diff --git a/lib/npg_tracking/data/reference/find.pm b/lib/npg_tracking/data/reference/find.pm index 11b9a380..2e96d48b 100644 --- a/lib/npg_tracking/data/reference/find.pm +++ b/lib/npg_tracking/data/reference/find.pm @@ -222,7 +222,7 @@ sub refs { $spiked_phix_index = $self->lims->spiked_phix_tag_index; } - my @alims = $self->lims->associated_lims; + my @alims = $self->lims->descendants; if (!@alims) { @alims = ($self->lims); } @@ -471,7 +471,7 @@ Marina Gourtovaia Emg8@sanger.ac.ukE =head1 LICENSE AND COPYRIGHT -Copyright (C) 2017 GRL +Copyright (C) 2013,2014,2015,2016,2017,2018,2019,2023 Genome Research Ltd. This file is part of NPG. diff --git a/lib/st/api/lims.pm b/lib/st/api/lims.pm index 2790c40e..432d96eb 100644 --- a/lib/st/api/lims.pm +++ b/lib/st/api/lims.pm @@ -543,7 +543,7 @@ sub _build_required_insert_size { my $is_hash = {}; if (defined $self->position) { - my @alims = $self->associated_lims; + my @alims = $self->descendants; @alims = @alims ? @alims : ($self); foreach my $lims (@alims) { if ($lims->is_control) { @@ -563,32 +563,6 @@ sub _build_required_insert_size { return $is_hash; } - -=head2 seq_qc_state - - 1 for passes, 0 for failed, undef if the value is not set. - - This method is deprecated as of 08 March 2016. It should not be used in any - new code. The only place where this method is used in production code is - the old warehouse loader. Deprecation warning is not appropriate because the - old wh loader logs will be flooded. - -=cut -sub seq_qc_state { - my $self = shift; - my $state = $self->driver ? $self->driver->qc_state : q[]; - if (!defined $state || $state eq '1' || $state eq '0') { - return $state; - } - if ($state eq q[]) { - return; - } - if (!exists $QC_EVAL_MAPPING{$state}) { - croak qq[Unexpected value '$state' for seq qc state in ] . $self->to_string; - } - return $QC_EVAL_MAPPING{$state}; -} - =head2 reference_genome Read-only accessor, not possible to set from the constructor. @@ -1038,20 +1012,6 @@ sub descendants { return @lims; } -=head2 associated_lims - -The same as descendants. Retained for backward compatibility - -=cut -*associated_lims = \&descendants; #backward compat - -=head2 associated_child_lims - -The same as children. Retained for backward compatibility - -=cut -*associated_child_lims = \&children; #backward compat - =head2 children_ia Method providing fast (index-based) access to child lims object. @@ -1097,13 +1057,6 @@ sub sample_publishable_name { return $self->sample_accession_number() || $self->sample_public_name() || $self->sample_name(); } -=head2 associated_child_lims_ia - -The same as children_ia. Retained for backward compatibility - -=cut -*associated_child_lims_ia = \&children_ia; #backward compat - sub _list_of_attributes { my ($self, $attr_name, $with_spiked_control) = @_; my @l = (); @@ -1422,7 +1375,7 @@ Marina Gourtovaia Emg8@sanger.ac.ukE =head1 LICENSE AND COPYRIGHT -Copyright (C) 2013,2014,2015,2016,2017,2018,2019,2020,2021 Genome Research Ltd. +Copyright (C) 2013,2014,2015,2016,2017,2018,2019,2020,2021,2023 Genome Research Ltd. This file is part of NPG.