added data for transcript count in genome_statistics test data
added test for get_transcripts and get_alt_transcripts in genomecontainer

generated test data for patch test database
database patched up to release 75

checking total length, not ref

revisions to CliHelper to support dbs where no production name is set, and to improve default behaviour where single_species mode not specified. Also expanded test coverage to support this, adding the nameless and test_collection test dbs for this purpose

switch to using the local as default. otherwise we cannot have a test passing until we have committed to version control

switch to using ENV variables. Otherwise we run the risk of not being able to run the tests in any kind of test harness tool

A number of params are missing their - flag. That means the new XS rearrange does not work (it is a bug not a feature)

also, when adding_mapping_path, do not expect the method to order coord systems by rank, it will use the first argument as assembled, the second argument as component

There was code in the GeneAdaptor which could be handled by the DBEntryAdaptor
and would be more reusable by others if it was there. Also added a test
case for the new method get_distinct_external_dbs() in DBEntryAdaptor.

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.