From 504b684a884bc71914c28630aec1e4fbe8c862ab Mon Sep 17 00:00:00 2001
From: Marina Gourtovaia <mg8@sanger.ac.uk>
Date: Tue, 19 Mar 2024 13:58:20 +0000
Subject: [PATCH] Add run-lane annotations to a search

---
 lib/npg/model/search.pm | 18 ++++++++++------
 t/10-model-search.t     | 33 +++++++++++++++++++++--------
 t/20-view-search.t      | 46 +++++++++++++----------------------------
 3 files changed, 50 insertions(+), 47 deletions(-)

diff --git a/lib/npg/model/search.pm b/lib/npg/model/search.pm
index 8425ec64..86fb9818 100644
--- a/lib/npg/model/search.pm
+++ b/lib/npg/model/search.pm
@@ -1,7 +1,3 @@
-#########
-# Author:        rmp
-# Created:       2008-01
-#
 package npg::model::search;
 use strict;
 use warnings;
@@ -77,7 +73,7 @@ sub results {
                        AND    content LIKE ?), "%$term%"];
 
   #########
-  # search run annotations
+  # search annotations
   #
   push @{$queries}, [q(SELECT 'run'        AS type,
                               ra.id_run    AS primary_key,
@@ -89,6 +85,16 @@ sub results {
                        AND    a.comment LIKE   ?
                        ORDER BY date DESC
                        LIMIT 100), "%$term%"];
+  push @{$queries}, [q(SELECT 'run_lane'        AS type,
+                              rla.id_run_lane   AS primary_key,
+                              'annotation' AS location,
+                              a.comment    AS context
+                       FROM   annotation     a,
+                              run_lane_annotation rla
+                       WHERE  rla.id_annotation = a.id_annotation
+                       AND    a.comment LIKE   ?
+                       ORDER BY date DESC
+                       LIMIT 100), "%$term%"];
 
   #########
   # search instrument annotations & statuses
@@ -492,7 +498,7 @@ Roger Pettett, E<lt>rmp@sanger.ac.ukE<gt>
 
 =head1 LICENSE AND COPYRIGHT
 
-Copyright (C) 2007 GRL, by Roger Pettett
+Copyright (C) 2007, 2013, 2014, 2017, 2024 Genome Research Ltd.
 
 This library is free software; you can redistribute it and/or modify
 it under the same terms as Perl itself, either Perl version 5.8.4 or,
diff --git a/t/10-model-search.t b/t/10-model-search.t
index 44add79b..b1bcf09b 100644
--- a/t/10-model-search.t
+++ b/t/10-model-search.t
@@ -1,22 +1,37 @@
 use strict;
 use warnings;
-use Test::More tests => 6;
+use Test::More tests => 13;
+use List::MoreUtils qw/uniq/;
 use t::util;
 
 use_ok('npg::model::search');
 
-my $util = t::util->new({
-       fixtures => 1,
-      });
+my $util = t::util->new({fixtures => 1,});
 
 {
-  my $search = npg::model::search->new({
-          util => $util,
-               });
+  my $search = npg::model::search->new({util => $util,});
 
-  $search->query('Lack of clusters');
+  my $query = 'Lack of clusters';
+  $search->query($query);
   my $results = $search->results();
-  is((scalar @{$results}), 1, 'exact run annotation');
+  is((scalar @{$results}), 2, 'run and run-lane annotations');
+  is($results->[0]->[0], 'run', 'run annotation first');
+  is($results->[1]->[0], 'run_lane', 'run-lane annotation second');
+  my @annotations = uniq map { $_->[3] } @{$results}; 
+  ok((@annotations == 1) && ($annotations[0] eq "${query} - run cancelled"),
+    'correct annotations are retrieved');
+
+  $query = 'Training flow';
+  $search->query($query);
+  $results = $search->results();
+  is((scalar @{$results}), 7, 'run and run-lane annotations');
+  my $n = grep { $_->[0] eq 'run' } @{$results};
+  is($n, 3, 'three run annotation');
+  $n = grep { $_->[0] eq 'run_lane' } @{$results};
+  is($n, 4, 'four run-lane annotation');
+  @annotations = uniq map { $_->[3] } @{$results};
+  ok((@annotations == 1) && ($annotations[0] eq 'Training Flowcell'),
+    'correct annotations are retrieved');
 }
 
 {
diff --git a/t/20-view-search.t b/t/20-view-search.t
index d5f201b2..ca574338 100644
--- a/t/20-view-search.t
+++ b/t/20-view-search.t
@@ -1,53 +1,35 @@
 use strict;
 use warnings;
-use Test::More tests => 4;
+use Test::More tests => 3;
 use t::util;
 use t::request;
 use npg::model::search;
 
 use_ok('npg::view::search');
 
-my $util = t::util->new({
-       fixtures => 1,
-      });
+my $util = t::util->new({fixtures => 1,});
 
 {
   my $str = t::request->new({
-                             PATH_INFO      => '/search',
-                             REQUEST_METHOD => 'GET',
+           PATH_INFO      => '/search',
+           REQUEST_METHOD => 'GET',
            username       => 'public',
-                             util           => $util,
-           cgi_params     => {
-            query => 'TriosP',
-                 },
-                            });
+           util           => $util,
+           cgi_params     => {query => 'TriosP',},
+  });
   ok($util->test_rendered($str, 't/data/rendered/search.html'), 'list render');
 }
 
 {
   my $str = t::request->new({
-                             PATH_INFO      => '/search',
-                             REQUEST_METHOD => 'GET',
+           PATH_INFO      => '/search',
+           REQUEST_METHOD => 'GET',
            username       => 'public',
-                             util           => $util,
-           cgi_params     => {
-            query => '  TriosP',
-                 },
-                            });
-  ok($util->test_rendered($str, 't/data/rendered/search.html'), 'list render leading whitespace');
-}
-
-{
-  my $str = t::request->new({
-                             PATH_INFO      => '/search',
-                             REQUEST_METHOD => 'GET',
-           username       => 'public',
-                             util           => $util,
-           cgi_params     => {
-            query => 'TriosP ',
-                 },
-                            });
-  ok($util->test_rendered($str, 't/data/rendered/search.html'), 'list render trailing whitespace');
+           util           => $util,
+           cgi_params     => {query => '  TriosP ',},
+  });
+  ok($util->test_rendered($str, 't/data/rendered/search.html'),
+    'list render leading and trailing whitespace');
 }
 
 1;