Merge pull request #473 from wtsi-npg/devel

release 64.4 prep

Changes

@@ -1,5 +1,9 @@
 LIST OF CHANGES FOR NPG-QC PACKAGE
 
+ - utility QC feature: db tables, DBIx classes, retrieval
+ - Add STAR aligner bams as a valid RNA alignments - also added tests for it
+ - update bam_flagstats to be able run when no markdups metrics file exists
+
 release 64.3.1
  - error in a statement for data update is fixed
 

MANIFEST

@@ -174,6 +174,9 @@ lib/npg_qc/Schema/Result/TagMetrics.pm
 lib/npg_qc/Schema/Result/TagsReporters.pm
 lib/npg_qc/Schema/Result/TileScore.pm
 lib/npg_qc/Schema/Result/UpstreamTags.pm
+lib/npg_qc/Schema/Result/UqcOutcomeDict.pm
+lib/npg_qc/Schema/Result/UqcOutcomeEnt.pm
+lib/npg_qc/Schema/Result/UqcOutcomeHist.pm
 lib/npg_qc/Schema/Result/VerifyBamId.pm
 lib/npg_qc/Schema/ResultSet.pm
 lib/npg_qc/Schema/ResultSet/MqcOutcomeEnt.pm
@@ -245,6 +248,9 @@ t/50-schema-result-VerifyBamId.t
 t/50-schema-result-SamtoolsStats.t
 t/50-schema-result-SeqComposition.t
 t/50-schema-result-SequenceSummary.t
+t/50-schema-result-UqcOutcomeDict.t
+t/50-schema-result-UqcOutcomeEnt.t
+t/50-schema-result-UqcOutcomeHist.t
 t/50-schema-resultset.t
 t/50-schema-resultset-MqcOutcomeEnt.t
 t/60-autoqc-autoqc.t
@@ -297,14 +303,15 @@ t/60-autoqc-results-verify_bam_id.t
 t/70-mqc-reporter.t
 t/70-mqc-outcomes.t
 t/80-autoqc-qc-script.t
-t/autoqc_util.pm
 t/data/config.ini
 t/data/api_dbic_fixtures/npg_qc/RunTimeline.yml
 t/data/api_dbic_fixtures/npg/RunStatusDict.yml
 t/data/api_dbic_fixtures/npg/RunStatus.yml
 t/data/api_dbic_fixtures/npg/Run.yml
 t/data/autoqc/bam_flagstats/16960_1_0.tar.gz
 t/data/autoqc/bam_flagstats/17448_1_9.tar.gz
+t/data/autoqc/bam_flagstats/24135_1#1.bam_flagstats.json
+t/data/autoqc/bam_flagstats/24135_1#1.flagstat
 t/data/autoqc/bam_flagstats/4783_5_bam_flagstats.json
 t/data/autoqc/bam_flagstats/4783_5_metrics_optical.txt
 t/data/autoqc/bam_flagstats/4783_5.flagstat
@@ -579,6 +586,7 @@ t/data/fixtures/000-analysis.yml
 t/data/fixtures/000-image_store.yml
 t/data/fixtures/000-mqc_outcome_dict.yml
 t/data/fixtures/000-mqc_library_outcome_dict.yml
+t/data/fixtures/000-uqc_outcome_dict.yml
 t/data/fixtures/000-run_tile.yml
 t/data/fixtures/100-analysis_lane.yml
 t/data/fixtures/100-cache_query.yml
@@ -646,6 +654,7 @@ t/data/nfs/sf44/ILorHSany_sf25/incoming/100925_HS8_05330_B_205NNABXX/Data/Intens
 t/data/nfs/sf44/ILorHSany_sf25/incoming/100925_HS8_05330_B_205NNABXX/RunInfo.xml
 t/data/qcoutcomes/fixtures/000-mqc_library_outcome_dict.yml
 t/data/qcoutcomes/fixtures/000-mqc_outcome_dict.yml
+t/data/qcoutcomes/fixtures/000-uqc_outcome_dict.yml
 t/data/reporter/npg_qc/mqc_outcome_dict.yml
 t/data/reporter/npg_qc/mqc_outcome_ent.yml
 t/data/reporter/npg_qc/seq_component.yml

lib/npg_qc/Schema/Mqc/OutcomeEntity.pm

@@ -10,7 +10,6 @@ with 'npg_qc::Schema::Composition';
 
 our $VERSION = '0';
 
-requires 'mqc_outcome';
 requires 'update';
 requires 'insert';
 
