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/makeItemsItem.c src/hg/lib/makeItemsItem.c
index 91a724b..da9e033 100644
--- src/hg/lib/makeItemsItem.c
+++ src/hg/lib/makeItemsItem.c
@@ -1,243 +1,243 @@
 /* makeItemsItem.c was originally generated by the autoSql program, which also
  * generated makeItemsItem.h and makeItemsItem.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 "makeItemsItem.h"
 
 
 void makeItemsItemStaticLoad(char **row, struct makeItemsItem *ret)
 /* Load a row from makeItemsItem table into ret.  The contents of ret will
  * be replaced at the next call to this function. */
 {
 
 ret->bin = sqlUnsigned(row[0]);
 ret->chrom = row[1];
 ret->chromStart = sqlUnsigned(row[2]);
 ret->chromEnd = sqlUnsigned(row[3]);
 ret->name = row[4];
 ret->score = sqlUnsigned(row[5]);
 safecpy(ret->strand, sizeof(ret->strand), row[6]);
 ret->thickStart = sqlUnsigned(row[7]);
 ret->thickEnd = sqlUnsigned(row[8]);
 ret->itemRgb = sqlUnsigned(row[9]);
 ret->description = row[10];
 ret->id = sqlUnsigned(row[11]);
 }
 
 struct makeItemsItem *makeItemsItemLoadByQuery(struct sqlConnection *conn, char *query)
 /* Load all makeItemsItem 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 makeItemsItemFreeList(). */
 {
 struct makeItemsItem *list = NULL, *el;
 struct sqlResult *sr;
 char **row;
 
 sr = sqlGetResult(conn, query);
 while ((row = sqlNextRow(sr)) != NULL)
     {
     el = makeItemsItemLoad(row);
     slAddHead(&list, el);
     }
 slReverse(&list);
 sqlFreeResult(&sr);
 return list;
 }
 
 void makeItemsItemSaveToDb(struct sqlConnection *conn, struct makeItemsItem *el, char *tableName, int updateSize)
 /* Save makeItemsItem 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 ( %u,'%s',%u,%u,'%s',%u,'%s',%u,%u,%u,%s,%u)",
 	tableName,  el->bin,  el->chrom,  el->chromStart,  el->chromEnd,  el->name,  el->score,  el->strand,  el->thickStart,  el->thickEnd,  el->itemRgb,  el->description,  el->id);
 sqlUpdate(conn, update->string);
-freeDyString(&update);
+dyStringFree(&update);
 }
 
 
 struct makeItemsItem *makeItemsItemLoad(char **row)
 /* Load a makeItemsItem from row fetched with select * from makeItemsItem
  * from database.  Dispose of this with makeItemsItemFree(). */
 {
 struct makeItemsItem *ret;
 
 AllocVar(ret);
 ret->bin = sqlUnsigned(row[0]);
 ret->chrom = cloneString(row[1]);
 ret->chromStart = sqlUnsigned(row[2]);
 ret->chromEnd = sqlUnsigned(row[3]);
 ret->name = cloneString(row[4]);
 ret->score = sqlUnsigned(row[5]);
 safecpy(ret->strand, sizeof(ret->strand), row[6]);
 ret->thickStart = sqlUnsigned(row[7]);
 ret->thickEnd = sqlUnsigned(row[8]);
 ret->itemRgb = sqlUnsigned(row[9]);
 ret->description = cloneString(row[10]);
 ret->id = sqlUnsigned(row[11]);
 return ret;
 }
 
 struct makeItemsItem *makeItemsItemLoadAll(char *fileName)
 /* Load all makeItemsItem from a whitespace-separated file.
  * Dispose of this with makeItemsItemFreeList(). */
 {
 struct makeItemsItem *list = NULL, *el;
 struct lineFile *lf = lineFileOpen(fileName, TRUE);
 char *row[12];
 
 while (lineFileRow(lf, row))
     {
     el = makeItemsItemLoad(row);
     slAddHead(&list, el);
     }
 lineFileClose(&lf);
 slReverse(&list);
 return list;
 }
 
 struct makeItemsItem *makeItemsItemLoadAllByChar(char *fileName, char chopper)
 /* Load all makeItemsItem from a chopper separated file.
  * Dispose of this with makeItemsItemFreeList(). */
 {
 struct makeItemsItem *list = NULL, *el;
 struct lineFile *lf = lineFileOpen(fileName, TRUE);
 char *row[12];
 
