Disallow emply applicability criteria (wtsi-npg#879)

Changes

@@ -1,5 +1,13 @@
 LIST OF CHANGES FOR NPG-QC PACKAGE
 
+ - Previously the code allowed for an empty applicability_criteria hash, which
+   resulted in a particular set of QC criteria being applied to every and any
+   product. Very early on this was an intended behaviour for UKB data. The main
+   filter was the study id. The default section of the product configuration
+   file does not have an external filter, so there is a real danger of the
+   review check being run indiscriminately for any product. While this will
+   never be an intention, small errors in the YML file might have this effect.
+
 release 72.2.1 (2024-10-04)
  - Added .github/dependabot.yml file to auto-update GitHub actions
  - GitHub CI - updated deprecated v2 runner action to v3

MANIFEST

@@ -520,6 +520,8 @@ 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/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/uqc_type/product_release.yml
 t/data/autoqc/review/default_and_study_section/product_release.yml

lib/npg_qc/autoqc/checks/review.pm

@@ -29,6 +29,9 @@ Readonly::Scalar my $QC_TYPE_KEY      => q[qc_type];
 Readonly::Scalar my $APPLICABILITY_CRITERIA_KEY => q[applicability_criteria];
 Readonly::Scalar my $LIMS_APPLICABILITY_CRITERIA_KEY => q[lims];
 Readonly::Scalar my $SEQ_APPLICABILITY_CRITERIA_KEY => q[sequencing_run];
+Readonly::Array  my @APPLICABILITY_CRITERIA_TYPES => (
+  $LIMS_APPLICABILITY_CRITERIA_KEY, $SEQ_APPLICABILITY_CRITERIA_KEY
+                                                     );
 Readonly::Scalar my $ACCEPTANCE_CRITERIA_KEY    => q[acceptance_criteria];
 
 Readonly::Scalar my $QC_TYPE_DEFAULT  => q[mqc];
@@ -514,31 +517,42 @@ has '_applicable_criteria' => (
 sub _build__applicable_criteria {
   my $self = shift;
 
-  my $criteria_objs = $self->_robo_config->{$CRITERIA_KEY};
   my @applicable = ();
-  foreach my $co ( @{$criteria_objs} ) {
+  foreach my $criteria_definition ( @{$self->_robo_config->{$CRITERIA_KEY}} ) {
+
+    my $applicability_definition = $criteria_definition->{$APPLICABILITY_CRITERIA_KEY};
+    $applicability_definition or croak
+      "$APPLICABILITY_CRITERIA_KEY is not defined for one of RoboQC criteria";
+
     my $c_applicable = 1;
-    for my $c_type ($LIMS_APPLICABILITY_CRITERIA_KEY, $SEQ_APPLICABILITY_CRITERIA_KEY) {
-      my $c = $co->{$APPLICABILITY_CRITERIA_KEY}->{$c_type};
-      if ($c && !$self->_applicability($c, $c_type)) {
-        $c_applicable = 0;
-        last;
-      }
+    my $one_found = 0;
+    for my $c_type (@APPLICABILITY_CRITERIA_TYPES) {
+      exists $applicability_definition->{$c_type} or next;
+      $one_found = 1;
+      my $ac = $applicability_definition->{$c_type};
+      (defined $ac and keys %{$ac}) or croak
+        "$c_type type applicability criteria is not defined";
+      $c_applicable = $self->_is_applicable($c_type, $ac);
+      !$c_applicable && last; # Stop on the first non applicable.
     }
-    $c_applicable or next;
-    push @applicable, $co;
+    $one_found or croak 'None of known applicability type criteria is defined. ' .
+      'Known types: ' . join q[, ], @APPLICABILITY_CRITERIA_TYPES;
+    $c_applicable && push @applicable, $criteria_definition; # Save if fully applicable.
   }
 
   return \@applicable;
 }
 
-sub _applicability {
-  my ($self, $acriteria, $criteria_type) = @_;
+sub _is_applicable {
+  my ($self, $criteria_type, $acriteria) = @_;
 
-  ($acriteria && $criteria_type) or croak
-    'The criterium and its type type should be defined';
+  $criteria_type or croak
+    'Applicability criteria type is not defined';
+  $acriteria or croak
+    "$criteria_type applicability criteria is not defined";
   (ref $acriteria eq 'HASH') or croak sprintf
-    '%s section should be a hash in a robo config for %', $criteria_type, $self->_entity_desc;
+    '%s section should be a hash in a robo config for %',
+    $criteria_type, $self->_entity_desc;
 
   my $test = {};
   foreach my $prop ( keys %{$acriteria} ) {

t/60-autoqc-checks-review.t

@@ -33,7 +33,7 @@ my $criteria_list = [
 ];
 
 subtest 'constructing object, deciding whether to run' => sub {
-  plan tests => 29;
+  plan tests => 33;
 
   my $check = npg_qc::autoqc::checks::review->new(
     conf_path => $test_data_dir,
@@ -147,8 +147,10 @@ subtest 'constructing object, deciding whether to run' => sub {
     conf_path => "$test_data_dir/no_applicability4single",
     qc_in     => $test_data_dir,
     rpt_list  => '27483:1:2');
-  ok ($check->can_run, 'can_run returns true');
-  ok (!$check->result->comments, 'No comments logged');
+  ok (!$check->can_run, 'can_run returns false');
+  like ($check->result->comments,
+    qr/applicability_criteria is not defined for one of RoboQC criteria/,
+    'Error logged');
 
