GitLab

change to api version

Added a defualt set of aliases for the load_registry_from_db subroutine. Also added no_version_check getter/setter to allow configuration of wether the version checking is done. So you can specifiy in configuration script that you do not want to do the version checking.

version_check changed to only check when adaptors are instantiated or not at all if special file exists

load_registry_from_db will now only load the databases that match the correct software version and not necessarily the latest versions

replaced do with eval require for better error messages. Added optional argument to load_all to write to stderr what configuration file is being used. This was always reported before but defualt is now not to

merged adaptors removed and more docs added. load_registry_with_web_adaptors deprecated as new web does not allow this to work anymore, but Use load_registry_from_db can now be used instead

pretty much a rewrite of the sub get_all_adaptors. Now takes the optional species, group and type pairs. The adaptors are returned instantiated now.

subroutine clear, now added which will drop all database connections and reset the registry.  NOTE: if you load_all and the registry is loaded the subroutine clear is now automatically called first to clear out the old configuration before loading the new one.

made all registry calls case INsensetive as it was very annoying having to have species, group and type all in the correct case. Also added load_registry_from_db which will load the latest ensembl databases given a database host (and optionally port, user, pass) to search. At prsent only core,variation,estgene,compara and go adaptors are loaded via this method.

fix for no species being specified and more than one core database bring called (connection was not dropped)

changes to ensembl code to handle disconnecting databases properly - disconnect_all, checking for reconnection when doing do and prepare and finishing statement handles in generic_fetch

set_disconnect_when_inactive method added which will disconnect ALL DBConnections and set the flag for disconnect_when_inactive to 1