GitLab

Test DBs: fix broken application of the Compara schema-version bump

The last time we ran patch_test_databases for release 98 it somehow managed
to apply compara's patch_97_98_b without applying patch_97_98_a. I don't
even.

Release-98 version bump

Source: release/98 branch of ols-ensembl-loader and master branches
of all other relevant Ensembl repositories, pulled a few minutes ago.
Compara, Variation and ontology schemas all have already been bumped to
version 98.

The ontology schema patches have been moved from ensembl/misc_scripts…

ENSCORESW-3132: Limited implementation of Intervals with start > end …

The ontology schema patches have been moved from ensembl/misc_scripts/ontology/sql to ols-ensembl-loader/sql

ENSCORESW-3132: Limited implementation of Intervals with start > end (i.e. spanning the origin of a circular chromosome)

Remove deprecated GOTermAdaptor and SOTermAdaptor modules

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

Enable VGNC xrefs for felis_catus, macaca_mulatta and microcebus_murinus

Deprecated since 2011, non-functional since March 2018. See ENSCORESW-2871.

Note that there is still a reference to GOTermAdaptor in the xref parser
GOSlimParser. However, the parser in question seems to be no longer used
and in any case has not been updated, other than changing the copyright
notices, for years.

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.

Make the Coveralls badge in the README work

ENSCORESW-3147: correctly capture all required fields from file

The new Coveralls URI points to SVG so let us stick with a single format
for all badges.

The Coveralls URI need to contain the branch name for the badge to work,
moreover URIs for GitHub repositories are (now?) different. The URIs use
now both are what Coveralls Web site suggests and have been demonstrated
to work in case of ensembl-xref.

Registry: add support for versioned ensembl_metadata DBs [master]

appris method on Transcript

See ENSCORESW-3119. If both a versioned and an unversioned database are
present, use the versioned one if the version number matches that of the
software.

Store web_data without newlines

Changed attribute code length to 14 characters.

Add support for stop codon readthrough as a type of edit. 

Code updated to implement review comments. There is a new package to handle stop codon readthrough in a sequence. Test case has been updated with new regex

The previous test-database update missed some patches for the core and
variation schemas, which is why Travis jobs keep failing these days.

ENSCORESW-3110- Code to handle stop codon readthrough in 12 transcripts. The code edits the amino acid sequence to display the stop codon readthrough with an X

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