Skip to content

Tweak handling of strain, Pan and subtree export #1074

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Merged

Conversation

twalsh-ebi
Copy link
Contributor

@twalsh-ebi twalsh-ebi commented Apr 21, 2025

Description

This PR would:

  • add a GENE_TREE_CONSTANTS function in the EnsEMBL::Web::Constants module;
  • make use of the GENE_TREE_CONSTANTS function to pass appropriate cdb, action, component and strain parameters in "Tree or Alignment" or "Sequences" export URLs in gene-tree node ZMenus;
  • ensure that node and strain parameters are passed when the Back button is used in a gene-tree download modal window.

The effects of this would be that:

  • clicking the "Tree or Alignment" or "Sequences" subtree export options in a strain, Pan or Metazoa gene-tree node Zmenu would lead to the tree/alignment or sequences (respectively) of the subtree rooted at the given node;
  • when previewing data for a strain/subtree, if a user clicks the Back button and clicks the Preview button again, they will return to a preview of the given strain/subtree. Currently, in this scenario, the user is presented with data for the full default gene tree.

Views affected

This change would affect gene-tree export previews/downloads for internal tree nodes, strain gene trees, and internal nodes of strain/Pan gene trees.

In conjunction with eg-web-metazoa PR 42, it would also benefit gene-tree export previews/downloads for internal nodes of Metazoa gene trees.

Example of a Newick preview for a subtree (node_id: 3002982674) of the cultivar gene tree of Rice gene Os05g0421750:
rice_cultivar_subtree_preview_3002982674

Possible complications

None expected.

Merge conflicts

None detected.

Related JIRA Issues (EBI developers only)

N/A

@azangru azangru merged commit 0d92b20 into Ensembl:postreleasefix/114 Apr 29, 2025
azangru pushed a commit that referenced this pull request Apr 29, 2025
* postreleasefix/114:
  Tweak handling of strain, Pan and subtree export (#1074)
  Load underlying slices iff needed for alignslice view (#1076)
  Update Apache access logs format: print request ips (#1077)
azangru pushed a commit that referenced this pull request Apr 29, 2025
* postreleasefix/114:
  Tweak handling of strain, Pan and subtree export (#1074)
  Load underlying slices iff needed for alignslice view (#1076)
  Update Apache access logs format: print request ips (#1077)
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Labels
None yet
Projects
None yet
Development

Successfully merging this pull request may close these issues.

2 participants