QC type should be defined, default fallback is removed

mgcam · Sep 13, 2024 · 230b33f · 230b33f
1 parent fa8ae77
commit 230b33f
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Showing 8 changed files with 22 additions and 9 deletions.
diff --git a/lib/npg_qc/autoqc/checks/review.pm b/lib/npg_qc/autoqc/checks/review.pm
@@ -106,9 +106,9 @@ RoboQC definitions. Library Manual QC is configured as C<qc_type: "mqc">.
 The other recognised type is C<mqc_lane>, which is only compatible with
 lane-level entities.
 
-If the Robo QC type is not defined directly in the top-level section,
-it should be defined for each of the criteria individually. The definition
-on teh criteria level takes precedence.
+If the QC type is not defined directly in the top-level section, it should
+be defined for each of the criteria individually. The definition on the
+criteria level takes precedence.
 
 =head2 Rules for assignment of the QC outcome
 
@@ -598,7 +598,10 @@ sub _build__outcome_type {
   if (!$outcome_type) {
     $outcome_type = $self->_robo_config()->{$QC_TYPE_KEY};
   }
-  $outcome_type ||= $QC_TYPE_LIB;
+
+  if (!$outcome_type) {
+    croak 'QC type is not defined in a RoboQC config for ' . $self->_entity_desc;
+  }
 
   if (none { $outcome_type eq $_ } @VALID_QC_TYPES) {
     croak "Invalid QC type '$outcome_type' in a RoboQC config for " .

diff --git a/t/data/autoqc/review/default_and_study_section/product_release.yml b/t/data/autoqc/review/default_and_study_section/product_release.yml
@@ -8,6 +8,7 @@ default:
     enable: true
     notify: false
   robo_qc:
+    qc_type: "mqc"
     criteria:
       - applicability_criteria:
           lims:

diff --git a/t/data/autoqc/review/default_section/product_release.yml b/t/data/autoqc/review/default_section/product_release.yml
@@ -3,8 +3,10 @@ default:
   irods:
     enable: true
   robo_qc:
+    qc_type: "mqc_lane"
     criteria:
-      - applicability_criteria:
+      - qc_type: "mqc"
+        applicability_criteria:
           lims:
             library_type:
               - "HiSeqX PCR free"

diff --git a/t/data/autoqc/review/generic/product_release.yml b/t/data/autoqc/review/generic/product_release.yml
@@ -31,15 +31,17 @@ study:
         pp_staging_root: "{{ lustre_mount }}/climb_upload"
     robo_qc:
       criteria:
-        - applicability_criteria:
+        - qc_type: "mqc"
+          applicability_criteria:
             lims:
               sample_is_control:
                 - 0
                 - ""
           acceptance_criteria :
             - &heron_robo_realsample_ac1 "generic:ncov2019_artic_nf.doc->{meta}->{'num_input_reads'} and (generic:ncov2019_artic_nf.doc->{'QC summary'}->{qc_pass} eq 'TRUE')"
             - &heron_robo_realsample_ac2 "(generic:ncov2019_artic_nf.doc->{meta}->{'max_negative_control_filtered_read_count'} < 100) or ((generic:ncov2019_artic_nf.doc->{meta}->{'max_negative_control_filtered_read_count'} <= 1000) and (generic:ncov2019_artic_nf.doc->{'QC summary'}->{num_aligned_reads} > 100 * generic:ncov2019_artic_nf.doc->{meta}->{'max_negative_control_filtered_read_count'}))"
-        - applicability_criteria:
+        - qc_type: "mqc"
+          applicability_criteria:
             lims:
               sample_is_control:
                 - 1
@@ -48,7 +50,8 @@ study:
           acceptance_criteria :
             - *heron_robo_realsample_ac1
             - *heron_robo_realsample_ac2
-        - applicability_criteria:
+        - qc_type: "mqc"
+          applicability_criteria:
             lims:
               sample_is_control:
                 - 1

diff --git a/t/data/autoqc/review/no_applicability4single/product_release.yml b/t/data/autoqc/review/no_applicability4single/product_release.yml
@@ -24,6 +24,7 @@ study:
     merge:
       component_cache_dir: "/merge_component_cache/5392/"
     robo_qc:
+      qc_type: "mqc"
       criteria:
         - applicability_criteria:
           acceptance_criteria:

diff --git a/t/data/autoqc/review/product_release.yml b/t/data/autoqc/review/product_release.yml
@@ -25,7 +25,8 @@ study:
       component_cache_dir: "/merge_component_cache/5392/"
     robo_qc:
       criteria:
-        - applicability_criteria:
+        - qc_type: "mqc"
+          applicability_criteria:
             lims:
               library_type:
                 - "HiSeqX PCR free"

diff --git a/t/data/autoqc/review/with_criteria/product_release.yml b/t/data/autoqc/review/with_criteria/product_release.yml
@@ -23,6 +23,7 @@ study:
     merge:
       component_cache_dir: "/merge_component_cache/4042/"
     robo_qc:
+      qc_type: "mqc"
       criteria:
         - applicability_criteria:
             lims:

diff --git a/t/data/autoqc/review/wrong_default_and_study_section/product_release.yml b/t/data/autoqc/review/wrong_default_and_study_section/product_release.yml
@@ -27,6 +27,7 @@ study:
     merge:
       component_cache_dir: "/merge_component_cache/5392/"
     robo_qc:
+      qc_type: "mqc"
       criteria:
         - applicability_criteria:
             lims: