From f99dca4c06301594b8464fb36d0eaf8491a22315 Mon Sep 17 00:00:00 2001
From: Kim Rutherford <kmr@aska.gen.nz>
Date: Fri, 10 Jan 2025 00:09:28 +1300
Subject: [PATCH] Add importer for GO-CAM JSON file

Refs pombase/pombase-chado#1174
---
 lib/PomBase/Import/GoCamJson.pm | 173 ++++++++++++++++++++++++++++++++
 script/pombase-import.pl        |   1 +
 2 files changed, 174 insertions(+)
 create mode 100644 lib/PomBase/Import/GoCamJson.pm

diff --git a/lib/PomBase/Import/GoCamJson.pm b/lib/PomBase/Import/GoCamJson.pm
new file mode 100644
index 00000000..ff3621e8
--- /dev/null
+++ b/lib/PomBase/Import/GoCamJson.pm
@@ -0,0 +1,173 @@
+package PomBase::Import::GoCamJson;
+
+=head1 NAME
+
+PomBase::Import::GoCamJson - Read the GO-CAM JSON file from SVN in Chado
+
+=head1 SYNOPSIS
+
+=head1 AUTHOR
+
+Kim Rutherford C<< <kmr44@cam.ac.uk> >>
+
+=head1 BUGS
+
+Please report any bugs or feature requests to C<kmr44@cam.ac.uk>.
+
+=head1 SUPPORT
+
+You can find documentation for this module with the perldoc command.
+
+    perldoc PomBase::Import::GoCamJson
+
+=over 4
+
+=back
+
+=head1 COPYRIGHT & LICENSE
+
+Copyright 2025 Kim Rutherford, all rights reserved.
+
+This program is free software; you can redistribute it and/or modify it
+under the same terms as Perl itself.
+
+=head1 FUNCTIONS
+
+=cut
+
+use strict;
+use warnings;
+use Carp;
+
+use utf8;
+
+use Moose;
+use JSON;
+use Getopt::Long qw(GetOptionsFromArray);
+
+
+with 'PomBase::Role::ChadoUser';
+with 'PomBase::Role::ConfigUser';
+with 'PomBase::Role::DbQuery';
+with 'PomBase::Role::CvQuery';
+with 'PomBase::Role::FeatureFinder';
+with 'PomBase::Role::OrganismFinder';
+with 'PomBase::Role::XrefStorer';
+with 'PomBase::Role::CvtermCreator';
+with 'PomBase::Role::FeatureCvtermCreator';
+with 'PomBase::Role::FeatureStorer';
+with 'PomBase::Role::Embl::FeatureRelationshipStorer';
+
+has verbose => (is => 'ro');
+has options => (is => 'ro', isa => 'ArrayRef', required => 1);
+
+has organism => (is => 'rw', init_arg => undef);
+has null_pub => (is => 'rw', init_arg => undef);
+
+sub BUILD
+{
+  my $self = shift;
+
+  my $organism_taxonid = undef;
+
+  my @opt_config = ("organism-taxonid=s" => \$organism_taxonid);
+
+  if (!GetOptionsFromArray($self->options(), @opt_config)) {
+    croak "option parsing failed";
+  }
+
+  if (!defined $organism_taxonid || length $organism_taxonid == 0) {
+    die "no --organism-taxonid passed to the importer\n";
+  }
+
+  my $organism = $self->find_organism_by_taxonid($organism_taxonid);
+
+  if (!defined $organism) {
+    die "can't find organism with taxon ID: $organism_taxonid\n";
+  }
+
+  $self->organism($organism);
+
+  my $null_pub = $self->find_or_create_pub('null');
+
+  $self->null_pub($null_pub);
+}
+
+sub store_process_terms {
+  my $self = shift;
+  my $gocam_feature = shift;
+  my $process_terms = shift;
+
+  my $chado = $self->chado();
+
+  for my $process_term_id (@$process_terms) {
+    my $process_term =
+      $self->find_cvterm_by_term_id($process_term_id);
+
+    $self->create_feature_cvterm($gocam_feature, $process_term,
+                                 $self->null_pub(), 0);
+  }
+}
+
+sub store_model_genes {
+  my $self = shift;
+  my $gocam_feature = shift;
+  my $genes = shift;
+
+  my $chado = $self->chado();
+
+  for my $gene_uniquename (@$genes) {
+    my $gene_feature =
+      $self->find_chado_feature($gene_uniquename, 1, 0,
+                                $self->organism(), ['gene']);
+
+    $self->store_feature_rel($gene_feature, $gocam_feature, 'part_of');
+  }
+}
+
+sub load {
+  my $self = shift;
+  my $fh = shift;
+
+  my $chado = $self->chado();
+  my $organism = $self->organism();
+
+  my $decoder = JSON->new();
+
+  my $json_text;
+
+  {
+    local $/ = undef;
+    $json_text = <$fh>;
+  }
+
+  my $data = $decoder->decode($json_text);
+
+  while (my ($gocam_id, $details) = each %$data) {
+    my $title = $details->{title};
+    my $gocam_feature =
+      $self->store_feature("$gocam_id", $title, [], 'gocam_model',
+                           $organism);
+
+    $self->store_model_genes($gocam_feature, $details->{genes});
+    $self->store_process_terms($gocam_feature, $details->{process_terms});
+
+    if (my $gocam_date = $details->{date}) {
+      $self->store_featureprop($gocam_feature, 'gocam_date', $gocam_date);
+    }
+
+    for my $gocam_contributor (@{$details->{contributors} // []}) {
+      $self->store_featureprop($gocam_feature, 'gocam_contributor',
+                               $gocam_contributor);
+    }
+  }
+}
+
+sub results_summary {
+  my $self = shift;
+  my $results = shift;
+
+  return '';
+}
+
+1;
diff --git a/script/pombase-import.pl b/script/pombase-import.pl
index 2c87abfb..264ab8f8 100755
--- a/script/pombase-import.pl
+++ b/script/pombase-import.pl
@@ -40,6 +40,7 @@
   'references-file' => 'PomBase::Import::ReferencesFile',
   'kegg-pathway' => 'PomBase::Import::KEGGMapping',
   'names-and-products' => 'PomBase::Import::NameAndProduct',
+  'go-cam-json' => 'PomBase::Import::GoCamJson',
 );
 
 sub usage