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/oreganno.c src/hg/cgilib/oreganno.c
index 6124496..4677984 100644
--- src/hg/cgilib/oreganno.c
+++ src/hg/cgilib/oreganno.c
@@ -1,531 +1,531 @@
 /* oreganno.c was originally generated by the autoSql program, which also 
  * generated oreganno.h and oreganno.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 "oreganno.h"
 
 
 void oregannoStaticLoad(char **row, struct oreganno *ret)
 /* Load a row from oreganno 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->id = row[4];
 strcpy(ret->strand, row[5]);
 ret->name = row[6];
 }
 
 struct oreganno *oregannoLoad(char **row)
 /* Load a oreganno from row fetched with select * from oreganno
  * from database.  Dispose of this with oregannoFree(). */
 {
 struct oreganno *ret;
 
 AllocVar(ret);
 ret->bin = sqlUnsigned(row[0]);
 ret->chrom = cloneString(row[1]);
 ret->chromStart = sqlUnsigned(row[2]);
 ret->chromEnd = sqlUnsigned(row[3]);
 ret->id = cloneString(row[4]);
 strcpy(ret->strand, row[5]);
 ret->name = cloneString(row[6]);
 return ret;
 }
 
 struct oreganno *oregannoLoadAll(char *fileName) 
 /* Load all oreganno from a whitespace-separated file.
  * Dispose of this with oregannoFreeList(). */
 {
 struct oreganno *list = NULL, *el;
 struct lineFile *lf = lineFileOpen(fileName, TRUE);
 char *row[7];
 
 while (lineFileRow(lf, row))
     {
     el = oregannoLoad(row);
     slAddHead(&list, el);
     }
 lineFileClose(&lf);
 slReverse(&list);
 return list;
 }
 
 struct oreganno *oregannoLoadAllByChar(char *fileName, char chopper) 
 /* Load all oreganno from a chopper separated file.
  * Dispose of this with oregannoFreeList(). */
 {
 struct oreganno *list = NULL, *el;
 struct lineFile *lf = lineFileOpen(fileName, TRUE);
 char *row[7];
 
 while (lineFileNextCharRow(lf, chopper, row, ArraySize(row)))
     {
     el = oregannoLoad(row);
     slAddHead(&list, el);
     }
 lineFileClose(&lf);
 slReverse(&list);
 return list;
 }
 
 struct oreganno *oregannoLoadByQuery(struct sqlConnection *conn, char *query)
 /* Load all oreganno 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 oregannoFreeList(). */
 {
 struct oreganno *list = NULL, *el;
 struct sqlResult *sr;
 char **row;
 
 sr = sqlGetResult(conn, query);
 while ((row = sqlNextRow(sr)) != NULL)
     {
     el = oregannoLoad(row);
     slAddHead(&list, el);
     }
 slReverse(&list);
 sqlFreeResult(&sr);
 return list;
 }
 
 void oregannoSaveToDb(struct sqlConnection *conn, struct oreganno *el, char *tableName, int updateSize)
 /* Save oreganno 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','%s','%s')", 
 	tableName,  el->bin,  el->chrom,  el->chromStart,  el->chromEnd,  el->id,  el->strand,  el->name);
 sqlUpdate(conn, update->string);
-freeDyString(&update);
+dyStringFree(&update);
 }
 
 
 struct oreganno *oregannoCommaIn(char **pS, struct oreganno *ret)
 /* Create a oreganno out of a comma separated string. 
  * This will fill in ret if non-null, otherwise will
  * return a new oreganno */
 {
 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->id = sqlStringComma(&s);
 sqlFixedStringComma(&s, ret->strand, sizeof(ret->strand));
 ret->name = sqlStringComma(&s);
 *pS = s;
 return ret;
 }
 
 void oregannoFree(struct oreganno **pEl)
 /* Free a single dynamically allocated oreganno such as created
  * with oregannoLoad(). */
 {
 struct oreganno *el;
 
