Merge branch 'master' into testing

canto.yaml

@@ -25,7 +25,7 @@ header_image: logos/curation_tool.png
 
 canto_url: https://curation.pombase.org/
 
-app_version: v1797
+app_version: v1798
 
 schema_version: 35
 

lib/Canto/Chado/FeaturePubLookup.pm

@@ -0,0 +1,118 @@
+package Canto::Chado::FeaturePubLookup;
+
+=head1 NAME
+
+Canto::Chado::FeaturePubLookup - Look up publication to feature relations and
+                                 sources in Chado
+
+=head1 SYNOPSIS
+
+=head1 AUTHOR
+
+Kim Rutherford C<< <[email protected]> >>
+
+=head1 BUGS
+
+Please report any bugs or feature requests to C<[email protected]>.
+
+=head1 SUPPORT
+
+You can find documentation for this module with the perldoc command.
+
+    perldoc Canto::Chado::FeaturePubLookup
+
+=over 4
+
+=back
+
+=head1 COPYRIGHT & LICENSE
+
+Copyright 2024 University of Cambridge, all rights reserved.
+
+Canto is free software: you can redistribute it and/or modify
+it under the terms of the GNU General Public License as published by
+the Free Software Foundation, either version 3 of the License, or
+(at your option) any later version.
+
+=head1 FUNCTIONS
+
+=cut
+
+use feature qw(state);
+
+use Moose;
+
+use Canto::Curs::Utils;
+
+with 'Canto::Role::Configurable';
+with 'Canto::Chado::ChadoLookup';
+
+
+=head2 lookup
+
+ Usage   : my $feature_pub_lookup = Canto::Track::get_adaptor($config, 'feature_pub');
+           my $results = $allele_lookup->lookup(publication_uniquename => 'PMID:31563844',
+                                                feature_type => 'gene')
+ Function: Look up the features and feature_pub_source props in Chado
+ Args    : publication_uniquename - a PMID
+           feature_type - a SO term name
+ Return  : [ { gene_uniquename => 'SPBC685.02'
+               gene_name => 'exo5',
+               feature_pub_source => 'contig_file_dbxref' }
+             { ... },
+             ...
+           ]
+=cut
+
+sub lookup
+{
+  my $self = shift;
+
+  my %args = @_;
+
+  my $publication_uniquename = $args{publication_uniquename};
+
+  if (!defined $publication_uniquename) {
+    die "no publication_uniquename passed to lookup()";
+  }
+
+  my $feature_type = $args{feature_type};
+  if (!defined $feature_type) {
+    die "no feature_type parameter passed to lookup()";
+  }
+
+  my $schema = $self->schema();
+
+  my $chado_dbh = $schema->storage()->dbh();
+
+  my $query = <<'EOQ';
+SELECT f.uniquename AS gene_uniquename,
+       f.name AS gene_name,
+       fcp.value AS feature_pub_source
+FROM feature f
+JOIN feature_pub ON feature_pub.feature_id = f.feature_id
+JOIN pub ON pub.pub_id = feature_pub.pub_id
+JOIN cvterm t ON f.type_id = t.cvterm_id
+JOIN feature_pubprop fcp ON fcp.feature_pub_id = feature_pub.feature_pub_id
+JOIN cvterm fcpt ON fcp.type_id = fcpt.cvterm_id
+WHERE pub.uniquename = ?
+  AND t.name = ?
+  AND fcpt.name = 'feature_pub_source'
+EOQ
+
+  my $sth = $chado_dbh->prepare($query);
+  $sth->execute($publication_uniquename, $feature_type)
+    or die "Couldn't execute: " . $sth->errstr;
+
+  my @rows = ();
+
+  while (my ($gene_uniquename, $gene_name, $feature_pub_source) = $sth->fetchrow_array()) {
+    push @rows, {
+      gene_uniquename => $gene_uniquename,
+      gene_name => $gene_name,
+      feature_pub_source => $feature_pub_source,
+    };
+  }
+
+  return @rows;
+}