Deactivate strain menu items for genes without strain tree

[twalsh-ebi]

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Description

In conjunction with eg-web-common PR 166, this pull request would deactivate strain-level homology menu items for genes lacking a strain-level gene tree.

A gene can have inferred strain homologies even if it lacks an inferred gene tree within the strain dataset. For example, if a strain gene-trees pipeline assigns a gene to a cluster containing only genes that are in the default collection, the cluster may be deleted from the strain gene-tree dataset, though homologies may have been inferred between its gene members in the default gene-trees pipeline.

In these cases, the homologies may be available through both the default and strain-level menu items. As the strain-level homology view is redundant with the default homology view, deactivating its menu item will not necessarily negatively impact the accessibility of the relevant homology data.

Views affected

This change would affect homology views for a subset of genes in strain gene-tree collections:

Examples:

• Sheep gene ENSOARG00020066301 on Vertebrates sandbox and staging: strain-level menu items are inactive on the sandbox
• Avena sativa OT3098 on Plants sandbox and staging sites: strain-level menu items are inactive on the sandbox
• D. melanogaster gene 'corto' on Metazoa sandbox and staging sites: In short, this is unaffected because Metazoa orthologues and paralogues are pooled from the various gene-tree collections, and because the strain-level comparative menu is deleted (here) if present.
• Barley gene HORVU.MOREX.r3.4HG0411430 on Plants sandbox and staging sites: This gene has orthologues but no gene tree in the Oat pangenome, while it has both gene tree and orthologues in the Barley pangenome.
  Because the Barley pangenome is the preferred gene-tree collection for this species, its strain-level menu items are unaffected by the changes in this pull request.
• Barley gene HORVU.MOREX.r3.1HG0000270 on Plants sandbox and staging sites: This gene has orthologues but no gene tree in the Barley pangenome — the preferred gene-tree collection for this species — so its strain menu links are made inactive by the changes in this PR.

Possible complications

None expected.

Merge conflicts

None detected.

Related JIRA Issues (EBI developers only)

N/A