 if ((el = *pEl) == NULL) return;
 freeMem(el->chrom);
 freeMem(el->id);
 freeMem(el->name);
 freez(pEl);
 }
 
 void oregannoFreeList(struct oreganno **pList)
 /* Free a list of dynamically allocated oreganno's */
 {
 struct oreganno *el, *next;
 
 for (el = *pList; el != NULL; el = next)
     {
     next = el->next;
     oregannoFree(&el);
     }
 *pList = NULL;
 }
 
 void oregannoOutput(struct oreganno *el, FILE *f, char sep, char lastSep) 
 /* Print out oreganno.  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->id);
 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->name);
 if (sep == ',') fputc('"',f);
 fputc(lastSep,f);
 }
 
 void oregannoAttrStaticLoad(char **row, struct oregannoAttr *ret)
 /* Load a row from oregannoAttr table into ret.  The contents of ret will
  * be replaced at the next call to this function. */
 {
 
 ret->id = row[0];
 ret->attribute = row[1];
 ret->attrVal = row[2];
 }
 
 struct oregannoAttr *oregannoAttrLoad(char **row)
 /* Load a oregannoAttr from row fetched with select * from oregannoAttr
  * from database.  Dispose of this with oregannoAttrFree(). */
 {
 struct oregannoAttr *ret;
 
 AllocVar(ret);
 ret->id = cloneString(row[0]);
 ret->attribute = cloneString(row[1]);
 ret->attrVal = cloneString(row[2]);
 return ret;
 }
 
 struct oregannoAttr *oregannoAttrLoadAll(char *fileName) 
 /* Load all oregannoAttr from a whitespace-separated file.
  * Dispose of this with oregannoAttrFreeList(). */
 {
 struct oregannoAttr *list = NULL, *el;
 struct lineFile *lf = lineFileOpen(fileName, TRUE);
 char *row[3];
 
 while (lineFileRow(lf, row))
     {
     el = oregannoAttrLoad(row);
     slAddHead(&list, el);
     }
 lineFileClose(&lf);
 slReverse(&list);
 return list;
 }
 
 struct oregannoAttr *oregannoAttrLoadAllByChar(char *fileName, char chopper) 
 /* Load all oregannoAttr from a chopper separated file.
  * Dispose of this with oregannoAttrFreeList(). */
 {
 struct oregannoAttr *list = NULL, *el;
 struct lineFile *lf = lineFileOpen(fileName, TRUE);
 char *row[3];
 
 while (lineFileNextCharRow(lf, chopper, row, ArraySize(row)))
     {
     el = oregannoAttrLoad(row);
     slAddHead(&list, el);
     }
 lineFileClose(&lf);
 slReverse(&list);
 return list;
 }
 
 struct oregannoAttr *oregannoAttrLoadByQuery(struct sqlConnection *conn, char *query)
 /* Load all oregannoAttr 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 oregannoAttrFreeList(). */
 {
 struct oregannoAttr *list = NULL, *el;
 struct sqlResult *sr;
 char **row;
 
 sr = sqlGetResult(conn, query);
 while ((row = sqlNextRow(sr)) != NULL)
     {
     el = oregannoAttrLoad(row);
     slAddHead(&list, el);
     }
 slReverse(&list);
 sqlFreeResult(&sr);
 return list;
 }
 
 void oregannoAttrSaveToDb(struct sqlConnection *conn, struct oregannoAttr *el, char *tableName, int updateSize)
 /* Save oregannoAttr 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','%s','%s')", 
 	tableName,  el->id,  el->attribute,  el->attrVal);
 sqlUpdate(conn, update->string);
-freeDyString(&update);
+dyStringFree(&update);
 }
 
 
 struct oregannoAttr *oregannoAttrCommaIn(char **pS, struct oregannoAttr *ret)
 /* Create a oregannoAttr out of a comma separated string. 
  * This will fill in ret if non-null, otherwise will
  * return a new oregannoAttr */
 {
 char *s = *pS;
 
