"Stuck Run" functionality dropped

Changes

@@ -9,6 +9,8 @@ LIST OF CHANGES
    - npg::model_run_status -
        current_run_statuses, latest_current_run_status,
        active_runs_over_last_30_days, epoch
+ - Deleted 'Stuck Runs' button from the admin top-level menu,
+   the associated template and the view and model methods.
 
 release 102.1.0 (2025-01-16)
  - Fixed perlbrew installation by installing libdevel-patchperl-perl in

MANIFEST

@@ -71,7 +71,6 @@ data/templates/run_lane_list_tag.tt2
 data/templates/run_lane_read.tt2
 data/templates/run_lane_update_tags.tt2
 data/templates/run_list.tt2
-data/templates/run_list_stuck_runs.tt2
 data/templates/run_read.tt2
 data/templates/run_status_create.tt2
 data/templates/run_status_table.tt2
@@ -548,7 +547,6 @@ t/data/rendered/run.html-POST
 t/data/rendered/run.html;add
 t/data/rendered/run/1.html;update_tags
 t/data/rendered/run/1.html;update_tags-no-tags
-t/data/rendered/run/list_stuck_runs.html
 t/data/rendered/run/runs_on_instrument.html
 t/data/rendered/run_annotation_add_ajax.html
 t/data/rendered/run_lane/1;update_tags

data/templates/actions.tt2

@@ -70,9 +70,6 @@
 <ul class="inline">
  <li><a class="npg_menu" href="[% SCRIPT_NAME %]/run/">Runs</a></li>
  <li><a class="npg_menu" href="[% SCRIPT_NAME %]/instrument/">Instruments</a></li>
-[%- IF requestor.is_member_of('loaders') || requestor.is_member_of('annotators') %]
- <li><a class="npg_menu" href="[% SCRIPT_NAME %]/run/stuck_runs">Stuck Runs</a></li>
-[% END -%]
 [%- IF requestor.is_member_of('engineers') || requestor.is_member_of('admin') %]
  <li><a class="npg_menu" href="[% SCRIPT_NAME %]/administration/">Admin</a></li>
 [% END -%]

lib/npg/model/run.pm

@@ -896,14 +896,6 @@ sub has_analysis_in_progress {
   return 0;
 }
 
-sub potentially_stuck_runs {
-  my ( $self ) = @_;
-  if ( ! $self->{potentially_stuck_runs} ) {
-    $self->{potentially_stuck_runs} = $self->runs()->[0]->current_run_status()->potentially_stuck_runs();
-  }
-  return $self->{potentially_stuck_runs};
-}
-
 sub teams {
   my $self = shift;
   return map {$TEAMS{$_}} (sort {$a <=> $b} keys %TEAMS);
@@ -1149,10 +1141,6 @@ npg::model::run
 
 =head2 num_reads - calculate number of reads of this run based on multplex_run and paired read or not
 
-=head2 potentially_stuck_runs
-
-return runs which are potentially stuck due to the length of time at their current run status - see method in model::run_status
-
 =head2 run_status_dict
 
 provides a short cut method to the run status dict object providing the description for the current run status

lib/npg/model/run_status.pm

@@ -4,9 +4,6 @@ use strict;
 use warnings;
 use English qw(-no_match_vars);
 use Carp;
-use Date::Parse;
-use DateTime;
-use Readonly;
 
 use npg::model::event;
 use npg::model::run_status_dict;
@@ -15,19 +12,6 @@ use base qw(npg::model);
 
 our $VERSION = '0';
 
-Readonly::Hash our %DAYS_PER_STATUS => (
-  'run complete' => 1,
-  'run mirrored' => 1,
-  'analysis pending' => 1,
-  'analysis in progress' => 2,
-  'secondary analysis in progress' => 3,
-  'analysis complete' => 1,
-  'archival pending' => 1,
-  'analysis in progress' => 1,
-  'analysis complete' => 1,
-  'archival in progress' => 2,
-);
-
 __PACKAGE__->mk_accessors(fields());
 __PACKAGE__->has_a([qw(run user run_status_dict)]);
 
