Reverted Production DB dependency in order to allow Xref pipeline to run. Changes can be reinstated once slightly more mature.

The code did not attempt to build the additional lookup before fetching from
it. Our solution is to switch to requesting the cache in get_????_additional_lookup()
which will trigger the building of the additional lookup.

[ENSCORESW-577]. Fixing a logical hole where we reqiured a method to be defined but did nothing with it.

Looks like I was between implementations. Now switched to requesting the
additional lookup keys and if the hash was empty then skipping
any additional work. Seems to behave a lot better and means users need
only override one method in the object.

(ie, include the duplicated sequence Y has in common with X rather than the two sequences unique to Y)

DensityType is not a feature but is the object storing the analysis related
to the DensityFeature

unlike other features, the related analysis is stored in the density type table

added test for 'fetch_all_by_feature_class' with density features

Other schemas may need this which do not go through a process of removing
old/retired seq region ids in favour of their new ids. When querying by a slice
this is automatically delt with. When fetching by an ID you now need to
force the search on.

Fixed a warning that was testing the wrong value and failing to verify a store_alt_alleles call properly

It seems that $DBI::errstr has a very strange life. We can get the error message
recived by incorrect connections or bad drivers (DBD::mysql is missing) when we
just warn the error. However concatenating it into another string makes the
message disapear. Even assignment and then concat will not work. Instead we
have switched to using the $@. This has the error in it.

The optimise tree step can take a very long time and cause web timeouts. We have
added a time limit expressed in floting-point seconds. If an optimisation is
taking longer than the specified time we will abort any more attempts.

The optimise tree step can take a very long time and cause web timeouts. We have
added a time limit expressed in floting-point seconds. If an optimisation is
taking longer than the specified time we will abort any more attempts.

The original code decalred a max of 2K ids because of max allowed packet concerns
and wanted the packet to stay close to 256KB. However the actual figure was off
by a factor of 8 as the max packet is 1MB not 1Mbit. We have increased the limit
to 16K when working with numerics. Strings are still at 2K due to their possible
large size.

Fixes for the alt alleles code. We needed to make sure we used the right variables in the code. Also needed to make sure an array is actually defined during construction

Fixing an issue raised by vega and non-standard DBAdaptor group names. Vega use ensembl to denote the ensembl db. We assumed incorrectly that core could always be used. That would always fail the moment a different group name was used

replaced ok tests with is where possible
replaced core test database with patch database

by farm3.

small queue for exonerate to finish.  Also added spaces after -R and -J
switches.

Making consistent through plants species the use of ncRNA_EG source for maintaining ncRNA genes xrefs asscoiated with logic_name ncrna_eg