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/landmark.c src/hg/lib/landmark.c
index 8f8d2a6..ecb690b 100644
--- src/hg/lib/landmark.c
+++ src/hg/lib/landmark.c
@@ -1,508 +1,508 @@
 /* landmark.c was originally generated by the autoSql program, which also 
  * generated landmark.h and landmark.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 "landmark.h"
 
 
 void landmarkStaticLoad(char **row, struct landmark *ret)
 /* Load a row from landmark 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->landmarkId = sqlUnsigned(row[5]);
 ret->landmarkType = row[6];
 }
 
 struct landmark *landmarkLoad(char **row)
 /* Load a landmark from row fetched with select * from landmark
  * from database.  Dispose of this with landmarkFree(). */
 {
 struct landmark *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->landmarkId = sqlUnsigned(row[5]);
 ret->landmarkType = cloneString(row[6]);
 return ret;
 }
 
 struct landmark *landmarkLoadAll(char *fileName) 
 /* Load all landmark from a whitespace-separated file.
  * Dispose of this with landmarkFreeList(). */
 {
 struct landmark *list = NULL, *el;
 struct lineFile *lf = lineFileOpen(fileName, TRUE);
 char *row[7];
 
 while (lineFileRow(lf, row))
     {
     el = landmarkLoad(row);
     slAddHead(&list, el);
     }
 lineFileClose(&lf);
 slReverse(&list);
 return list;
 }
 
 struct landmark *landmarkLoadAllByChar(char *fileName, char chopper) 
 /* Load all landmark from a chopper separated file.
  * Dispose of this with landmarkFreeList(). */
 {
 struct landmark *list = NULL, *el;
 struct lineFile *lf = lineFileOpen(fileName, TRUE);
 char *row[7];
 
 while (lineFileNextCharRow(lf, chopper, row, ArraySize(row)))
     {
     el = landmarkLoad(row);
     slAddHead(&list, el);
     }
 lineFileClose(&lf);
 slReverse(&list);
 return list;
 }
 
 struct landmark *landmarkLoadByQuery(struct sqlConnection *conn, char *query)
 /* Load all landmark 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 landmarkFreeList(). */
 {
 struct landmark *list = NULL, *el;
 struct sqlResult *sr;
 char **row;
 
 sr = sqlGetResult(conn, query);
 while ((row = sqlNextRow(sr)) != NULL)
     {
     el = landmarkLoad(row);
     slAddHead(&list, el);
     }
 slReverse(&list);
 sqlFreeResult(&sr);
 return list;
 }
 
 void landmarkSaveToDb(struct sqlConnection *conn, struct landmark *el, char *tableName, int updateSize)
 /* Save landmark 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')", 
 	tableName,  el->bin,  el->chrom,  el->chromStart,  el->chromEnd,  el->name,  el->landmarkId,  el->landmarkType);
 sqlUpdate(conn, update->string);
-freeDyString(&update);
+dyStringFree(&update);
 }
 
 
 struct landmark *landmarkCommaIn(char **pS, struct landmark *ret)
 /* Create a landmark out of a comma separated string. 
  * This will fill in ret if non-null, otherwise will
  * return a new landmark */
 {
 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->landmarkId = sqlUnsignedComma(&s);
 ret->landmarkType = sqlStringComma(&s);
 *pS = s;
 return ret;
 }
 
 void landmarkFree(struct landmark **pEl)
 /* Free a single dynamically allocated landmark such as created
  * with landmarkLoad(). */
 {
 struct landmark *el;
 
 if ((el = *pEl) == NULL) return;
 freeMem(el->chrom);
 freeMem(el->name);
 freeMem(el->landmarkType);
 freez(pEl);
 }
 
 void landmarkFreeList(struct landmark **pList)
 /* Free a list of dynamically allocated landmark's */
 {
 struct landmark *el, *next;
 
 for (el = *pList; el != NULL; el = next)
     {
     next = el->next;
     landmarkFree(&el);
     }
 *pList = NULL;
 }
 
 void landmarkOutput(struct landmark *el, FILE *f, char sep, char lastSep) 
 /* Print out landmark.  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->landmarkId);
 fputc(sep,f);
 if (sep == ',') fputc('"',f);
 fprintf(f, "%s", el->landmarkType);
 if (sep == ',') fputc('"',f);
 fputc(lastSep,f);
 }
 
 void landmarkAttrStaticLoad(char **row, struct landmarkAttr *ret)
 /* Load a row from landmarkAttr table into ret.  The contents of ret will
  * be replaced at the next call to this function. */
 {
 
 ret->landmarkId = sqlUnsigned(row[0]);
 ret->linkId = sqlUnsigned(row[1]);
 ret->attribute = row[2];
 ret->attrVal = row[3];
 }
 
 struct landmarkAttr *landmarkAttrLoad(char **row)
 /* Load a landmarkAttr from row fetched with select * from landmarkAttr
  * from database.  Dispose of this with landmarkAttrFree(). */
 {
 struct landmarkAttr *ret;
 