@@ -77,7 +61,7 @@ sub create {
 
     my $desc = $self->run_status_dict->description();
 
-    my $msg = qq($desc for run @{[$self->run->name()]}\nhttp://sfweb.internal.sanger.ac.uk:9000/perl/npg/run/@{[$self->run->name()]}\n$history\n\n$contents_of_lanes);
+    my $msg = qq($desc for run @{[$self->run->name()]}\nhttp://sfweb.internal.sanger.ac.uk:12443/perl/npg/run/@{[$self->run->name()]}\n$history\n\n$contents_of_lanes);
     my $event = npg::model::event->new({
                                       run                => $self->run(),
                                       status_description => $desc,
@@ -113,57 +97,6 @@ sub create {
   return 1;
 }
 
-sub potentially_stuck_runs {
-  my ( $self ) = @_;
-  my $return = {};
-
-  my $rows = $self->_runs_at_requested_statuses();
-
-  my $dtnow = $self->_datetime_now();
-
-  foreach my $row ( @{ $rows } ) {
-    my ( $id_run, $date, $status, $priority ) = @{ $row };
-    my ( $year, $month, $day ) = $date =~ /(\d{4})-(\d{2})-(\d{2})/xms;
-    my $dt = DateTime->new(
-      year => $year, month => $month, day => $day, time_zone => 'UTC',
-    );
-    my $days = $dtnow->delta_days($dt)->in_units( q{days} );
-    if ( $days >= $DAYS_PER_STATUS{$status} ) {
-      push @{ $return->{$status} }, { id_run => $id_run, days => $days, priority => $priority };
-    }
-  }
-
-  return $return;
-}
-
-sub _runs_at_requested_statuses {
-  my ( $self ) = @_;
-
-  if ( ! $self->{_runs_at_requested_statuses} ) {
-    my @statuses_for_query = keys %DAYS_PER_STATUS;
-    my $query_string = q{'} . ( join q{','}, keys %DAYS_PER_STATUS ) . q{'};
-
-    my $query =  qq{SELECT rs.id_run, rs.date, rsd.description, r.priority
-                    FROM run_status rs, run_status_dict rsd, run r
-                    WHERE  rs.iscurrent = 1
-                    AND    rs.id_run_status_dict = rsd.id_run_status_dict
-                    AND    rs.id_run = r.id_run
-                    AND    rsd.description IN ($query_string)
-                    ORDER BY rsd.id_run_status_dict, rs.id_run};
-
-    $self->{_runs_at_requested_statuses} = $self->util->dbh->selectall_arrayref( $query );
-  }
-  return $self->{_runs_at_requested_statuses};
-}
-
-sub _datetime_now {
-  my ( $self ) = @_;
-  if ( ! $self->{_datetime_now} ) {
-    $self->{_datetime_now} = DateTime->now( time_zone => 'UTC' );
-  }
-  return $self->{_datetime_now};
-}
-
 1;
 __END__
 
@@ -204,29 +137,6 @@ npg::model::run_status
   Sets all other run_status for this id_run to iscurrent=0
   Sets this iscurrent=1 (whatever was set/unset in the object);
 
-=head2 potentially_stuck_runs
-
-returns a hashref, keyed on status, which contains all the runs that are over a certain time period within a current run status
-
-  i.e. run complete => 1 day
-       run mirrored => 1 day
-       analysis pending => 1 day
-       analysis in progress => 2 days
-       secondary analysis in progress => 3 days
-       analysis complete => 1 day
-       archival pending => 1 day
-       analysis in progress => 1 day
-       analysis complete => 1 day
-
-You get back a hashref as follows
-
-  {
-    'run complete' => [ { id_run => 1234, days => 2 }, { id_run => 2341, days => 3 } ],
-    ...
-  }
-
-  my $hPotentiallyStuckRuns = $oRunStatus->potentially_stuck_runs();
-
 =head1 DIAGNOSTICS
 
 =head1 CONFIGURATION AND ENVIRONMENT
@@ -251,8 +161,6 @@ You get back a hashref as follows
 
