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Add run-lane annotations to a search #815

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Apr 3, 2024
Merged

Add run-lane annotations to a search #815

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18 changes: 12 additions & 6 deletions lib/npg/model/search.pm
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Original file line number Diff line number Diff line change
@@ -1,7 +1,3 @@
#########
# Author: rmp
# Created: 2008-01
#
package npg::model::search;
use strict;
use warnings;
Expand Down Expand Up @@ -77,7 +73,7 @@ sub results {
AND content LIKE ?), "%$term%"];

#########
# search run annotations
# search annotations
#
push @{$queries}, [q(SELECT 'run' AS type,
ra.id_run AS primary_key,
Expand All @@ -89,6 +85,16 @@ sub results {
AND a.comment LIKE ?
ORDER BY date DESC
LIMIT 100), "%$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
Expand Down Expand Up @@ -492,7 +498,7 @@ Roger Pettett, E<lt>[email protected]<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,
Expand Down
33 changes: 24 additions & 9 deletions t/10-model-search.t
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Original file line number Diff line number Diff line change
@@ -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');
}

{
Expand Down
46 changes: 14 additions & 32 deletions t/20-view-search.t
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Original file line number Diff line number Diff line change
@@ -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;
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