 AllocVar(ret);
 ret->landmarkId = sqlUnsigned(row[0]);
 ret->linkId = sqlUnsigned(row[1]);
 ret->attribute = cloneString(row[2]);
 ret->attrVal = cloneString(row[3]);
 return ret;
 }
 
 struct landmarkAttr *landmarkAttrLoadAll(char *fileName) 
 /* Load all landmarkAttr from a whitespace-separated file.
  * Dispose of this with landmarkAttrFreeList(). */
 {
 struct landmarkAttr *list = NULL, *el;
 struct lineFile *lf = lineFileOpen(fileName, TRUE);
 char *row[4];
 
 while (lineFileRow(lf, row))
     {
     el = landmarkAttrLoad(row);
     slAddHead(&list, el);
     }
 lineFileClose(&lf);
 slReverse(&list);
 return list;
 }
 
 struct landmarkAttr *landmarkAttrLoadAllByChar(char *fileName, char chopper) 
 /* Load all landmarkAttr from a chopper separated file.
  * Dispose of this with landmarkAttrFreeList(). */
 {
 struct landmarkAttr *list = NULL, *el;
 struct lineFile *lf = lineFileOpen(fileName, TRUE);
 char *row[4];
 
 while (lineFileNextCharRow(lf, chopper, row, ArraySize(row)))
     {
     el = landmarkAttrLoad(row);
     slAddHead(&list, el);
     }
 lineFileClose(&lf);
 slReverse(&list);
 return list;
 }
 
 struct landmarkAttr *landmarkAttrLoadByQuery(struct sqlConnection *conn, char *query)
 /* Load all landmarkAttr 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 landmarkAttrFreeList(). */
 {
 struct landmarkAttr *list = NULL, *el;
 struct sqlResult *sr;
 char **row;
 
 sr = sqlGetResult(conn, query);
 while ((row = sqlNextRow(sr)) != NULL)
     {
     el = landmarkAttrLoad(row);
     slAddHead(&list, el);
     }
 slReverse(&list);
 sqlFreeResult(&sr);
 return list;
 }
 
 void landmarkAttrSaveToDb(struct sqlConnection *conn, struct landmarkAttr *el, char *tableName, int updateSize)
 /* Save landmarkAttr 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,%u,'%s','%s')", 
 	tableName,  el->landmarkId,  el->linkId,  el->attribute,  el->attrVal);
 sqlUpdate(conn, update->string);
-freeDyString(&update);
+dyStringFree(&update);
 }
 
 
 struct landmarkAttr *landmarkAttrCommaIn(char **pS, struct landmarkAttr *ret)
 /* Create a landmarkAttr out of a comma separated string. 
  * This will fill in ret if non-null, otherwise will
  * return a new landmarkAttr */
 {
 char *s = *pS;
 
 if (ret == NULL)
     AllocVar(ret);
 ret->landmarkId = sqlUnsignedComma(&s);
 ret->linkId = sqlUnsignedComma(&s);
 ret->attribute = sqlStringComma(&s);
 ret->attrVal = sqlStringComma(&s);
 *pS = s;
 return ret;
 }
 
 void landmarkAttrFree(struct landmarkAttr **pEl)
 /* Free a single dynamically allocated landmarkAttr such as created
  * with landmarkAttrLoad(). */
 {
 struct landmarkAttr *el;
 
 if ((el = *pEl) == NULL) return;
 freeMem(el->attribute);
 freeMem(el->attrVal);
 freez(pEl);
 }
 
 void landmarkAttrFreeList(struct landmarkAttr **pList)
 /* Free a list of dynamically allocated landmarkAttr's */
 {
 struct landmarkAttr *el, *next;
 
 for (el = *pList; el != NULL; el = next)
     {
     next = el->next;
     landmarkAttrFree(&el);
     }
 *pList = NULL;
 }
 
 void landmarkAttrOutput(struct landmarkAttr *el, FILE *f, char sep, char lastSep) 
 /* Print out landmarkAttr.  Separate fields with sep. Follow last field with lastSep. */
 {
 fprintf(f, "%u", el->landmarkId);
 fputc(sep,f);
 fprintf(f, "%u", el->linkId);
 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 landmarkAttrLinkStaticLoad(char **row, struct landmarkAttrLink *ret)
 /* Load a row from landmarkAttrLink table into ret.  The contents of ret will
  * be replaced at the next call to this function. */
 {
 
 ret->attrId = sqlUnsigned(row[0]);
 ret->raKey = row[1];
 ret->attrAcc = row[2];
 ret->displayVal = row[3];
 }
 
 struct landmarkAttrLink *landmarkAttrLinkLoad(char **row)
 /* Load a landmarkAttrLink from row fetched with select * from landmarkAttrLink
  * from database.  Dispose of this with landmarkAttrLinkFree(). */
 {
 struct landmarkAttrLink *ret;
 
 AllocVar(ret);
 ret->attrId = sqlUnsigned(row[0]);
 ret->raKey = cloneString(row[1]);
 ret->attrAcc = cloneString(row[2]);
 ret->displayVal = cloneString(row[3]);
 return ret;
 }
 
 struct landmarkAttrLink *landmarkAttrLinkLoadAll(char *fileName) 
 /* Load all landmarkAttrLink from a whitespace-separated file.
  * Dispose of this with landmarkAttrLinkFreeList(). */
 {
 struct landmarkAttrLink *list = NULL, *el;
 struct lineFile *lf = lineFileOpen(fileName, TRUE);
 char *row[4];
 
 while (lineFileRow(lf, row))
     {
     el = landmarkAttrLinkLoad(row);
     slAddHead(&list, el);
     }
 lineFileClose(&lf);
 slReverse(&list);
 return list;
 }
 
 struct landmarkAttrLink *landmarkAttrLinkLoadAllByChar(char *fileName, char chopper) 
 /* Load all landmarkAttrLink from a chopper separated file.
  * Dispose of this with landmarkAttrLinkFreeList(). */
 {
 struct landmarkAttrLink *list = NULL, *el;
 struct lineFile *lf = lineFileOpen(fileName, TRUE);
 char *row[4];
 
 while (lineFileNextCharRow(lf, chopper, row, ArraySize(row)))
     {
     el = landmarkAttrLinkLoad(row);
     slAddHead(&list, el);
     }
 lineFileClose(&lf);
 slReverse(&list);
 return list;
 }
 
 struct landmarkAttrLink *landmarkAttrLinkLoadByQuery(struct sqlConnection *conn, char *query)
 /* Load all landmarkAttrLink 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 landmarkAttrLinkFreeList(). */
 {
 struct landmarkAttrLink *list = NULL, *el;
 struct sqlResult *sr;
 char **row;
 
 sr = sqlGetResult(conn, query);
 while ((row = sqlNextRow(sr)) != NULL)
     {
     el = landmarkAttrLinkLoad(row);
     slAddHead(&list, el);
     }
 slReverse(&list);
 sqlFreeResult(&sr);
 return list;
 }
 
 void landmarkAttrLinkSaveToDb(struct sqlConnection *conn, struct landmarkAttrLink *el, char *tableName, int updateSize)
 /* Save landmarkAttrLink 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','%s','%s')", 
 	tableName,  el->attrId,  el->raKey,  el->attrAcc,  el->displayVal);
 sqlUpdate(conn, update->string);
-freeDyString(&update);
+dyStringFree(&update);
 }
 
 
 struct landmarkAttrLink *landmarkAttrLinkCommaIn(char **pS, struct landmarkAttrLink *ret)
 /* Create a landmarkAttrLink out of a comma separated string. 
  * This will fill in ret if non-null, otherwise will
  * return a new landmarkAttrLink */
 {
 char *s = *pS;
 
 if (ret == NULL)
     AllocVar(ret);
 ret->attrId = sqlUnsignedComma(&s);
 ret->raKey = sqlStringComma(&s);
 ret->attrAcc = sqlStringComma(&s);
 ret->displayVal = sqlStringComma(&s);
 *pS = s;
 return ret;
 }
 
 void landmarkAttrLinkFree(struct landmarkAttrLink **pEl)
 /* Free a single dynamically allocated landmarkAttrLink such as created
  * with landmarkAttrLinkLoad(). */
 {
 struct landmarkAttrLink *el;
 
 if ((el = *pEl) == NULL) return;
 freeMem(el->raKey);
 freeMem(el->attrAcc);
 freeMem(el->displayVal);
 freez(pEl);
 }
 
 void landmarkAttrLinkFreeList(struct landmarkAttrLink **pList)
 /* Free a list of dynamically allocated landmarkAttrLink's */
 {
 struct landmarkAttrLink *el, *next;
 
 for (el = *pList; el != NULL; el = next)
     {
     next = el->next;
     landmarkAttrLinkFree(&el);
     }
 *pList = NULL;
 }
 
 void landmarkAttrLinkOutput(struct landmarkAttrLink *el, FILE *f, char sep, char lastSep) 
 /* Print out landmarkAttrLink.  Separate fields with sep. Follow last field with lastSep. */
 {
 fprintf(f, "%u", el->attrId);
 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(sep,f);
 if (sep == ',') fputc('"',f);
 fprintf(f, "%s", el->displayVal);
 if (sep == ',') fputc('"',f);
 fputc(lastSep,f);
 }
 
 /* -------------------------------- End autoSql Generated Code -------------------------------- */