From 4ecbd3680b1fc2fb7d84db700ff9ab54f28b58ff Mon Sep 17 00:00:00 2001
From: Kim Rutherford <kmr@aska.gen.nz>
Date: Wed, 6 Sep 2023 17:35:31 +1200
Subject: [PATCH] Add script to set external_uniquename by details

Refs pombase/canto#2770
---
 etc/set_ids_from_chado.pl | 142 ++++++++++++++++++++++++++++++++++++++
 1 file changed, 142 insertions(+)
 create mode 100755 etc/set_ids_from_chado.pl

diff --git a/etc/set_ids_from_chado.pl b/etc/set_ids_from_chado.pl
new file mode 100755
index 000000000..ab246da50
--- /dev/null
+++ b/etc/set_ids_from_chado.pl
@@ -0,0 +1,142 @@
+#!/usr/bin/env perl
+
+use strict;
+use warnings;
+use Carp;
+
+use utf8;
+
+use File::Basename;
+
+BEGIN {
+  my $script_name = basename $0;
+
+  if (-f $script_name && -d "../etc") {
+    # we're in the scripts directory - go up
+    chdir "..";
+  }
+};
+
+use lib qw(lib);
+
+use Canto::Config;
+use Canto::Track;
+use Canto::TrackDB;
+use Canto::Meta::Util;
+
+my $app_name = Canto::Config::get_application_name();
+
+$ENV{CANTO_CONFIG_LOCAL_SUFFIX} ||= 'deploy';
+
+my $suffix = $ENV{CANTO_CONFIG_LOCAL_SUFFIX};
+
+if (!Canto::Meta::Util::app_initialised($app_name, $suffix)) {
+  die "The application is not yet initialised, try running the canto_start " .
+    "script\n";
+}
+
+my $config = Canto::Config::get_config();
+my $track_schema = Canto::TrackDB->new(config => $config);
+
+my $allele_lookup = Canto::Track::get_adaptor($config, 'allele');
+
+my $allele_config = $config->{allele_types};
+
+my $add_uniquenames = sub {
+  my $curs = shift;
+  my $curs_key = $curs->curs_key();
+  my $curs_schema = shift;
+  my $track_schema = shift;
+
+  my $status = $curs->prop_value('annotation_status') // 'UNKNOWN_STATUS';
+
+  return if $status ne 'APPROVED';
+
+  my $allele_rs = $curs_schema->resultset('Allele')
+    ->search({ external_uniquename => undef });
+
+  ALLELE: while (defined (my $allele = $allele_rs->next())) {
+    my $gene_primary_identifier = $allele->gene()->primary_identifier();
+
+    my $allele_name = ($allele->name() // '*NO_NAME*');
+    $allele_name =~ s/Δ|∆/delta/g;
+    my $allele_type = $allele->type();
+    my $allele_description = $allele->description() // '*NO_DESCRIPTION*';
+
+    if ($allele_type =~ /^wild[ _]type$/) {
+      $allele_name = 'wild_type';
+      $allele_description = 'wild type';
+    }
+
+    my $allele_export_type = $allele_config->{$allele_type}->{export_type};
+
+    if (!defined $allele_export_type) {
+      if (defined $config->{export_type_to_allele_type}->{$allele_type}) {
+        $allele_export_type = $allele_type;
+      } else {
+        warn "$curs_key: type not found: $gene_primary_identifier ",
+          ($allele->{name} // '*NO_NAME*'), " $allele_type $allele_description\n" ;
+        next ALLELE;
+      }
+    }
+
+    my @alleles = $allele_lookup->lookup_by_details($gene_primary_identifier,
+                                                    $allele_export_type,
+                                                    $allele_description);
+
+    if (@alleles > 1) {
+      for my $chado_allele (@alleles) {
+        if (($chado_allele->{name} // '*NO_NAME*') =~ s/Δ|∆/delta/gr eq $allele_name) {
+          my $chado_external_uniquename = $chado_allele->{external_uniquename};
+#          warn "$curs_key: found allele for: $gene_primary_identifier ", $allele_name,
+#            " $allele_type $allele_description - $chado_external_uniquename\n";
+
+          #    $allele->external_uniquename($chado_external_uniquename);
+          #    $allele->update();
+          next ALLELE;
+        }
+      }
+
+      warn "$curs_key: multiple alleles (", scalar(@alleles), ") for: $gene_primary_identifier ",
+        $allele_name, " $allele_type $allele_description\n";
+      next ALLELE;
+    }
+
+    if (@alleles == 0) {
+      warn "$curs_key: no alleles for: $gene_primary_identifier ",
+        $allele_name, " $allele_type $allele_description\n";
+      next ALLELE;
+    }
+
+    my $chado_allele = $alleles[0];
+    my $chado_allele_name = $chado_allele->{name} // '*NO_NAME*';
+    $chado_allele_name =~ s/Δ|∆/delta/g;
+
+    if ($chado_allele->{type} eq 'wild_type') {
+      $chado_allele_name = 'wild_type';
+    }
+
+    my $chado_external_uniquename = $chado_allele->{external_uniquename};
+
+#    warn "$curs_key: found allele for: $gene_primary_identifier $allele_type $allele_description - $chado_external_uniquename\n";
+
+    if ($allele_type ne 'deletion' &&
+        $chado_allele_name ne $allele_name) {
+
+      warn $curs_key, q|: Chado allele name doesn't match Canto DB: |,
+        "$allele_name ", $allele->type(), " $allele_description ",
+        $chado_allele_name, "\n";
+    }
+
+#    $allele->external_uniquename($chado_external_uniquename);
+#    $allele->update();
+  }
+};
+
+my $proc = sub {
+  Canto::Track::curs_map($config, $track_schema, $add_uniquenames);
+};
+
+$track_schema->txn_do($proc);
+
+