 =item npg::model::run_status_dict
 
-=item Date::Parse
-
 =back
 
 =head1 INCOMPATIBILITIES

lib/npg/view/run.pm

@@ -62,10 +62,6 @@ sub authorised {
     return 1;
   }
 
-  if (  $aspect eq q{list_stuck_runs} && ( $requestor->is_member_of( q{loaders} ) || $requestor->is_member_of( q{annotators} ) || $requestor->is_member_of( q{manual_qc} ) ) ) {
-    return 1;
-  }
-
   return $self->SUPER::authorised();
 }
 
@@ -355,11 +351,6 @@ sub update {
   return $self->SUPER::update(@args);
 }
 
-sub list_stuck_runs {
-  my ( $self ) = @_;
-  return 1;
-}
-
 1;
 
 __END__
@@ -397,10 +388,6 @@ npg::view::run - view handling for runs
 
 =head2 update - handling for tile-layout updates
 
-=head2 list_stuck_runs
-
-handling for the stuck runs page
-
 =head1 DIAGNOSTICS
 
 =head1 CONFIGURATION AND ENVIRONMENT

t/10-model-run.t

@@ -14,15 +14,13 @@ use_ok ('npg::model::annotation');
 my $util  = t::util->new({fixtures  => 1});
 
 subtest 'model object that is not linked to a run' => sub {
-  plan tests => 7;
+  plan tests => 6;
 
   my $model = npg::model::run->new({util => $util});
   isa_ok($model, 'npg::model::run');
   my @fields = $model->fields();
   is((scalar @fields), 13, '$model->fields() size');
 
-  isa_ok( $model->potentially_stuck_runs(), q{HASH}, q{potentially_stuck_runs} );
-
   is($model->name(), 'UNKNOWN_0000', 'unknown name if no instrument name and no id_run');
 
   is($model->attach_annotation('test annotation'), 1, '$model->attach_annotation() with annotation, but no $model->id_run()');

t/10-model-run_status.t

@@ -1,6 +1,6 @@
 use strict;
 use warnings;
-use Test::More tests => 15;
+use Test::More tests => 10;
 use Test::Exception;
 
 use npg::model::run;
@@ -10,47 +10,6 @@ use_ok('npg::model::run_status');
 
 my $util = t::util->new({ fixtures  => 1,});
 
-{
-  my $rs = npg::model::run_status->new({
-          util => $util,
-               });
-  isa_ok($rs, 'npg::model::run_status');
-  my $expected_data = [
-    [ '9948', '2010-01-01 10:10:30', 'run complete',      1 ],
-    [ '9949', '2010-01-01 10:10:33', 'run complete',      1 ],
-    [ '9950', '2010-01-01 10:10:34', 'run complete',      1 ],
-    [ '9951', '2010-01-01 10:10:34', 'run complete',      1 ],
-    [ '1',    '2007-06-05 12:22:32', 'analysis complete', 1 ],
-    [ '95',   '2007-06-05 12:22:32', 'analysis complete', 4 ],
-    [ '5',    '2007-06-05 12:32:28', 'run mirrored',      1 ],
-    [ '11',   '2007-06-05 12:31:44', 'run mirrored',      1 ],
-    [ '12',   '2007-06-05 12:32:27', 'run mirrored',      1 ],
-  ];
-
-  is_deeply( $rs->_runs_at_requested_statuses(), $expected_data, q{correct data from _runs_at_requested_statuses obtained} );
-
-  my $datetime = $rs->_datetime_now();
-  is( $datetime, $rs->_datetime_now(), q{_datetime_now is cached correctly} );
-
-  $datetime->set_day(28);
-  $datetime->set_month(2);
-  $datetime->set_year(2011);
-
-  $expected_data = {
-    'analysis complete' => [ { 'days' => 1364, 'id_run' => '1',  priority => 1 },
-                             { 'days' => 1364, 'id_run' => '95', priority => 4 }, ],
-    'run complete' => [ { 'days' => 423,  'id_run' => '9948', priority => 1 },
-                        { 'days' => 423,  'id_run' => '9949', priority => 1 },
-                        { 'days' => 423,  'id_run' => '9950', priority => 1 },
-                        { 'days' => 423,  'id_run' => '9951', priority => 1 }, ],
-    'run mirrored' => [ { 'days' => 1364, 'id_run' => '5',    priority => 1 },
-                        { 'days' => 1364, 'id_run' => '11',   priority => 1 },
-                        { 'days' => 1364, 'id_run' => '12',   priority => 1 }, ]
-  };
-
-  is_deeply( $rs->potentially_stuck_runs(), $expected_data, q{potentially_stuck_runs returns the expected data} );
-}
-
 {
   my $rs = npg::model::run_status->new({
           util => $util,
@@ -102,12 +61,4 @@ my $util = t::util->new({ fixtures  => 1,});
     'no croak on create for id_run_status_dict = 4 for id_run 1';
 }
 