 while (lineFileNextCharRow(lf, chopper, row, ArraySize(row)))
     {
     el = makeItemsItemLoad(row);
     slAddHead(&list, el);
     }
 lineFileClose(&lf);
 slReverse(&list);
 return list;
 }
 
 struct makeItemsItem *makeItemsItemCommaIn(char **pS, struct makeItemsItem *ret)
 /* Create a makeItemsItem out of a comma separated string.
  * This will fill in ret if non-null, otherwise will
  * return a new makeItemsItem */
 {
 char *s = *pS;
 
 if (ret == NULL)
     AllocVar(ret);
 ret->bin = sqlUnsignedComma(&s);
 ret->chrom = sqlStringComma(&s);
 ret->chromStart = sqlUnsignedComma(&s);
 ret->chromEnd = sqlUnsignedComma(&s);
 ret->name = sqlStringComma(&s);
 ret->score = sqlUnsignedComma(&s);
 sqlFixedStringComma(&s, ret->strand, sizeof(ret->strand));
 ret->thickStart = sqlUnsignedComma(&s);
 ret->thickEnd = sqlUnsignedComma(&s);
 ret->itemRgb = sqlUnsignedComma(&s);
 ret->description = sqlStringComma(&s);
 ret->id = sqlUnsignedComma(&s);
 *pS = s;
 return ret;
 }
 
 void makeItemsItemFree(struct makeItemsItem **pEl)
 /* Free a single dynamically allocated makeItemsItem such as created
  * with makeItemsItemLoad(). */
 {
 struct makeItemsItem *el;
 
 if ((el = *pEl) == NULL) return;
 freeMem(el->chrom);
 freeMem(el->name);
 freeMem(el->description);
 freez(pEl);
 }
 
 void makeItemsItemFreeList(struct makeItemsItem **pList)
 /* Free a list of dynamically allocated makeItemsItem's */
 {
 struct makeItemsItem *el, *next;
 
 for (el = *pList; el != NULL; el = next)
     {
     next = el->next;
     makeItemsItemFree(&el);
     }
 *pList = NULL;
 }
 
 void makeItemsItemOutput(struct makeItemsItem *el, FILE *f, char sep, char lastSep)
 /* Print out makeItemsItem.  Separate fields with sep. Follow last field with lastSep. */
 {
 fprintf(f, "%u", el->bin);
 fputc(sep,f);
 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);
 fprintf(f, "%u", el->score);
 fputc(sep,f);
 if (sep == ',') fputc('"',f);
 fprintf(f, "%s", el->strand);
 if (sep == ',') fputc('"',f);
 fputc(sep,f);
 fprintf(f, "%u", el->thickStart);
 fputc(sep,f);
 fprintf(f, "%u", el->thickEnd);
 fputc(sep,f);
 fprintf(f, "%u", el->itemRgb);
 fputc(sep,f);
 if (sep == ',') fputc('"',f);
 fprintf(f, "%s", el->description);
 if (sep == ',') fputc('"',f);
 fputc(sep,f);
 fprintf(f, "%u", el->id);
 fputc(lastSep,f);
 }
 
 /* -------------------------------- End autoSql Generated Code -------------------------------- */
 
 static char *makeItemsItemAutoSqlString =
 "table makeItemsItem\n"
 "\"An item in a makeItems type track.\"\n"
 "    (\n"
 "    uint bin;	       \"Bin for range index\"\n"
 "    string chrom;      \"Reference sequence chromosome or scaffold\"\n"
 "    uint   chromStart; \"Start position in chromosome\"\n"
 "    uint   chromEnd;   \"End position in chromosome\"\n"
 "    string name;       \"Name of item - up to 16 chars\"\n"
 "    uint  score;	\"0-1000.  Higher numbers are darker.\"\n"
 "    char[1] strand;     \"+ or - for strand\"\n"
 "    uint   thickStart; \"Start of thick part\"\n"
 "    uint   thickEnd;   \"End position of thick part\"\n"
 "    uint itemRgb;	\"RGB 8 bits each as in bed\"\n"
 "    lstring description; \"Longer item description\"\n"
 "    uint id;		\"Unique ID for item\"\n"
 "    )\n"
    ;
 
 struct asObject *makeItemsItemAsObj()
 // Return asObject describing fields of makeItemsItem
 {
 return asParseText(makeItemsItemAutoSqlString);
 }