GitLab

104 versionbump in testdb

Mysql 8 comressed data import

103 test db patch

test db patching, version bump

patching compara ref https://github.com/Ensembl/ensembl/pull/476

(cherry picked from commit 9c97de88)

patch test db for 101

Yearly copyright update

Add prototype Gitlab-CI configuration

Patch test databases

Our Perl images are now all based on Debian Buster so there is no longer
a need to try and install Jessie packages.

Seeing as they were to run even in the event of any of the local
test jobs having failed, no real point in waiting until after the local
jobs have completed.

What I have done here is take .gitlab-ci.yml and
MultiTestDB.conf.gitlabci.mysql from ensembl (my own development version
in case of the former), modify the before_script section of the former
to account for differences in dependencies between the two projects,
create a dependent-build trigger attempting to launch one on
ensembl-gh-mirror/ensembl (i.e.  already on EBI Gitlab), and fix the
declaration of same because it has turned out variable expansion
in trigger declarations works only in the branch field, not in "project".

Note that all of this results in a somewhat different build
matrix than on Travis but unlike there, on GitLab we have got
consistency between ensembl and ensembl-test.

patch_test_databases.pl: add an option for restricting the patching to specific DB types

Added the biotype table to the list of "global" tables

Note that said option takes precedence over the hard-coded list of types
to exclude so it _is_ possible to, should one be inclined to do so,
attempt the patching of 'hive' and 'web' databases.

Issue: ENSCORESW-3259

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

It is needed in order to get the bioytpe group of a gene / transcript

Bump test-database schema versions to 99/100

This updates the core test DBs from 90 to 100 and the compara one from
90 to 99. Moreover, we now actually have SQLite test DBs instead of
empty directories.

Fixed bug when core dbs don't have contigs

Removed assumption that the 3 levels of assembly are chromosome,
supercontig and contig, as there are many other species with different
coord_system sequence level (e.g. primary assembly, scaffold).

A similar error might be raised in the future regarding supercontigs,
and since 'toplevel' and 'seqlevel' are linked in the assembly table,
that part of the code has also been removed.

Travis: explicitly use Ubuntu Trusty for builds

Matthieu Muffato's experiments with ensembl-hive have shown that in
spite of https://docs.travis-ci.com/user/languages/perl/ claiming
Travis supporting perl-5.8 and newer, the oldest version supported under
the Xenial environment is 5.22. This has since been confirmed by a post
on Travis community forums:
https://travis-ci.community/t/failure-with-perl-5-16-5-18-5-20/2458 .

We are presently not ready to drop support for Perl versions older than
what Travis makes available under Xenial, therefore let us for the time
being make sure we continue to use Trusty for now.

Add a README with the Travis badge

Travis: Add mysql to the list of services [master]

Ubuntu Xenial, which is now being rolled out as the default Linux distro
for Travis builds following the end of life of Ubuntu Trusty, does not
start services such as MySQL unless told to. We use the default distro
in our builds so we are likely to be affected.

[ENSCORESW-3077] Travis: Unify configuration of Slack notifications