080a160c7b9595d516c9c70e83689a09b60839d0
galt
  Mon Jun 3 12:16:53 2013 -0700
fix SQL Injection
diff --git src/hg/lib/protVar.c src/hg/lib/protVar.c
index 60bb398..1270028 100644
--- src/hg/lib/protVar.c
+++ src/hg/lib/protVar.c
@@ -89,68 +89,39 @@
 while ((row = sqlNextRow(sr)) != NULL)
     {
     el = protVarLoad(row);
     slAddHead(&list, el);
     }
 slReverse(&list);
 sqlFreeResult(&sr);
 return list;
 }
 
 void protVarSaveToDb(struct sqlConnection *conn, struct protVar *el, char *tableName, int updateSize)
 /* Save protVar 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. Note that strings must be escaped to allow insertion into the database.
- * For example "autosql's features include" --> "autosql\'s features include" 
- * If worried about this use protVarSaveToDbEscaped() */
+ * inserted as NULL. Strings are automatically escaped to allow insertion into the database. */
 {
 struct dyString *update = newDyString(updateSize);
-dyStringPrintf(update, "insert into %s values ( '%s','%s','%s','%s','%s',%u)", 
+sqlDyStringPrintf(update, "insert into %s values ( '%s','%s','%s','%s','%s',%u)", 
 	tableName,  el->id,  el->name,  el->srcId,  el->baseChangeType,  el->location,  el->coordinateAccuracy);
 sqlUpdate(conn, update->string);
 freeDyString(&update);
 }
 
-void protVarSaveToDbEscaped(struct sqlConnection *conn, struct protVar *el, char *tableName, int updateSize)
-/* Save protVar 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. Automatically 
- * escapes all simple strings (not arrays of string) but may be slower than protVarSaveToDb().
- * For example automatically copies and converts: 
- * "autosql's features include" --> "autosql\'s features include" 
- * before inserting into database. */ 
-{
-struct dyString *update = newDyString(updateSize);
-char  *id, *name, *srcId, *baseChangeType, *location;
-id = sqlEscapeString(el->id);
-name = sqlEscapeString(el->name);
-srcId = sqlEscapeString(el->srcId);
-baseChangeType = sqlEscapeString(el->baseChangeType);
-location = sqlEscapeString(el->location);
-
-dyStringPrintf(update, "insert into %s values ( '%s','%s','%s','%s','%s',%u)", 
-	tableName,  id,  name,  srcId,  baseChangeType,  location,  el->coordinateAccuracy);
-sqlUpdate(conn, update->string);
-freeDyString(&update);
-freez(&id);
-freez(&name);
-freez(&srcId);
-freez(&baseChangeType);
-freez(&location);
-}
 
 struct protVar *protVarCommaIn(char **pS, struct protVar *ret)
 /* Create a protVar out of a comma separated string. 
  * This will fill in ret if non-null, otherwise will
  * return a new protVar */
 {
 char *s = *pS;
 
 if (ret == NULL)
     AllocVar(ret);
 ret->id = sqlStringComma(&s);
 ret->name = sqlStringComma(&s);
 ret->srcId = sqlStringComma(&s);
 ret->baseChangeType = sqlStringComma(&s);
 ret->location = sqlStringComma(&s);
@@ -296,66 +267,39 @@
 while ((row = sqlNextRow(sr)) != NULL)
     {
     el = protVarPosLoad(row);
     slAddHead(&list, el);
     }
 slReverse(&list);
 sqlFreeResult(&sr);
 return list;
 }
 
 void protVarPosSaveToDb(struct sqlConnection *conn, struct protVarPos *el, char *tableName, int updateSize)
 /* Save protVarPos 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. Note that strings must be escaped to allow insertion into the database.
- * For example "autosql's features include" --> "autosql\'s features include" 
- * If worried about this use protVarPosSaveToDbEscaped() */
+ * inserted as NULL. Strings are automatically escaped to allow insertion into the database. */
 {
 struct dyString *update = newDyString(updateSize);
-dyStringPrintf(update, "insert into %s values ( %u,'%s',%u,%u,'%s','%s','%s')", 
+sqlDyStringPrintf(update, "insert into %s values ( %u,'%s',%u,%u,'%s','%s','%s')", 
 	tableName,  el->bin,  el->chrom,  el->chromStart,  el->chromEnd,  el->name,  el->strand,  el->label);
 sqlUpdate(conn, update->string);
 freeDyString(&update);
 }
 
-void protVarPosSaveToDbEscaped(struct sqlConnection *conn, struct protVarPos *el, char *tableName, int updateSize)
-/* Save protVarPos 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. Automatically 
- * escapes all simple strings (not arrays of string) but may be slower than protVarPosSaveToDb().
- * For example automatically copies and converts: 
- * "autosql's features include" --> "autosql\'s features include" 
- * before inserting into database. */ 
-{
-struct dyString *update = newDyString(updateSize);
-char  *chrom, *name, *strand, *label;
-chrom = sqlEscapeString(el->chrom);
-name = sqlEscapeString(el->name);
-strand = sqlEscapeString(el->strand);
-label = sqlEscapeString(el->label);
-
-dyStringPrintf(update, "insert into %s values ( %u,'%s',%u,%u,'%s','%s','%s')", 
-	tableName,  el->bin,  chrom,  el->chromStart,  el->chromEnd,  name,  strand,  label);
-sqlUpdate(conn, update->string);
-freeDyString(&update);
-freez(&chrom);
-freez(&name);
-freez(&strand);
-freez(&label);
-}
 
