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Tweak handling of strain, Pan and subtree export #1074

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Merged
merged 2 commits into from
Apr 29, 2025
Merged

Tweak handling of strain, Pan and subtree export #1074

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8f91d41
Tweak handling of strain, Pan and subtree export
twalsh-ebi Apr 21, 2025
807b50a
Centralise gene-tree constants
twalsh-ebi Apr 28, 2025
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2 changes: 1 addition & 1 deletion modules/EnsEMBL/Web/Command/DataExport/Output.pm
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Original file line number Diff line number Diff line change
Expand Up @@ -157,7 +157,7 @@ sub process {
$url_params->{'__clear'} = 1;
## Pass parameters needed for Back button to work
my @core_params = keys %{$hub->core_object('parameters')};
push @core_params, qw(export_action data_type data_action component align g1);
push @core_params, qw(export_action data_type data_action component align g1 node strain);
push @core_params, $self->config_params;
foreach (@core_params) {
my @values = $component->param($_);
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31 changes: 31 additions & 0 deletions modules/EnsEMBL/Web/Constants.pm
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Expand Up @@ -199,6 +199,37 @@ sub GENE_JOIN_TYPES {
}
}

sub GENE_TREE_CONSTANTS {
### Compara lookup for various gene-tree views
my ($cdb, $strain, $clusterset_id) = @_;

my $GENE_TREE_CONSTANTS = {
compara_pan_ensembl => {
action => 'PanComparaTree',
component => 'PanComparaTree',
},
compara_strain => {
action => 'Strain_Compara_Tree',
component => 'ComparaTree',
},
compara => {
action => 'Compara_Tree',
component => 'ComparaTree',
},
};

my $gene_tree_view_key;
if ($cdb eq 'compara_pan_ensembl') {
$gene_tree_view_key = 'compara_pan_ensembl';
} elsif ($strain) {
$gene_tree_view_key = 'compara_strain';
} else {
$gene_tree_view_key = 'compara';
}

return $GENE_TREE_CONSTANTS->{$gene_tree_view_key};
}

sub ALIGNMENT_FORMATS {
### Metadata for alignment export formats
return (
Expand Down
32 changes: 9 additions & 23 deletions modules/EnsEMBL/Web/ZMenu/ComparaTreeNode.pm
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Expand Up @@ -26,14 +26,17 @@ use URI::Escape qw(uri_escape);
use IO::String;
use Bio::AlignIO;

use EnsEMBL::Web::Constants;

use base qw(EnsEMBL::Web::ZMenu);

sub content {
my $self = shift;
my $cdb = shift || 'compara';
my $hub = $self->hub;
my $object = $self->object;
my $strain_tree = $hub->species_defs->get_config($self->hub->species,'RELATED_TAXON') if $hub->param('strain');
my $is_strain = $hub->param('strain');
my $strain_tree = $hub->species_defs->get_config($self->hub->species,'RELATED_TAXON') if $is_strain;
my $tree = $object->isa('EnsEMBL::Web::Object::GeneTree') ? $object->tree : $object->get_GeneTree($cdb, "", $strain_tree);

die 'No tree for gene' unless $tree;
Expand Down Expand Up @@ -165,6 +168,7 @@ sub content {

}

my $gene_tree_constants = EnsEMBL::Web::Constants::GENE_TREE_CONSTANTS($cdb, $is_strain, $tree->tree->clusterset_id);
my $lookup = $hub->species_defs->prodnames_to_urls_lookup;
if ($is_leaf and $is_supertree) {

Expand All @@ -177,9 +181,6 @@ sub content {

my $link_gene = $node->{_sub_reference_gene};

## Strain trees and other trees are very different!
my $action = $hub->param('strain') ? 'Strain_Compara_Tree' : 'Compara_Tree';

my $that_subtree_link;
if ($tree_stable_id) {
$that_subtree_link = $hub->url({
Expand All @@ -193,27 +194,10 @@ sub content {
my $link_gene = $node->{_sub_reference_gene};
my $species = $lookup->{$link_gene->genome_db->name};

# This is not the most elegant approach, but it will change the $action
# only where gene-tree constants are available (e.g. Metazoa),
# and only for non-default protein trees that lack a stable ID.
require EnsEMBL::Web::Component::Gene::ComparaOrthologs;
if (defined $EnsEMBL::Web::Component::Gene::ComparaOrthologs::GENE_TREE_CONSTANTS) {
my $gene_tree_constants = $EnsEMBL::Web::Component::Gene::ComparaOrthologs::GENE_TREE_CONSTANTS;
if (defined $gene_tree_constants) {
my $clusterset_id = $tree->tree->clusterset_id;
if (exists $gene_tree_constants->{$clusterset_id}) {
my $clusterset_specific_action = $gene_tree_constants->{$clusterset_id}{url_part};
if (defined $clusterset_specific_action) {
$action = $clusterset_specific_action;
}
}
}
}

$that_subtree_link = $hub->url({
species => $species,
type => 'Gene',
action => $action,
action => $gene_tree_constants->{action},
__clear => 1,
g => $link_gene->stable_id,
});
Expand Down Expand Up @@ -387,11 +371,13 @@ sub content {
my $params = {
'type' => 'DataExport',
'action' => 'GeneTree',
'cdb' => $cdb,
'data_type' => 'Gene',
'component' => 'ComparaTree',
'component' => $gene_tree_constants->{component},
'gene_name' => $gene_name,
'align' => 'tree',
'node' => $node_id,
'strain' => $is_strain,
};

$self->add_entry({
Expand Down