql Generated Code -------------------------------- */
 
 void gencodeIntronTableCreate(struct sqlConnection *conn, char *tableName, int indexSize)
 /* Create a gencodeIntron table with the given name */
 {
 char *createString =
 "CREATE TABLE %s (\n"
 "       chrom varchar(255) not null,	# Chromosome\n"
 "       chromStart int unsigned not null,	# Start position in chromosome\n"
 "       chromEnd int unsigned not null,	# End position in chromosome\n"
 "       name varchar(255) not null,	# Intron ID\n"
 "       status enum('not_tested', 'RT_positive','RT_negative','RT_wrong_junction','RT_submitted', 'RACE_validated'),      # Status\n"
 "       strand char(1) not null,	# + or -\n"
 "       transcript varchar(255) not null,	# Transcript ID from GTF\n"
 "       geneId varchar(255) not null,	# Gene ID from GTF\n"
 "    INDEX(chrom(%d),chromStart),\n"
 "    INDEX(chrom(%d),chromEnd)\n"
 ")\n";
-struct dyString *dy = newDyString(1024);
+struct dyString *dy = dyStringNew(1024);
 sqlDyStringPrintf(dy, createString, tableName, indexSize, indexSize, indexSize);
 sqlRemakeTable(conn, tableName, dy->string);
 dyStringFree(&dy);
 }