Access more homology metadata via multi packed file

[twalsh-ebi]

Description

This PR aims to mitigate issues with a long-running database query — particularly affecting Ensembl Fungi — by avoiding calling the API method(s) triggering it.

It adds method ConfigPacker::_build_gene_tree_stats_mlss to populate GENE_TREE_STATS_MLSS_IDS, which is used in EnsEMBL::Web::Document::HTML::Compara::GeneTrees::format_gene_tree_stats to fetch the species tree of a gene-tree collection without going through its MethodLinkSpeciesSet.

It adds method ConfigPacker::_build_homology_mlss_tags to populate HOMOLOGY_MLSS_TAGS, which is used in Ensembl::Web::Object::Gene::fetch_homology_species_hash to fetch GOC/WGA thresholds with instantiating a MethodLinkSpeciesSet object.

Views affected

These changes would affect respectively gene-tree stats views and homology pages.

Examples are given below of test and baseline sandbox pages, all in sandbox sites in which calls to Compara method SpeciesSetAdaptor::_left_join throw an error. The error is not thrown on the test pages because SpeciesSetAdaptor::_left_join is not being called.

test_page	baseline_page
Orthologues page of D. melanogaster gene FBgn0013679	Orthologues page of D. melanogaster gene FBgn0013679
Fungi protein-tree stats page	Metazoa protein-tree stats page

Possible complications

This change would require repacking of all MULTI.db.packed files.

Without repacking:

• method format_gene_tree_stats would revert to previous behaviour, selecting a species tree dynamically;
• method fetch_homology_species_hash would return undefined GOC/WGA thresholds.

Merge conflicts

None detected.

Related JIRA Issues (EBI developers only)

• ENSCOMPARASW-9255