GitLab

added fetch_stable_id_event and get_event methods for archivestableid, in adaptor and object modules respectively
allows to get the specific event of an archive stable id related to a given stable id
finally gives access to score

Ordering only by the session's created date failed to realise we could have more than one entry for the same stable id. Ordering now by the score as a way of getting rid of this ambiguity. Issue was picked up by Rhoda running the code on an older MySQL version which consistently exhibited different behaviour to later MySQL versions

<ensembl-dev@ebi.ac.uk> to <dev@ensembl.org>.

Formatting of SYNOPSIS code.

Passes unit tests.

  implementation
- added fetch_associated_archived()
- removed deprecated methods

- rewrote fetch_by_stable_id*() methods to look up current versions of stable
  IDs in *_stable_id tables
- new method lookup_current() to assist the former (also replaces
  _lookup_version())
- new method add_all_current_to_history() to implement this behaviour for
  StableIdHistoryTree

- new methods to get properties of current db:
  - get_current_release()
  - get_current_assembly()

- fixed _resolve_type() to copy with non Ensembl-style stable IDs (e.g.
  Anopheles)

- removed deprecated methods

score is no longer an attribute of ArchiveStableId (this is now handled by StableIdEvent); history tree consolitation and untangling calls

improved retrieval of associated ArchiveStableIds for a given ArchiveStableIds (e.g. transcripts and translation for genes)

fetch_by_stable_id_version() now checks if this stable_id.version is actually in the database, and retrieves dbname, release and assembly of latest incarnation of this ID

modified execute calls to make compatible with other databases. Need to use bind_param first, with the type of the parameter, and execute later