package LIMS::Model::Storage; use Moose; extends 'LIMS::Model::Base'; use namespace::clean -except => 'meta'; __PACKAGE__->meta->make_immutable; use Data::Dumper; use LIMS::Local::Utils; #------------------------------------------------------------------------------- sub input_storage { my ($self, $data) = @_; # warn Dumper $data; { # add specimen.id: my $o = LIMS::DB::Specimen::Manager->get_specimens(); my %map = map { $_->sample_code => $_->id } @$o; my $specimen = $data->{specimen}; $data->{specimen_id} = $map{$specimen}; } # warn Dumper $data; my $vialID = $data->{vialId}; # 10 chars, or multiples of (input validated) if ( length $vialID > 10 ) { # have multiple vials my (@ids) = $vialID =~ /([A-Z]{2}\d{8})/g; # warn Dumper \@ids; for my $vial_id(@ids) { # warn $vial_id; my $c = LIMS::Local::Utils::clone($data); $c->{vialId} = $vial_id; # warn Dumper $c; my $rtn = $self->update_object({ class => 'RequestStorage', data => $c }); return $rtn if $rtn; # only returns true on error } return 0; } else { return $self->update_object({ class => 'RequestStorage', data => $data }); } } #------------------------------------------------------------------------------- sub output_storage { my ($self, $data) = @_; # warn Dumper $data; my $request_id = $data->{request_id}; my $vial_id = $data->{vialId}; my $o = LIMS::DB::RequestStorage->new(vialId => $vial_id)->load_speculative || return { error => "vialId $vial_id does not exist" }; # first check vialId belongs to request_id: unless ( $o->request_id eq $request_id ) { return { error => "vialId $vial_id does not belong to this request" } } $o->signed_out(LIMS::Local::Utils::time_now); $o->save(changes_only => 1); return 'OK'; } #------------------------------------------------------------------------------- sub void_plate { my ($self, $plateId) = @_; # warn Dumper $plateId; my $rack = LIMS::DB::StorageRack->new(plateId => $plateId)->load; my $rack_id = $rack->id or die 'cannot find a plate with ID ' . $plateId; # warn $rack_id; my $db = $self->lims_db; # ie LIMS::DB->new_or_cached; my $tx = sub { LIMS::DB::RequestStorage::Manager->update_objects( set => { vial_location => undef, rack_id => undef, }, where => [ rack_id => $rack_id ], # where => [ plateId => $plateId ], # require_objects => 'rack', # can't do this ); # delete rack ID for possible re-scan: $rack->delete; # die; }; return $db->do_transaction($tx) ? 0 : 'void_plate() error - ' . $db->error; } #------------------------------------------------------------------------------- sub update_storage_vial { my ($self, $data) = @_; # warn Dumper $data; my $o = LIMS::DB::RequestStorage->new(vialId => $data->{vialId})->load; # warn Dumper $o->as_tree; my @cols = $o->meta->column_names; # warn Dumper \@cols; while ( my ($key, $val) = each %$data ) { next unless grep $key eq $_, @cols; # skip non-table fields (eg specimen) next if $o->$key eq $val; # skip if not changed $o->$key($val); } my $db = $self->lims_db; # ie LIMS::DB->new_or_cached; my $tx = sub { $o->save(changes_only => 1) }; return $db->do_transaction($tx) ? 0 : 'update_storage_vial() error - ' . $db->error; } #------------------------------------------------------------------------------- sub update_storage_rack { my ($self, $data) = @_; # warn Dumper $data; my $rack_id = $data->{rack_id}; # warn Dumper $rack_id; my $plate = $data->{plate}; # href of vialId => location (A1 - F12) my $db = $self->lims_db; # ie LIMS::DB->new_or_cached; my %data; # keys = success & fail my $update = sub { while ( my($vialId, $location) = each %$plate ) { # warn Dumper [$vialId,$location]; my $o = LIMS::DB::RequestStorage->new(vialId => $vialId)->load; # warn Dumper $o->as_tree; $o->rack_id($rack_id); $o->vial_location($location); my $request_id = $o->request_id; my %h = ( vialId => $vialId, request_id => $request_id ); $o->save(changes_only => 1) ? $data{success}{$location} = \%h : $data{fail}{$location} = \%h; $data{requests}{$request_id}++; # add request_id } # warn Dumper \%data; }; return $db->do_transaction($update) ? \%data # no errors, but maybe some failed to update : 'update_storage_rack() error - ' . $db->error; } #------------------------------------------------------------------------------- sub sign_out_storage_rack { my ($self, $data) = @_; # warn Dumper $data; my $rack_id = $data->{rack_id}; # warn Dumper $rack_id; my $vial_id = $data->{vial_id}; # arrayref of vialIds my $db = $self->lims_db; # ie LIMS::DB->new_or_cached; my $NOW = $self->time_now; my $rs = do { # get all request_storage rows from vial_id array: my @q = ( vialId => $vial_id ); LIMS::DB::RequestStorage::Manager->get_objects( query => \@q ); }; my %data; # keys = success & fail my $update = sub { for my $ref (@$rs) { # warn $id; $ref->signed_out($NOW); my $request_id = $ref->request_id; my $location = $ref->vial_location; my %h = ( vialId => $ref->vialId, request_id => $request_id ); $ref->save(changes_only => 1) ? $data{success}{$location} = \%h : $data{fail}{$location} = \%h; $data{requests}{$request_id}++; # add request_id } # warn Dumper \%data; { # set plate inactive: my $o = LIMS::DB::StorageRack->new(id => $rack_id)->load; $o->is_active('no'); $o->save(changes_only => 1); } }; return $db->do_transaction($update) ? \%data # no errors, but maybe some failed to update : 'sign_out_storage_rack() error - ' . $db->error; } #------------------------------------------------------------------------------- sub get_request_storage { my ($self, $request_id) = @_; my @args = ( query => [ request_id => $request_id ], with_objects => ['specimen', 'rack' ], sort_by => 'created_at', ); my $o = LIMS::DB::RequestStorage::Manager->get_objects(@args); return $o; } #------------------------------------------------------------------------------- sub get_storage_vial { my ($self, $vial_id) = @_; my $o = LIMS::DB::RequestStorage->new(vialId => $vial_id)->load; return $o; } #------------------------------------------------------------------------------- sub delete_storage_vial { my ($self, $vialId) = @_; my $o = LIMS::DB::RequestStorage->new(vialId => $vialId)->load; return 'cannot delete vial when rack Id exists' if $o->rack_id; my $db = $self->lims_db; # ie LIMS::DB->new_or_cached; my $delete = sub { $o->delete; }; return $db->do_transaction($delete) ? 0 : 'delete_storage_vial() error - ' . $db->error; } #------------------------------------------------------------------------------- sub get_storage_rack { my ($self, $plateId) = @_; my $o = LIMS::DB::StorageRack->new( plateId => $plateId )->load_speculative; return $o ? $o->as_tree : 0; # return hashref for use in session } #------------------------------------------------------------------------------- sub new_storage_rack { my ($self, $plateId) = @_; # return id if exists, otherwise create new object first: my $o = LIMS::DB::StorageRack->new( plateId => $plateId )->load_or_insert; return $o->id; } #------------------------------------------------------------------------------- sub get_rack_contents { # find rack contents by rack.id, or list of vialId's: my ($self, $args) = @_; my $query; if ( my $rack_id = $args->{rack_id} ) { $query = [ rack_id => $rack_id ]; } elsif ( my $vial_ids = $args->{vial_ids} ) { $query = [ vialId => $vial_ids ]; } my @args = ( query => $query ); my $o = LIMS::DB::RequestStorage::Manager->get_objects(@args); return $o; } 1;