Enhanced a textual listing of instruments.

data/templates/instrument_list_textual.tt2

@@ -13,6 +13,7 @@
    <th>Current Status</th>
    <th>Status Comment</th>
    <th>Laboratory</th>
+   <th>Staging Volume</th>
   </tr>
  </thead>
  <tbody>
@@ -26,6 +27,7 @@
    <td>[% instrument.current_instrument_status.instrument_status_dict.description %]</td>
    <td>[% instrument.current_instrument_status.comment %]</td>
    <td>[% instrument.lab %]</td>
+   <td>[% instrument.recent_staging_volumes.join(', ') %]</td>
   </tr>
 [% END %]
  </tbody>

lib/npg/model/instrument.pm

@@ -2,9 +2,15 @@ package npg::model::instrument;
 
 use strict;
 use warnings;
-use base qw(npg::model);
 use English qw(-no_match_vars);
+use File::Spec;
 use Carp;
+use DateTime;
+use DateTime::Duration;
+use DateTime::Format::MySQL;
+use List::MoreUtils qw(any uniq);
+use base qw(npg::model);
+
 use npg::model::user;
 use npg::model::run;
 use npg::model::instrument_format;
@@ -15,10 +21,6 @@ use npg::model::instrument_annotation;
 use npg::model::annotation;
 use npg::model::instrument_designation;
 use npg::model::designation;
-use DateTime;
-use DateTime::Duration;
-use DateTime::Format::MySQL;
-use List::MoreUtils qw/any/;
 
 our $VERSION = '0';
 
@@ -380,6 +382,42 @@ sub latest_annotation {
   return $self->{latest_annotation};
 }
 
+sub recent_staging_volumes {
+  my $self = shift;
+
+  my $run_status = q[run in progress];
+  my $query = q[SELECT folder_path_glob FROM instrument
+                JOIN run USING(id_instrument)
+                JOIN run_status USING(id_run)
+                JOIN run_status_dict USING(id_run_status_dict)
+                WHERE folder_path_glob IS NOT NULL
+                AND LENGTH(folder_path_glob) != 0
+                AND id_instrument=? AND description=?
+                ORDER BY date DESC];
+  my $dbh = $self->util->dbh();
+  # Four rather than two latest runs since NovaSeq(X) instruments have
+  # two sides, which write to the same staging server.
+  my $rows = $dbh->selectall_arrayref($query, {RaiseError => 1, MaxRows => 4},
+    $self->id_instrument(), $run_status);
+  my @globs = uniq map { $_->[0] } @{$rows};
+  # We do not need more that two unique globs.
+  while (scalar @globs > 2) {
+    pop @globs
+  }
+
+  my @volumes = ();
+  foreach my $area (@globs) {
+    my @dirs = File::Spec->splitdir($area);
+    # Current (May 2024) folder path globs look like
+    # /{export,nfs}/esa-sv-20201215-03/IL_seq_data/*/
+    ##no critic (ValuesAndExpressions::ProhibitMagicNumbers)
+    push @volumes, (@dirs >= 3 and $dirs[0] eq q[]) ? $dirs[2] : $area;
+    ##use critic
+  }
+
+  return @volumes;
+}
+
 sub does_sequencing {
   my $self = shift;
   return ($self->instrument_format->model &&
@@ -595,9 +633,9 @@ npg::model::instrument
 
 =head1 DESCRIPTION
   Clearpress model for an instrument.
-  To be replaced by DBIx model. Contains duplicates of functions in
-  npg_tracking::Schema::Result::Instrument. When editing the code
-  of this module consider if any changes are meeded in the other module. 
+  Contains duplicates of functions in npg_tracking::Schema::Result::Instrument.
+  When editing the code of this module consider if any changes are needed in
+  the other module. 
 
