Merge pull request #739 from wtsi-npg/devel

pull from devel to master to create release 69.5.0

Changes

@@ -1,5 +1,14 @@
 LIST OF CHANGES FOR NPG-QC PACKAGE
 
+release 69.5.0
+ - measures to speed-up generation of SeqQC pages:
+   - add a prefetch for compositions and components when retrieving autoqc
+     results from a database;
+   - use in-line custom sort function instead of a closure for ref_match
+     result objects  
+   - disable a check for circular references in serialization of autoqc
+     result objects
+
 release 69.4.0
  - mqc skipper not to consider runs tagged 'no_auto' or 'no_mqc_skipper'
 

lib/npg_qc/autoqc/qc_store.pm

@@ -260,7 +260,7 @@ autoqc result objects corresponding to JSON files.
 
  my $query = npg_qc::autoqc::qc_store::query_non_tracking->new(
              id_run => 123);
- my $c     = $obj->load_from_staging_archive($query, $archive_dir); 
+ my $c     = $obj->load_from_staging_archive($query, $archive_dir);
 
 =cut
 
@@ -515,6 +515,14 @@ sub _build__available_classes {
   return \@names;
 }
 
+=head2 _db_collection4compositions
+
+Takes a listref of composition dbIDs, and queries all available QC result types
+for each composition. Returns a collection of result objects of mixed QC
+types
+
+=cut
+
 sub _db_collection4compositions {
   my ($self, $composition_ids) = @_;
 
@@ -525,7 +533,20 @@ sub _db_collection4compositions {
   if (@{$composition_ids}) {
     foreach my $name (@{$self->_available_classes}) {
       push @rows, $self->qc_schema()->resultset($name)
-        ->search({'me.id_seq_composition' => $composition_ids})->all();
+        ->search(
+          {
+            'me.id_seq_composition' => $composition_ids
+          },
+          {
+            # later uses of this collection will need access to components
+            # and prefetching halves the overhead
+            prefetch => {
+              'seq_composition' => {
+                'seq_component_compositions' => 'seq_component'
+              }
+            }
+          }
+        )->all();
     }
   }
 

lib/npg_qc/autoqc/role/ref_match.pm

@@ -32,14 +32,11 @@ sub ranked_organisms {
   # Deterministic ranking of organisms:
   # reverse numerical comparison of alignment results
   # followed, if necessary, by string comparison of names.
-  my $compare = sub {
-    my ($org1, $org2) = @_;
-    my $result = $ratings->{$org2} <=> $ratings->{$org1};
-    $result  ||= $org1 cmp $org2;
-    return $result;
-  };
-
-  my @ranked_organisms = sort { $compare->($a, $b) } keys %{$ratings};
+  ## no critic (BuiltinFunctions::ProhibitReverseSortBlock)
+  my @ranked_organisms = sort {
+    $ratings->{$b} <=> $ratings->{$a}
+    || $a cmp $b
+  } keys %{$ratings};
 
   return \@ranked_organisms;
 }

lib/npg_qc/autoqc/role/result.pm

@@ -9,7 +9,7 @@ use Readonly;
 use List::MoreUtils qw(none uniq);
 use Digest::MD5 qw/md5_hex/;
 
-with Storage( 'traits' => ['OnlyWhenBuilt'],
+with Storage( 'traits' => [qw/OnlyWhenBuilt DisableCycleDetection/],
               'format' => 'JSON',
               'io'     => 'File' ), 'npg_qc::autoqc::role::rpt_key';
 
@@ -380,7 +380,7 @@ Marina Gourtovaia E<lt>[email protected]<gt>
 
 =head1 LICENSE AND COPYRIGHT
 
-Copyright (C) 2014,2015,2016,2017,2018,2019,2020 Genome Research Ltd.
+Copyright (C) 2014,2015,2016,2017,2018,2019,2020,2021 Genome Research Ltd.
 
 This file is part of NPG.
 

t/60-autoqc-checks-check.t

@@ -30,10 +30,10 @@ subtest 'validation of attributes' => sub {
     plan tests => 36;
 ;
     throws_ok {npg_qc::autoqc::checks::check->new(path => $path)}
-        qr/Either id_run or position key is undefined/,
+        qr/'id_run' key is undefined/,
         'error on instantiating an object without any id';
     throws_ok {npg_qc::autoqc::checks::check->new(path => $path, id_run => $idrun)}
-        qr/Either id_run or position key is undefined/,
+        qr/'position' key is undefined/,
         'error on instantiating an object without either a position or rpt_list attr';
     throws_ok {npg_qc::autoqc::checks::check->new(
         position => 17, path => $path, id_run => $idrun)}
@@ -58,7 +58,7 @@ subtest 'validation of attributes' => sub {
     lives_ok {npg_qc::autoqc::checks::check->new(position => 2, id_run => $idrun)}
         'no error on instantiating an object without a path/qc_in attr';
     throws_ok {npg_qc::autoqc::checks::check->new(position => 2, qc_in => 't')}
-        qr/Either id_run or position key is undefined/,
+        qr/'id_run' key is undefined/,
         'error on instantiating an object without either a run id or an rpt_list attr';
     throws_ok {npg_qc::autoqc::checks::check->new(
         position => 1, path => 'nonexisting', id_run => -1)}