 if (ret == NULL)
     AllocVar(ret);
 ret->id = sqlStringComma(&s);
 ret->attribute = sqlStringComma(&s);
 ret->attrVal = sqlStringComma(&s);
 *pS = s;
 return ret;
 }
 
 void oregannoAttrFree(struct oregannoAttr **pEl)
 /* Free a single dynamically allocated oregannoAttr such as created
  * with oregannoAttrLoad(). */
 {
 struct oregannoAttr *el;
 
 if ((el = *pEl) == NULL) return;
 freeMem(el->id);
 freeMem(el->attribute);
 freeMem(el->attrVal);
 freez(pEl);
 }
 
 void oregannoAttrFreeList(struct oregannoAttr **pList)
 /* Free a list of dynamically allocated oregannoAttr's */
 {
 struct oregannoAttr *el, *next;
 
 for (el = *pList; el != NULL; el = next)
     {
     next = el->next;
     oregannoAttrFree(&el);
     }
 *pList = NULL;
 }
 
 void oregannoAttrOutput(struct oregannoAttr *el, FILE *f, char sep, char lastSep) 
 /* Print out oregannoAttr.  Separate fields with sep. Follow last field with lastSep. */
 {
 if (sep == ',') fputc('"',f);
 fprintf(f, "%s", el->id);
 if (sep == ',') fputc('"',f);
 fputc(sep,f);
 if (sep == ',') fputc('"',f);
 fprintf(f, "%s", el->attribute);
 if (sep == ',') fputc('"',f);
 fputc(sep,f);
 if (sep == ',') fputc('"',f);
 fprintf(f, "%s", el->attrVal);
 if (sep == ',') fputc('"',f);
 fputc(lastSep,f);
 }
 
 void oregannoLinkStaticLoad(char **row, struct oregannoLink *ret)
 /* Load a row from oregannoLink table into ret.  The contents of ret will
  * be replaced at the next call to this function. */
 {
 
 ret->id = row[0];
 ret->attribute = row[1];
 ret->raKey = row[2];
 ret->attrAcc = row[3];
 }
 
 struct oregannoLink *oregannoLinkLoad(char **row)
 /* Load a oregannoLink from row fetched with select * from oregannoLink
  * from database.  Dispose of this with oregannoLinkFree(). */
 {
 struct oregannoLink *ret;
 
 AllocVar(ret);
 ret->id = cloneString(row[0]);
 ret->attribute = cloneString(row[1]);
 ret->raKey = cloneString(row[2]);
 ret->attrAcc = cloneString(row[3]);
 return ret;
 }
 
 struct oregannoLink *oregannoLinkLoadAll(char *fileName) 
 /* Load all oregannoLink from a whitespace-separated file.
  * Dispose of this with oregannoLinkFreeList(). */
 {
 struct oregannoLink *list = NULL, *el;
 struct lineFile *lf = lineFileOpen(fileName, TRUE);
 char *row[4];
 
 while (lineFileRow(lf, row))
     {
     el = oregannoLinkLoad(row);
     slAddHead(&list, el);
     }
 lineFileClose(&lf);
 slReverse(&list);
 return list;
 }
 
 struct oregannoLink *oregannoLinkLoadAllByChar(char *fileName, char chopper) 
 /* Load all oregannoLink from a chopper separated file.
  * Dispose of this with oregannoLinkFreeList(). */
 {
 struct oregannoLink *list = NULL, *el;
 struct lineFile *lf = lineFileOpen(fileName, TRUE);
 char *row[4];
 
 while (lineFileNextCharRow(lf, chopper, row, ArraySize(row)))
     {
     el = oregannoLinkLoad(row);
     slAddHead(&list, el);
     }
 lineFileClose(&lf);
 slReverse(&list);
 return list;
 }
 
 struct oregannoLink *oregannoLinkLoadByQuery(struct sqlConnection *conn, char *query)
 /* Load all oregannoLink 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 oregannoLinkFreeList(). */
 {
 struct oregannoLink *list = NULL, *el;
 struct sqlResult *sr;
 char **row;
 