 =head1 SUBROUTINES/METHODS
 
@@ -621,11 +659,6 @@ npg::model::instrument
 
   my $arAllInstruments = $oInstrument->instruments();
 
-=head2 instrument_by_ipaddr - npg::model::instrument by its IP address
-
-  my $oInstrument = $oInstrument->instrument_by_ipaddr('127.0.0.1');
-instrument_by_instrument_comp
-
 =head2 instrument_by_instrument_comp - npg::model::instrument by its instrument_comp name
 
 =head2 current_instruments - arrayref of all npg::model::instruments with iscurrent=1
@@ -637,16 +670,6 @@ instrument_by_instrument_comp
   my $lab = 'Sulston';
   my $arCurrentSulstonInstruments = $oInstrument->current_instruments_from_lab($lab);
 
-=head2 last_wash_instrument_status - npg::model::instrument_status (or undef) corresponding to the last 'wash performed' state
-
-  my $oInstrumentStatus = $oInstrument->last_wash_instrument_status();
-
-=head2 check_wash_status - boolean whether this instrument needs washing
-
-Has a side-effect of updating an instrument's current instrument_status to 'wash required'
-
- $bNeedAWash = $oInstrument->check_wash_status();
-
 =head2 runs - arrayref of npg::model::runs for this instrument
 
   my $arRuns = $oInstrument->runs();
@@ -719,6 +742,10 @@ Has a side-effect of updating an instrument's current instrument_status to 'wash
 
 =head2 fc_slots2blocking_runs - a hash reference mapping instrument flowcell slots to blocking runs; tags for slots are used as keys
 
+=head2 recent_staging_volumes - returns a list of names of staging volumes
+this instrument most recently transferred data to, most recently used volume
+first. The list might be empty and cannot have more than two volume names.
+
 =head2 does_sequencing - returns true is the instrument does sequencing, false otherwise
 
 =head2 is_two_slot_instrument - returns true if this instrument has two slots, false otherwise
@@ -729,7 +756,7 @@ returns true if the instrument is a MiSeq, false otherwise
 
 =head2 is_cbot_instrument - returns true if this instrument is CBot, false otherwise
 
-=head2 current_run_by_id - returns one of current runs with teh argument id or nothing if a list of current runs does not contain a run with this id
+=head2 current_run_by_id - returns one of current runs with the argument id or nothing if a list of current runs does not contain a run with this id
 
  my $id_run = 22;
  my $run = $oInstrument->current_run_by_id($id_run);
@@ -761,27 +788,21 @@ returns true if the instrument is a MiSeq, false otherwise
 
 =item base
 
-=item npg::model
+=item File::Spec
 
 =item English
 
 =item Carp
 
-=item npg::model::user
-
-=item npg::model::run
-
-=item npg::model::instrument_format
-
-=item npg::model::instrument_status
+=item Readonly
 
-=item npg::model::instrument_status_dict
+=item DateTime
 
-=item npg::model::instrument_mod
+=item DateTime::Duration
 
-=item DateTime
+=item DateTime::Format::MySQL
 
-=item Readonly
+=item List::MoreUtils
 
 =back
 
@@ -793,15 +814,15 @@ returns true if the instrument is a MiSeq, false otherwise
 
 =over
 
-=item Roger Pettett, E<lt>[email protected]<gt>
+=item Roger Pettett
 
 =item Marina Gourtovaia
 
 =back
 
 =head1 LICENSE AND COPYRIGHT
 
-Copyright (C) 2006,2008,2013,2014,2016,2018,2021 Genome Research Ltd.
+Copyright (C) 2006,2008,2013,2014,2016,2018,2021,2024 Genome Research Ltd.
 
 This file is part of NPG.
 

t/10-model-instrument.t

@@ -1,7 +1,7 @@
 use strict;
 use warnings;
 use t::util;
-use Test::More tests => 141;
+use Test::More tests => 142;
 use Test::Deep;
 use Test::Exception;
 
@@ -191,7 +191,6 @@ my $util = t::util->new({ fixtures => 1 });
       qq[status changed automatically to "$auto_status"]);
 }
 
-
 {
   my $instr = npg::model::instrument->new({
     util          => $util,
@@ -312,7 +311,6 @@ lives_ok {$util->fixtures_path(q[t/data/fixtures]); $util->load_fixtures;} 'a fr
   ok (!$model->autochange_status_if_needed('analysis in progress'), 'no autochange status');
 }
 