   $check = npg_qc::autoqc::checks::review->new(
     conf_path => "$test_data_dir/with_na_criteria",
@@ -158,10 +160,31 @@ subtest 'constructing object, deciding whether to run' => sub {
   is ($check->result->comments,
     'None of the RoboQC applicability criteria is satisfied',
     'Comment logged');
+
+  local $ENV{NPG_CACHED_SAMPLESHEET_FILE} =
+    't/data/autoqc/review/samplesheet_29524.csv';
+
+  $check = npg_qc::autoqc::checks::review->new(
+    conf_path => "$test_data_dir/no_known_applicability_type",
+    qc_in     => $test_data_dir,
+    rpt_list  => '27483:1:2');
+  ok (!$check->can_run, 'can_run returns false');
+  like ($check->result->comments,
+    qr/None of known applicability type criteria is defined/,
+    'Error logged');
+
+  $check = npg_qc::autoqc::checks::review->new(
+    conf_path => "$test_data_dir/lims_applicability_empty",
+    qc_in     => $test_data_dir,
+    rpt_list  => '27483:1:2');
+  ok (!$check->can_run, 'can_run returns false');
+  like ($check->result->comments,
+    qr/lims type applicability criteria is not defined/,
+    'Error logged');    
 };
 
 subtest 'caching appropriate criteria object' => sub {
-  plan tests => 3;
+  plan tests => 2;
 
   my $check = npg_qc::autoqc::checks::review->new(
     conf_path => "$test_data_dir/with_criteria",
@@ -171,13 +194,6 @@ subtest 'caching appropriate criteria object' => sub {
   is_deeply ($check->_criteria, {'and' => \@list},
     'criteria parsed correctly');
 
-  $check = npg_qc::autoqc::checks::review->new(
-    conf_path => "$test_data_dir/no_applicability4single",
-    qc_in     => $test_data_dir,
-    rpt_list  => '27483:1:2');
-  is_deeply ($check->_criteria, {'and' => $criteria_list},
-    'criteria parsed correctly');
-
   $check = npg_qc::autoqc::checks::review->new(
     conf_path => "$test_data_dir/with_na_criteria",
     qc_in     => $test_data_dir,

t/data/autoqc/review/lims_applicability_empty/product_release.yml

@@ -0,0 +1,36 @@
+---
+default:
+  s3:
+    enable: false
+    url: null
+    notify: false
+  irods:
+    enable: true
+    notify: false
+
+study:
+  - study_id: "5392"
+    s3:
+      enable: true
+      url: "gs://profile_one-europe-west2"
+      date_binning: true
+      customer_name: "UK Organisation"
+      profile: "profile_one"
+      notify: true
+      receipts: "/data_product_receipts/5392/"
+    irods:
+      enable: false
+      notify: true
+    merge:
+      component_cache_dir: "/merge_component_cache/5392/"
+    robo_qc:
+      qc_type: "mqc"
+      criteria:
+        - applicability_criteria:
+            lims:
+          acceptance_criteria :
+            - "( bam_flagstats.target_proper_pair_mapped_reads / bam_flagstats.target_mapped_reads ) > 0.95"
+            - "bam_flagstats.target_mapped_bases > 85_000_000_000"
+            - "bam_flagstats.target_percent_gt_coverage_threshold > 95"
+            - "verify_bam_id.freemix < 0.01"
+            - "( bcfstats.genotypes_nrd_dividend / bcfstats.genotypes_nrd_divisor ) < 0.02"

t/data/autoqc/review/mqc_type/product_release.yml

@@ -27,6 +27,8 @@ study:
       qc_type: "mqc"
       criteria:
         - applicability_criteria:
+            lims:
+              library_type: "HiSeqX PCR free"
           acceptance_criteria :
             - "( bam_flagstats.target_proper_pair_mapped_reads / bam_flagstats.target_mapped_reads ) > 0.95"
             - "bam_flagstats.target_mapped_bases > 85_000_000_000"

t/data/autoqc/review/no_known_applicability_type/product_release.yml

@@ -0,0 +1,37 @@
+---
+default:
+  s3:
+    enable: false
+    url: null
+    notify: false
+  irods:
+    enable: true
+    notify: false
+
+study:
+  - study_id: "5392"
+    s3:
+      enable: true
+      url: "gs://profile_one-europe-west2"
+      date_binning: true
+      customer_name: "UK Organisation"
+      profile: "profile_one"
+      notify: true
+      receipts: "/data_product_receipts/5392/"
+    irods:
+      enable: false
+      notify: true
+    merge:
+      component_cache_dir: "/merge_component_cache/5392/"
+    robo_qc:
+      qc_type: "mqc"
+      criteria:
+        - applicability_criteria:
+            libs:
+              library_type: "HiSeqX PCR free"
+          acceptance_criteria :
+            - "( bam_flagstats.target_proper_pair_mapped_reads / bam_flagstats.target_mapped_reads ) > 0.95"
+            - "bam_flagstats.target_mapped_bases > 85_000_000_000"
+            - "bam_flagstats.target_percent_gt_coverage_threshold > 95"
+            - "verify_bam_id.freemix < 0.01"
+            - "( bcfstats.genotypes_nrd_dividend / bcfstats.genotypes_nrd_divisor ) < 0.02"