 sr = sqlGetResult(conn, query);
 while ((row = sqlNextRow(sr)) != NULL)
     {
     el = oregannoLinkLoad(row);
     slAddHead(&list, el);
     }
 slReverse(&list);
 sqlFreeResult(&sr);
 return list;
 }
 
 void oregannoLinkSaveToDb(struct sqlConnection *conn, struct oregannoLink *el, char *tableName, int updateSize)
 /* Save oregannoLink 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','%s','%s','%s')", 
 	tableName,  el->id,  el->attribute,  el->raKey,  el->attrAcc);
 sqlUpdate(conn, update->string);
-freeDyString(&update);
+dyStringFree(&update);
 }
 
 
 struct oregannoLink *oregannoLinkCommaIn(char **pS, struct oregannoLink *ret)
 /* Create a oregannoLink out of a comma separated string. 
  * This will fill in ret if non-null, otherwise will
  * return a new oregannoLink */
 {
 char *s = *pS;
 
 if (ret == NULL)
     AllocVar(ret);
 ret->id = sqlStringComma(&s);
 ret->attribute = sqlStringComma(&s);
 ret->raKey = sqlStringComma(&s);
 ret->attrAcc = sqlStringComma(&s);
 *pS = s;
 return ret;
 }
 
 void oregannoLinkFree(struct oregannoLink **pEl)
 /* Free a single dynamically allocated oregannoLink such as created
  * with oregannoLinkLoad(). */
 {
 struct oregannoLink *el;
 
 if ((el = *pEl) == NULL) return;
 freeMem(el->id);
 freeMem(el->attribute);
 freeMem(el->raKey);
 freeMem(el->attrAcc);
 freez(pEl);
 }
 
 void oregannoLinkFreeList(struct oregannoLink **pList)
 /* Free a list of dynamically allocated oregannoLink's */
 {
 struct oregannoLink *el, *next;
 
 for (el = *pList; el != NULL; el = next)
     {
     next = el->next;
     oregannoLinkFree(&el);
     }
 *pList = NULL;
 }
 
 void oregannoLinkOutput(struct oregannoLink *el, FILE *f, char sep, char lastSep) 
 /* Print out oregannoLink.  Separate fields with sep. Follow last field with lastSep. */
 {
 if (sep == ',') fputc('"',f);
 fprintf(f, "%s", el->id);
 if (sep == ',') fputc('"',f);
 fputc(sep,f);
 if (sep == ',') fputc('"',f);
 fprintf(f, "%s", el->attribute);
 if (sep == ',') fputc('"',f);
 fputc(sep,f);
 if (sep == ',') fputc('"',f);
 fprintf(f, "%s", el->raKey);
 if (sep == ',') fputc('"',f);
 fputc(sep,f);
 if (sep == ',') fputc('"',f);
 fprintf(f, "%s", el->attrAcc);
 if (sep == ',') fputc('"',f);
 fputc(lastSep,f);
 }
 
 /* -------------------------------- End autoSql Generated Code -------------------------------- */
 
 struct hash *oregannoLoadAttrHash(struct sqlConnection *conn)
 /* Construct a hash table of the entries in the oregannoAttr table, indexed by ID.
  * Free with hashFreeWithVals(&attrHash, oregannoAttrFree).
  */
 {
 struct hash *attrHash = hashNew(0);
 struct sqlResult *result = NULL;
 struct oregannoAttr *attr = NULL;
 char query[2048], **row = NULL;
 
 sqlSafef(query, sizeof(query), "select * from oregannoAttr where attribute = 'type'");
 result = sqlGetResult (conn, query);
 while ((row = sqlNextRow(result)) != NULL)
     {
     attr = oregannoAttrLoad(row);
     hashAdd (attrHash, attr->id, attr);
     }
 sqlFreeResult(&result);
 return attrHash;
 }