We now check the roundtripping of to_hash(). Should not have built this
method without a test case. Would have fixed the issue long ago!

Method in GeneAdaptor fetch_all_alt_alleles() was not working as it did prior to
our changes. It normally returned everything bar itself. That has been fixed.

Also stopped a warning which was driving the webteam mad.

[ENSCORESW-720] and [ENSCORESW-721]. Allowing default HashRef in execute() and sleep for less than a second.

First issue raised by Lee from EG. He wanted to be able to work with hash refs
in the same way you can do with ArrayRefs. Done and dusted.

Second issue raised by me. Want to sleep for periods less than 1 second for the test
suite sanity.

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.

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.

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.

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

We needed more methods to be able to handle alt allele group interactions. We also
needed to make sure a single gene could not be added more than once. Think we got
this one fixed

Removed dependencies on non-core APIs.

Added just a test for the new method filter_dir at the moment.

updated test cases to check integrity of api once deprecated tables, columns and methods have been removed
test databases patched to schema 74

Committing since we are now beyond the branch point in the API. This
allows a FullIdCache to key on various alternative identifiers/keys
generated by the implementing class. It means that if you want this
functionality you need to sub-class FullIdCache.

is not required for ontology database but allows for compatibility with metacontainer and schema version control like other databases

allows for future schema patching
added single table.sql file, replaces the need for individual sql files for each table

also updated existing tests to use is rather than ok whenever possible

The test schema was out of sync for ages due to it never being patched
using the patch sets. This is no longer the case. We needed a one
shot resynchronisation between the live schema and this test schema. All
test cases have been run and still pass. Assuming the processes
has not destroyed data. Any data changes seem to be related to different
levels of precision being emitted in the files.

Meta coord was updated.

patch was mentioned in meta table but not actually applied