-
 {
   my $model = npg::model::instrument->new({util => $util, id_instrument => 36,});
   ok($model->is_two_slot_instrument, 'is two_slot instrument');
@@ -351,7 +349,6 @@ lives_ok {$util->fixtures_path(q[t/data/fixtures]); $util->load_fixtures;} 'a fr
   cmp_deeply($model->fc_slots2blocking_runs, {fc_slotA => [], fc_slotB => [],}, 'empty mapping of both slots to blocking runs');
 }
 
-
 {
   my $run = npg::model::run->new({util => $util, id_run => 9950,});
   $run->id_instrument(36);
@@ -421,4 +418,84 @@ lives_ok {$util->fixtures_path(q[t/data/fixtures]); $util->load_fixtures;} 'a fr
   is (scalar @{$model->instrument_statuses()}, 3, 'number of statuses in total');
 }
 
+subtest 'recent staging volumes list' => sub {
+  plan tests => 14;
+
+  my $util4updates = t::util->new(); # need a new db handle
+  lives_ok {$util4updates->load_fixtures;} 'a fresh set of fixtures is loaded';
+  my $dbh = $util4updates->dbh;
+  $dbh->{AutoCommit} = 1;
+  $dbh->{RaiseError} = 1;
+
+  my $status = 'run in progress';
+
+  my $model = npg::model::instrument->new({
+             util          => $util,
+             id_instrument => 3,
+            });
+  is (join(q[ ], $model->recent_staging_volumes()), q[esa-sv-20201215-03],
+    qq[volume name for a single run that is associated with the "$status" status]);
+
+  $model = npg::model::instrument->new({
+             util          => $util,
+             id_instrument => 14,
+            });
+  is (scalar $model->recent_staging_volumes(), 0,
+    'empty list since no glob is available for a run that is associated with ' .
+    qq[the "$status" status]);
+
+  $model = npg::model::instrument->new({
+             util          => $util,
+             id_instrument => 13,
+            });
+  is (join(q[,], $model->recent_staging_volumes()), 'esa-sv-20201215-02',
+    'a list with one volume name');
+
+  my $new_glob = q[{export,nfs}/esa-sv-20201215-02/IL_seq_data/*/];
+  my $update = qq[update run set folder_path_glob='$new_glob' where id_run=15];
+  ok($dbh->do($update), 'folder path glob is updated');
+  $model = npg::model::instrument->new({
+             util          => $util,
+             id_instrument => 13,
+            });
+  is (join(q[,], $model->recent_staging_volumes()), $new_glob,
+    'a full glob is returned');
+
+  $new_glob = q[/{export,nfs}];
+  $update = qq[update run set folder_path_glob='$new_glob' where id_run=15];
+  ok($dbh->do($update), 'folder path glob is updated');
+  $model = npg::model::instrument->new({
+             util          => $util,
+             id_instrument => 13,
+            });
+  is (join(q[,], $model->recent_staging_volumes()), $new_glob,
+    'a full glob is returned');
+
+  $update = qq[update run set folder_path_glob='' where id_run=15];
+  ok($dbh->do($update), 'folder path glob is updated');
+  $model = npg::model::instrument->new({
+             util          => $util,
+             id_instrument => 13,
+            });
+  is (scalar $model->recent_staging_volumes(), 0,
+    'an empty list is returned for a zero length glob');
+
+  $update = q[update run_status set id_run_status_dict=2 where ] .
+    q[id_run in (3,4,5) and id_run_status_dict=4];
+  ok($dbh->do($update), 'run statuses are updated');
+  $update = qq[update run set folder_path_glob='volume5' where id_run=15];
+  ok($dbh->do($update), 'folder path glob is updated');
+  $update = qq[update run set id_instrument=3 where id_run=15];
+  ok($dbh->do($update), 'assign one more run to the instrument');
+
+  $model = npg::model::instrument->new({
+             util          => $util,
+             id_instrument => 3,
+            });
+  is (join(q[, ], $model->recent_staging_volumes()), q[volume5, /{export,nfs}],
+    'latest volumes list');
+
+  $dbh->disconnect;
+};
+
 1;