Merge pull request wtsi-npg#889 from mgcam/lane_type_qc4review_latest

Robo evaluation for lanes

Changes

@@ -1,5 +1,30 @@
 LIST OF CHANGES FOR NPG-QC PACKAGE
 
+ - npg_qc::autoqc::qc_store - changed loading of ORM classes into memory
+   to on demand at run time.
+ - Added lane-level assessment to RoboQC:
+    - Extended npg_qc::Schema::Result::Review class to enable saving of
+      sequencing (lane-level) QC outcomes to database
+    - Extended npg_qc::autoqc::check::review to enable lane-level assessment
+      and documented the new feature.
+    - Made redundant 'qc_type' key of the 'robo' configuration.
+    - Fixed a bug in creating a list of class names in
+      npg_qc::autoqc::check::review.
+      A list of names for result classes to be loaded was inferred
+      from all criteria in the 'robo' section under consideration.
+      Until now this did not pesent a problem since even when a number
+      of different criteria sections were present in the study RoboQC
+      section of the configuration file, it was possible to load all of
+      the AutoQC results for any given entity.
+      The bug is revealed when lane-level assessment is added to
+      the 'robo' section under the 'default' configuration. This
+      type of assessment might require presence of lane-level autoqc
+      results for checks that are never performed on sample level,
+      'tag_metrics' check being the most obvious example.
+      The fix is to infer the list of class names from the criteria,
+      which are going to be evaluated for the entity, rather than
+      from a collection of criteria from the whole 'robo' section.
+
 release 73.0.0 (2024-10-24)
  - Removed from the repository unused test data.
  - npg_qc::autoqc::check::review:

MANIFEST

@@ -519,10 +519,9 @@ t/data/autoqc/review/with_criteria/product_release.yml
 t/data/autoqc/review/with_na_criteria/product_release.yml
 t/data/autoqc/review/no_criteria_section/product_release.yml
 t/data/autoqc/review/not_hash/product_release.yml
-t/data/autoqc/review/mqc_type/product_release.yml
+t/data/autoqc/review/lib_type_scalar/product_release.yml
 t/data/autoqc/review/lims_applicability_empty/product_release.yml
 t/data/autoqc/review/no_known_applicability_type/product_release.yml
-t/data/autoqc/review/unknown_qc_type/product_release.yml
 t/data/autoqc/review/default_and_study_section/product_release.yml
 t/data/autoqc/review/default_section/product_release.yml
 t/data/autoqc/review/wrong_default_and_study_section/product_release.yml
@@ -672,6 +671,10 @@ t/data/qc_store/26291/plex3/qc/26291#3.bam_flagstats.json
 t/data/qc_store/26291/plex3/qc/26291#3_phix.bam_flagstats.json
 t/data/qc_store/26291/lane1/qc/26291_1.tag_metrics.json
 t/data/qc_store/26291/lane2/qc/26291_2.tag_metrics.json
+t/data/runfolder_49285/240802_A00537_1044_BHJKCGDSXC.tar.gz
+t/data/runfolder_49285/README
+t/data/runfolder_49285/product_release.yml
+t/data/runfolder_49285/samplesheet_49285.csv
 t/data/samtools_stats/26597_1_F0xB00.stats
 t/data/samtools_stats/26607_1#20_F0xB00.stats
 t/data/samtools_stats/26607_1#20_F0xB00.samtools_stats.json

lib/npg_qc/Schema/Result/Review.pm

@@ -275,16 +275,16 @@ __PACKAGE__->might_have (
   },
 );
 
-=head2 uqc_outcome_ent
+=head2 mqc_seq_outcome_ent
 
 Type: might_have
 Related object: L<npg_qc::Schema::Result::MqcLibraryOutcomeEnt>
 
 =cut
 
 __PACKAGE__->might_have (
-  'uqc_outcome_ent',
-  'npg_qc::Schema::Result::UqcOutcomeEnt',
+  'mqc_seq_outcome_ent',
+  'npg_qc::Schema::Result::MqcOutcomeEnt',
   { 'foreign.id_seq_composition' => 'self.id_seq_composition' },
   {
     is_deferrable => 1,
@@ -320,21 +320,15 @@ __PACKAGE__->has_many(
 Both update and insert methods are modified.
 
 If the qc outcome attribute is defined we will try saving this
-outcome as either library mqc outcome or uqc outcome.
+outcome as either library or sequencing mqc outcome.
 
-If a final library mqc outcome already exists for this product
-and we are trying to save a different final qc outcome, neither
-the review nor the mqc records are created and an error is raised.
+If a final mqc outcome already exists for this product and we are
+trying to save a different final qc outcome, neither the review nor
+the mqc records are created and an error is raised.
 
 Saving a review result with a preliminary outcome should always
-create or update a review row, but a library mqc outcome for the
-product will only be updated if there is no existing final mqc
-outcome.
-
-The type of existing qc outcome is not checked at the point of
-update. Therefore, it is possible to create by mistake a review
-record to which different types of roboqc-derived qc outcomes
-are linked.
+create or update a review row, but the mqc outcome itself is only
+updated if there is no existing final mqc outcome.
 
 =cut
 
@@ -391,13 +385,21 @@ sub _save_qc_outcome {
   my ($self, $qc_outcome) = @_;
   #####
   # What kind of qc outcome we need to update/create?
-  my $entity_type = (grep { $_ =~ /_outcome\Z/xms } keys %{$qc_outcome})[0];
+  # The value below can be either 'mqc_outcome' or 'mqc_seq_outcome'.
+  my $outcome_type = (grep { $_ =~ /_outcome\Z/xms } keys %{$qc_outcome})[0];
   #####
   # Find an existing qc outcome in the outcomes table or
   # create a new object.
-  my $qc_row = $self->find_or_new_related($entity_type . '_ent',
+  my $qc_row = $self->find_or_new_related($outcome_type . '_ent',
     {'id_seq_composition' => $self->id_seq_composition});
 
+  my $outcome_description = $qc_outcome->{$outcome_type};
+  # The outcome should be saved under the 'mqc_outcome' key.
+  if ($outcome_type ne 'mqc_outcome') {
+    $qc_outcome->{'mqc_outcome'} = $outcome_description;
+    delete $qc_outcome->{$outcome_type};
+  }
+
   my $update_or_create = 1;
   try {
     $update_or_create = $qc_row->valid4update($qc_outcome);
@@ -408,7 +410,7 @@ sub _save_qc_outcome {
     # no mqc update and no error. We might be archiving post-manual QC.
     if (($err =~ /Final\ outcome\ cannot\ be\ updated/xms) and
         (not $qc_row->mqc_outcome
-         ->is_final_outcome_description($qc_outcome->{'mqc_outcome'}))) {
+         ->is_final_outcome_description($outcome_description))) {
       $update_or_create = 0;
     } else {
       croak "Not saving review result. $err for " . $qc_row->composition->freeze();