From 3bab9549e64d6b77c6b9d0bc860503641426a9cc Mon Sep 17 00:00:00 2001
From: Kim Rutherford <kmr@aska.gen.nz>
Date: Sat, 6 Apr 2024 01:18:51 +1300
Subject: [PATCH] Add start of --change-gene-id admin action

Refs pombase/canto#2677
---
 lib/Canto/Track/TrackUtil.pm | 38 ++++++++++++++++++++++++++++++++++++
 script/canto_admin.pl        | 13 ++++++++++++
 2 files changed, 51 insertions(+)

diff --git a/lib/Canto/Track/TrackUtil.pm b/lib/Canto/Track/TrackUtil.pm
index ae29ab1ce..b127be4c2 100644
--- a/lib/Canto/Track/TrackUtil.pm
+++ b/lib/Canto/Track/TrackUtil.pm
@@ -426,4 +426,42 @@ sub update_annotation_curators
   Canto::Track::curs_map($self->config(), $track_schema, $proc);
 }
 
+=head2 change_gene_id
+
+ Usage   : $util->change_gene_id($from_id, $to_id)
+ Function: Change a gene ID (primary_identifier) in every session.
+           Also change allele IDs containing the $from_id.
+ Args    : $from_id - an existing primary_identifier
+           $to_id
+ Returns : nothing - dies on failures
+
+=cut
+
+sub change_gene_id
+{
+  my $self = shift;
+
+  my $from_id = shift;
+  my $to_id = shift;
+
+  my $track_schema = $self->schema();
+
+  my $proc = sub {
+    my $curs = shift;
+    my $cursdb = shift;
+
+    my $gene_rs = $cursdb->resultset('Gene');
+
+    while (defined (my $gene = $gene_rs->next())) {
+      if ($gene->primary_identifier() eq $from_id) {
+        print $curs->curs_key(), "\n";
+        $gene->primary_identifier($to_id);
+        $gene->update();
+      }
+    }
+  };
+
+  Canto::Track::curs_map($self->config(), $track_schema, $proc);
+}
+
 1;
diff --git a/script/canto_admin.pl b/script/canto_admin.pl
index d2a4217d4..e7ac5532a 100755
--- a/script/canto_admin.pl
+++ b/script/canto_admin.pl
@@ -39,6 +39,7 @@ BEGIN
 my $change_taxonid = undef;
 my $delete_unused_strains = undef;
 my $update_annotation_curators = undef;
+my $change_gene_id = undef;
 
 my $dry_run = 0;
 my $do_help = 0;
@@ -49,6 +50,7 @@ BEGIN
                          "change-taxonid" => \$change_taxonid,
                          "delete-unused-strains" => \$delete_unused_strains,
                          "update-annotation-curators" => \$update_annotation_curators,
+                         "change-gene-id" => \$change_gene_id,
                          "dry-run|d" => \$dry_run,
                          "help|h" => \$do_help);
 
@@ -84,6 +86,8 @@ sub usage
   Set the curator_orcid field of the annotations if available in the
   person table
 
+  $0 --change-gene-id <from_id> <to_id>
+  Change <from_id> to <to_id> for all genes and alleles in every session
 |;
 }
 
@@ -191,6 +195,15 @@ sub usage
       warn "failing to update annotation curator field: $_\n";
     };
   }
+
+  if (defined $change_gene_id) {
+    my $from_id = shift @ARGV;
+    my $to_id = shift @ARGV;
+
+    $util->change_gene_id($from_id, $to_id);
+
+    $exit_flag = 0;
+  }
 };
 
 if (defined $refresh_gene_cache) {