@@ -28,8 +27,9 @@ Readonly::Hash my %DELEGATION_TO_MQC_OUTCOME => {
 foreach my $this_class_method (keys %DELEGATION_TO_MQC_OUTCOME ) {
   __PACKAGE__->meta->add_method( $this_class_method, sub {
       my $self = shift;
+      my $outcome_type = $self->dict_relation();
       my $that_class_method = $DELEGATION_TO_MQC_OUTCOME{$this_class_method};
-      return $self->mqc_outcome->$that_class_method;
+      return $self->$outcome_type->$that_class_method;
     }
   );
 }
@@ -43,6 +43,17 @@ around [qw/update insert/] => sub {
   return $return_super;
 };
 
+sub dict_relation {
+  my $self = shift;
+  my $name = $self->_is_mqc_type_outcome() ? 'm' : 'u';
+  return $name . q[qc_outcome];
+}
+
+sub _is_mqc_type_outcome {
+  my $name = ref shift;
+  return $name =~ /::Mqc(?:Library)?OutcomeEnt\Z/smx;
+}
+
 sub get_time_now {
   return DateTime->now(time_zone => DateTime::TimeZone->new(name => q[local]));
 }
@@ -159,14 +170,19 @@ npg_qc::Schema::Mqc::OutcomeEntity
 
 =head1 DESCRIPTION
 
-Common functionality for lane and library manual qc outcome entity DBIx objects.
+Common functionality for lane and library manual qc and user utility outcomes
+entity DBIx objects.
 
 =head1 SUBROUTINES/METHODS
 
 =head2 composition
 
 A lazy-build attribute of type npg_tracking::glossary::composition.
-It is built by inspection the linked seq_composition row.
+It is built by inspecting the linked seq_composition row.
+
+=head2 dict_relation
+
+Returns the name of the relationship to the outcomes dictionary.
 
 =head2 update
 
@@ -208,15 +224,18 @@ otherwise returns false.
 =head2 update_outcome
 
 Updates the outcome of the entity with values provided. Stores a new row
-if this entity was not yet stored in database.
+if this entity was not yet stored in database. This method has not been yet
+extended to updating utility outcomes.
 
   $obj->update_outcome($outcome, $username);
   $obj->update_outcome($outcome, $username, $rt_ticket);
 
 =head2 toggle_final_outcome
 
 Updates the final accepted or rejected outcome to its opposite final outcome,
-i.e. accepted is changed to rejected and rejected to accepted.
+i.e. accepted is changed to rejected and rejected to accepted. This method is
+not applicable to utility qc outcomes since there is no concept of final
+for this type of outcome.
 
   $obj->toggle_final_outcome($username);
   $obj->toggle_final_outcome($username, $rt_ticket);

lib/npg_qc/Schema/Result/SeqComposition.pm

@@ -528,6 +528,36 @@ __PACKAGE__->might_have(
   { cascade_copy => 0, cascade_delete => 0 },
 );
 
+=head2 uqc_outcome_ent
+
+Type: might_have
+
+Related object: L<npg_qc::Schema::Result::UqcOutcomeEnt>
+
+=cut
+
+__PACKAGE__->might_have(
+  'uqc_outcome_ent',
+  'npg_qc::Schema::Result::UqcOutcomeEnt',
+  { 'foreign.id_seq_composition' => 'self.id_seq_composition' },
+  { cascade_copy => 0, cascade_delete => 0 },
+);
+
+=head2 uqc_outcome_hists
+
+Type: has_many
+
+Related object: L<npg_qc::Schema::Result::UqcOutcomeHist>
+
+=cut
+
+__PACKAGE__->has_many(
+  'uqc_outcome_hists',
+  'npg_qc::Schema::Result::UqcOutcomeHist',
+  { 'foreign.id_seq_composition' => 'self.id_seq_composition' },
+  { cascade_copy => 0, cascade_delete => 0 },
+);
+
 =head2 verify_bam_id
 
 Type: might_have
@@ -544,8 +574,8 @@ __PACKAGE__->might_have(
 );
 
 
-# Created by DBIx::Class::Schema::Loader v0.07047 @ 2017-09-15 14:33:12
-# DO NOT MODIFY THIS OR ANYTHING ABOVE! md5sum:j2lqJ9ZKV4Ps0eTABP7AXQ
+# Created by DBIx::Class::Schema::Loader v0.07047 @ 2017-10-06 15:50:03
+# DO NOT MODIFY THIS OR ANYTHING ABOVE! md5sum:7yXOqY10w/8mHVFgahi8YA
 
 
 # You can replace this text with custom code or comments, and it will be preserved on regeneration
@@ -556,7 +586,7 @@ our $VERSION = '0';
 
 =head2 create_composition
 
-A factory method returning a npg_tracking::glossary::composition object of illumina components. 
+A factory method returning a npg_tracking::glossary::composition object of illumina components.
 
 =cut