 struct protVarPos *protVarPosCommaIn(char **pS, struct protVarPos *ret)
 /* Create a protVarPos out of a comma separated string. 
  * This will fill in ret if non-null, otherwise will
  * return a new protVarPos */
 {
 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);
@@ -492,64 +436,39 @@
 while ((row = sqlNextRow(sr)) != NULL)
     {
     el = protVarAttrLoad(row);
     slAddHead(&list, el);
     }
 slReverse(&list);
 sqlFreeResult(&sr);
 return list;
 }
 
 void protVarAttrSaveToDb(struct sqlConnection *conn, struct protVarAttr *el, char *tableName, int updateSize)
 /* Save protVarAttr 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. Note that strings must be escaped to allow insertion into the database.
- * For example "autosql's features include" --> "autosql\'s features include" 
- * If worried about this use protVarAttrSaveToDbEscaped() */
+ * inserted as NULL. Strings are automatically escaped to allow insertion into the database. */
 {
 struct dyString *update = newDyString(updateSize);
-dyStringPrintf(update, "insert into %s values ( '%s','%s',%s)", 
+sqlDyStringPrintf(update, "insert into %s values ( '%s','%s',%s)", 
 	tableName,  el->id,  el->attrType,  el->attrVal);
 sqlUpdate(conn, update->string);
 freeDyString(&update);
 }
 
-void protVarAttrSaveToDbEscaped(struct sqlConnection *conn, struct protVarAttr *el, char *tableName, int updateSize)
-/* Save protVarAttr 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. Automatically 
- * escapes all simple strings (not arrays of string) but may be slower than protVarAttrSaveToDb().
- * For example automatically copies and converts: 
- * "autosql's features include" --> "autosql\'s features include" 
- * before inserting into database. */ 
-{
-struct dyString *update = newDyString(updateSize);
-char  *id, *attrType, *attrVal;
-id = sqlEscapeString(el->id);
-attrType = sqlEscapeString(el->attrType);
-attrVal = sqlEscapeString(el->attrVal);
-
-dyStringPrintf(update, "insert into %s values ( '%s','%s','%s')", 
-	tableName,  id,  attrType,  attrVal);
-sqlUpdate(conn, update->string);
-freeDyString(&update);
-freez(&id);
-freez(&attrType);
-freez(&attrVal);
-}
 
 struct protVarAttr *protVarAttrCommaIn(char **pS, struct protVarAttr *ret)
 /* Create a protVarAttr out of a comma separated string. 
  * This will fill in ret if non-null, otherwise will
  * return a new protVarAttr */
 {
 char *s = *pS;
 
 if (ret == NULL)
     AllocVar(ret);
 ret->id = sqlStringComma(&s);
 ret->attrType = sqlStringComma(&s);
 ret->attrVal = sqlStringComma(&s);
 *pS = s;
 return ret;
@@ -676,68 +595,39 @@
 while ((row = sqlNextRow(sr)) != NULL)
     {
     el = protVarLinkLoad(row);
     slAddHead(&list, el);
     }
 slReverse(&list);
 sqlFreeResult(&sr);
 return list;
 }
 
 void protVarLinkSaveToDb(struct sqlConnection *conn, struct protVarLink *el, char *tableName, int updateSize)
 /* Save protVarLink 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. Note that strings must be escaped to allow insertion into the database.
- * For example "autosql's features include" --> "autosql\'s features include" 
- * If worried about this use protVarLinkSaveToDbEscaped() */
+ * inserted as NULL. Strings are automatically escaped to allow insertion into the database. */
 {
 struct dyString *update = newDyString(updateSize);
-dyStringPrintf(update, "insert into %s values ( '%s','%s','%s','%s','%s')", 
+sqlDyStringPrintf(update, "insert into %s values ( '%s','%s','%s','%s','%s')", 
 	tableName,  el->id,  el->attrType,  el->raKey,  el->acc,  el->displayVal);
 sqlUpdate(conn, update->string);
 freeDyString(&update);
 }
 
-void protVarLinkSaveToDbEscaped(struct sqlConnection *conn, struct protVarLink *el, char *tableName, int updateSize)
-/* Save protVarLink 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. Automatically 
- * escapes all simple strings (not arrays of string) but may be slower than protVarLinkSaveToDb().
- * For example automatically copies and converts: 
- * "autosql's features include" --> "autosql\'s features include" 
- * before inserting into database. */ 
-{
-struct dyString *update = newDyString(updateSize);
-char  *id, *attrType, *raKey, *acc, *displayVal;
-id = sqlEscapeString(el->id);
-attrType = sqlEscapeString(el->attrType);
-raKey = sqlEscapeString(el->raKey);
-acc = sqlEscapeString(el->acc);
-displayVal = sqlEscapeString(el->displayVal);
-
-dyStringPrintf(update, "insert into %s values ( '%s','%s','%s','%s','%s')", 
-	tableName,  id,  attrType,  raKey,  acc,  displayVal);
-sqlUpdate(conn, update->string);
-freeDyString(&update);
-freez(&id);
-freez(&attrType);
-freez(&raKey);
-freez(&acc);
-freez(&displayVal);
-}
 
 struct protVarLink *protVarLinkCommaIn(char **pS, struct protVarLink *ret)
 /* Create a protVarLink out of a comma separated string. 
  * This will fill in ret if non-null, otherwise will
  * return a new protVarLink */
 {
 char *s = *pS;
 
 if (ret == NULL)
     AllocVar(ret);
 ret->id = sqlStringComma(&s);
 ret->attrType = sqlStringComma(&s);
 ret->raKey = sqlStringComma(&s);
 ret->acc = sqlStringComma(&s);
 ret->displayVal = sqlStringComma(&s);