-{
-  my $model = npg::model::run_status->new( {
-    util => $util,
-  } );
-  my $potentially_stuck_runs = $model->potentially_stuck_runs();
-  isa_ok( $potentially_stuck_runs, q{HASH}, q{$model->potentially_stuck_runs()} );
-}
-
 1;

t/20-view-run.t

@@ -1,6 +1,6 @@
 use strict;
 use warnings;
-use Test::More tests => 27;
+use Test::More tests => 26;
 use Test::Exception;
 use Test::Deep;
 use CGI;
@@ -54,19 +54,6 @@ my $util = t::util->new({fixtures  => 1,});
   is_deeply($view->staging_urls($name), $esa_urls, 'run on staging, esa urls');
 }
 
-{
-  my $view = npg::view::run->new({
-          util  => $util,
-          action => q{list},
-          aspect => q{list_stuck_runs},
-          model => npg::model::run->new({
-                 util   => $util,
-                 id_run => q(),
-                }),
-         });
-  ok($util->test_rendered($view->render(), 't/data/rendered/run/list_stuck_runs.html'), 'list_stuck_runs render is ok');
-}
-
 {
   my $str = t::request->new({
            PATH_INFO      => '/run;add',

t/data/rendered/actions_admin.html

@@ -4,7 +4,6 @@
 </div>
   <li><a class="npg_menu" href="/cgi-perl/npg/run/">Runs</a></li>
   <li><a class="npg_menu" href="/cgi-perl/npg/instrument/">Instruments</a></li>
-  <li><a class="npg_menu" href="/cgi-perl/npg/run/stuck_runs">Stuck Runs</a></li>
   <li><a class="npg_menu" href="/cgi-perl/npg/administration/">Admin</a></li>
   <li><a class="npg_menu_highlight" href="/cgi-perl/npg/run/;add">New Run</a></li>
   <li><a class="npg_menu" href="/cgi-perl/npg/search/">Search</a></li>

t/data/rendered/actions_annotator.html

@@ -4,7 +4,6 @@
 </div>
  <li><a class="npg_menu" href="/cgi-perl/npg/run/">Runs</a></li>
  <li><a class="npg_menu" href="/cgi-perl/npg/instrument/">Instruments</a></li>
- <li><a class="npg_menu" href="/cgi-perl/npg/run/stuck_runs">Stuck Runs</a></li>
  <li><a class="npg_menu" href="/cgi-perl/npg/search/">Search</a></li>
 
 

t/data/rendered/actions_loader.html

@@ -4,7 +4,6 @@
 
  <li><a class="npg_menu" href="/cgi-perl/npg/run/">Runs</a></li>
  <li><a class="npg_menu" href="/cgi-perl/npg/instrument/">Instruments</a></li>
- <li><a class="npg_menu" href="/cgi-perl/npg/run/stuck_runs">Stuck Runs</a></li>
  <li><a class="npg_menu_highlight" href="/cgi-perl/npg/run/;add">New Run</a></li>
  <li><a class="npg_menu" href="/cgi-perl/npg/search/">Search</a></li>