Patch test databases

Source: master branches of all relevant Ensembl repositories as of 10:00
today. This brings all test databases at hand to schema version 100.

Enscoresw 3267

Ameya Chaubal authored 5 years ago and Marek Szuba committed 5 years ago

Includes recent Variation schema updates.

Registry: add support for versioned ncbi_taxonomy DBs + improve support for versioned metadata DBs

Registry::get_species_and_object_type(): filter out versioned ensembl_metadata and ncbi_taxonomy DBs

Again, for ensembl_metadata this should have been part of ENSCORESW-3119.

For ensembl_metadata this should have been part of ENSCORESW-3119 but
alas, I missed it.

Not sure if ncbi_taxonomy is actually processed by this function but
let's play it safe, will have to confirm.

See ENSCORESW-3253. If both a versioned and an unversioned database are
present, use the versioned one if the version number matches that of the
software.

Add next-value buffering to Bio::EnsEMBL::Utils::Iterator

Fix fetch_all_by_outward_search

This is useful when working with coderefs that defer to
`$sth->fetchrow_arrayref`, which throws an error if called again after
having returned undef (which signifies the end of the data stream)

```
DBD::mysql::st fetchrow_arrayref failed: fetch() without execute()
```

Enable VGNC xrefs for callithrix_jacchus and papio_anubis [master]

E100 version bump

Travis: reactivate warnings about different API and schema versions

Deprecate Bio::EnsEMBL::DBSQL::GenomeContainer::get_total_length()

As per the Ensembl coding guidelines, i.e.: added a deprecation warning
to the method, tagged it as deprecated in the POD block, and listed it
as scheduled for removal in Ensembl 102.

Issue: ENSINT-283

Add an inactive proof-of-concept GitLab-CI config file

Patch non-core test databases to schema version 99

Since the Operations meeting on 2019-08-27 the bumping of Ensembl API
and DB-schema version numbers has been an Ensembl-wide policy.
Therefore, have Travis take notice of possible discrepancies in this
respect.

Note that simply removing the before_script line creating the file
disabling these checks is in general NOT sufficient - it might have
been left behind by a previous build in the event of runner re-use. It
is safer to make sure it does not exist regardless of initial conditions
of the runner.

cpanfile: require Try::Tiny

bugfix: should be sprintf here, as printf returns 1

(in case it isn't obvious, it has been deactivated by inserting
'.inactive' into the correct file name)

Unlike Ubuntu-based Travis builds, on GitLab-CI we use official Perl
images from Docker Hub. These are Debian-based so no major changes have
been required, support both perl-5.14 and perl-5.26 without any fuss
(and even if they eventually removed images for some version we could
always grab their relevant Dockerfiles and rebuild them ourselves), and
since they only contain core Perl they give us better control over our
dependency trees (i.e. much less risk of forgetting to add a non-core
module to cpanfile because it was already there as distro package on the
developer's machine).

What works:
 - the test suite runs and passes for both perl-5.14/sqlite and
   perl-5.26/mysql.

What still needs to be done to achieve full feature parity with Travis
builds:
 - enable Coveralls checks for 5.26/mysql jobs. Should work in theory but
   would require adju...

1. I must have set a branch wrong or something like that for the
   previous patching because it didn't update the version of the ontology
   schema. Fixed;
2. There is now an official variation schema-version patch;
3. For consistency between compara test DBs (officially still at 98) and
   all the rest (officially all at 99 now), apply the same unofficial
   compara schema-version patch as in ensembl-rest.