See ENSCORESW-3197. Have to think about the correct way of specifying
where to put that output file though, especially given the parser
doesn't actually delete it after it is done with it.

The initial value of the variable $counter is set to the highest
checksum_xref.checksum_xref_id found if the table in question is not
empty, or 0 if it is. This causes problems if $counter is only
incremented after each use in the input-file loop:
 - for a non-empty table the parser would attempt to re-use an existing
   value of checksum_xref_id for the first entry read from the input
   file. checksum_xref_id is the primary key of checksum_xref so its
   values have to be unique, therefore "LOAD DATA" silently discards the
   offending row;
 - for an empty table we lose one input row as well but it is the SECOND
   rather than the first one. Reason: 0 is not a valid value for
   auto_increment fields in MySQL, resulting in the first row being
   inserted with the first allowed ID value of 1 - which brings us back
   to the previous scenario when "LOAD DATA" attempts to insert the
   second row.

Incrementing $counter before use ought to address both forms of the
problem.

Remove misc_scripts/jira/*

schema_patcher.pl: Update location of ontology schema

Not used any more + at least partly out of date.

E99 version bump

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.

Yes, I *know* Compara, ontology and Variation schemas are still 98. It's
not that it could just happen, test databases have to be explicitly
patched - and in any case with Infra being at present the only team
which bumps versions to N+1 right after the branching of release/N
rather than just before the branching of release/N+1, it is only to be
expected. And call me weird but I like Test::Warnings tests to catch
warnings which really ARE unexpected.

Compara, Variation and ontology DBs haven't received their respective
version bumps yet so they remain at 98. Note that since API-DB
mismatches cause the Registry to produce warnings, test files using
Test::Warnings or equivalent will begin to report failures! At present
there are two such files - ontologyTerm.t and sequenceOntologyMapper.t,
both of them using the ontology database.

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