GitLab

Test DB: add missing ontology patches [release/97]

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

Make the Coveralls badge in the README work [release/97]

Travis: Add mysql to the list of services [release/97]

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

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.

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.

Registry: add support for versioned ensembl_metadata DBs [release/97]

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.

add feature_so_term to Slice.pm, as was added to Feature.pm

add feature_so_term to Slice.pm, as was added to Feature.pm

Patch test databases for release 97, part 2 [release/97]

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

Add support for mature RNA products of transcripts (e.g. MicroRNA) to the API and schema

See ENSCORESW-3054. Only really affects the test suite at this point,
in the code proper the prefix only appears in docstrings.

Apply patch_96_97_{c,d,e}, insert the necessary data into
homo_sapiens/core.

Three separate patches here:

1. Create Create tables for RNAProduct. Basically renamed copies of
Translation tables "translation" and "translation_attrib" plus a
new column rnaproduct_type_id, complete with a corresponding table
rnaproduct_type, which is used to distinguish between RNA-product
types;

2. Add type RNAProduct to object_xref.ensembl_object_type. This is
needed to support e.g. miRBase xrefs for microRNAs;

3. Add type rnaproduct to stable_id_event.type. This is needed to
support mature RNA products in stable-id mapping.

Quote noisy strings properly + avoid double-sigil dereferences.

Properties of specific types of mature RNA products such as microRNAs
are stored in the database as attributes (so that we needn't add
type-specific columns to the rnaproduct table) but have shorthand
accessors such as MicroRNA::arm() backed by cache member variables
in the API (for convenience and speed). In order for this to work
properly we have to push possible changes to the cache variables back
to attributes before they are stored in the database - which is what
this method does.

The synchronisation code itself is generic and has been implemented
in the superclass. Specialisation is handled by class-specific mappings
between member names and respective Attribute codes, provided
by RNAProductTypeMapper.

Limitations:
 - at present there can only be either zero or one target attribute;
   having many attributes with the same code results in an exception
   because we do not know which one(s) to update. In the future we might
   have to extend the mapping syntax to support multiple attributes, for
   now however (i.e. for microRNA arms) we do not need it;
 - chances are things will break badly if we fetch a MicroRNA object
   from the database, change the arm and push it back. Right now this is
   not a problem because RNAProducts do not support database updates at
   all, then again should we want to support them we will have to check
   how AttributeAdaptor handles updates of existing objects (as well as
   the same for DBEntryAdaptor, as a matter of fact).