I'm attempting to migrate a 0.7 biomart to 0.9 and am seeing problems with the code for migrating.
One thing I'm seeing is that when parsing the aliases (line 401)
String[] splitAlias = alias.split("=",-1);
There is no check on whether alias contains an = sign or on the size of splitAlias. The line
currentAliases.put(splitAlias[0], splitAlias[1]);
throws an ArrayOutOfBoundsException.
I'm not clear (yet) on how the aliases are pulled in from the existing mart, so I cannot say if our configuration is invalid. It appears that the alias that was generated the error was an empty string "". I've introduced a if (splitAlias.lenght > 1) test before putting the values into currentAliases.
I'm attempting to migrate a 0.7 biomart to 0.9 and am seeing problems with the code for migrating.
One thing I'm seeing is that when parsing the aliases (line 401)
String[] splitAlias = alias.split("=",-1);There is no check on whether alias contains an = sign or on the size of splitAlias. The linecurrentAliases.put(splitAlias[0], splitAlias[1]);throws anArrayOutOfBoundsException.I'm not clear (yet) on how the aliases are pulled in from the existing mart, so I cannot say if our configuration is invalid. It appears that the alias that was generated the error was an empty string "". I've introduced a
if (splitAlias.lenght > 1)test before putting the values into currentAliases.