comment out diag statements in tests

Activate Gitlab CI

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