Update handling of NCBI Taxonomy ranks in ComparaTree

[twalsh-ebi]

Description

This PR would change the ComparaTree to:

• update the NCBI Taxonomy rank_order with a current list of ranks;
• treat taxa of rank clade similarly to taxa of rank no rank; and
• borrow the rank of the closest ancestor of hierarchical rank for taxa of rank no rank or clade.

Views affected

This affects the Compara gene-tree view.

Example: sandbox vs live site

In the above example, if you select "Family" from the dropdown to "Collapse all the nodes at the taxonomic rank":

• the ancestor of genes OE9A017193 and FRAEX38873_v2_000040480 is linked to a taxon of rank "tribe", which is collapsed only on the sandbox view because this rank is in the updated rank_order;
• in the sandbox, the gene tree is collapsed at several nodes associated with the "50kb inversion clade" (a taxon of rank clade descending from a taxon of rank subfamily), while on the live site these are not collapsed.

Possible complications

None expected.

Merge conflicts

None detected.

Related JIRA Issues (EBI developers only)

• N/A