Merge pull request #822 from mgcam/qc_db_access

Removed pipeline dependency on npg_qc::Schema

MANIFEST

@@ -1030,14 +1030,6 @@ t/data/qc/references/Homo_sapiens/1000Genomes_hs37d5/all/fasta/hs37d5.fa
 t/data/qc/references/PhiX/default/all/fasta/PhiX.fasta
 t/data/qc/samplesheet_14043.csv
 t/data/qc/samplesheet_14353.csv
-t/data/qc_outcomes/fixtures/000-mqc_library_outcome_dict.yml
-t/data/qc_outcomes/fixtures/000-mqc_outcome_dict.yml
-t/data/qc_outcomes/fixtures/000-uqc_outcome_dict.yml
-t/data/qc_outcomes/fixtures/200-seq_component.yml
-t/data/qc_outcomes/fixtures/300-seq_component_composition.yml
-t/data/qc_outcomes/fixtures/300-seq_composition.yml
-t/data/qc_outcomes/fixtures/400-mqc_library_outcome_ent.yml
-t/data/qc_outcomes/fixtures/README
 t/data/release/config/archive_off/product_release.yml
 t/data/release/config/archive_on/product_release.yml
 t/data/release/config/bqsr_off/product_release.yml

lib/npg_pipeline/base.pm

@@ -60,22 +60,6 @@ within npg_pipeline package
 
 =head2 npg_tracking_schema
 
-=head2 qc_schema
-
-An attribute caching a connection to a QC database.
-The attribute is allowed to be undefined and is implicitly undefined
-since no default or build method is provided. This is done in order
-to prevent the automatic connection to a database in child classes.
-
-=cut
-
-has 'qc_schema' => (
-  metaclass  => 'NoGetopt',
-  isa        => 'Maybe[npg_qc::Schema]',
-  is         => 'ro',
-  required   => 0,
-);
-
 =head2 flowcell_id
 
 =head2 tracking_run

lib/npg_pipeline/product.pm

@@ -598,116 +598,6 @@ sub chunk_as_product {
   return __PACKAGE__->new($ref);
 }
 
-
-=head2 final_seqqc_objs
-
-  Returns a list of  DBIx row objects representing a sequencing QC outcomes
-  for component lanes of this product. If not all lanes have a final outcome,
-  an empty list is returned.
-
-  npg_qc::Schema object argument is required.
-
-    use List::MoreUtils qw/all any/;
-    my @seq_qc_objs = $p->final_seqqc_objs($schema);
-    my $passed = @seq_qc_objs && (all { $_->is_accepted } @seq_qc_objs);
-    my $failed = !@seq_qc_objs || (any { $_->is_rejected } @seq_qc_objs);
-=cut
-
-sub final_seqqc_objs {
-  my ($self, $schema) = @_;
-
-  $schema or croak 'qc schema argument is required';
-
-  my @lp = $self->lanes_as_products;
-  my @seqqc = grep { $_->has_final_outcome }
-              $schema->resultset('MqcOutcomeEnt')
-              ->search_via_composition([map{$_->composition}@lp])->all;
-  if (@lp != @seqqc) {
-    return;
-  }
-
-  return @seqqc;
-}
-
-=head2 seqqc_objs
-
-  Returns a list of  DBIx row objects representing a sequencing QC outcomes
-  for component lanes of this product, even if not all outcomes are final.
-
-  npg_qc::Schema object argument is required.
-
-    use List::MoreUtils qw/all any/;
-    my @seq_qc_objs = $p->seqqc_objs($schema);
-    #these may or may not be final outcomes
-    my $passed = @seq_qc_objs && (all { $_->is_accepted } @seq_qc_objs);
-    my $failed = !@seq_qc_objs || (any { $_->is_rejected } @seq_qc_objs);
-
-=cut
-
-sub seqqc_objs {
-  my ($self, $schema) = @_;
-
-  $schema or croak 'qc schema argument is required';
-
-  my @lp = $self->lanes_as_products;
-  my @seqqc = $schema->resultset('MqcOutcomeEnt')
-              ->search_via_composition([map{$_->composition}@lp])->all;
-  if (@lp != @seqqc) {
-    return;
-  }
-  return @seqqc;
-}
-
-=head2 final_libqc_obj
-
-  Returns a DBIx row object representing a final library QC outcome.
-  Returns an undefined value if the final library QC outcome is
-  not available for this product.
-
-  npg_qc::Schema object argument is required.
-
-    my $lib_qc_obj = $p->final_libqc_obj($schema);
-    print $lib_qc_obj->is_accepted;
-
-=cut
-
-sub final_libqc_obj {
-  my ($self, $schema) = @_;
-
-  $schema or croak 'qc schema argument is required';
-
-  my $libqc = $schema->resultset('MqcLibraryOutcomeEnt')
-                     ->search_via_composition([$self->composition])->next;
-  if ($libqc && $libqc->has_final_outcome) {
-    return $libqc;
-  }
-
-  return;
-}
-
-=head2 libqc_obj
-
-  Returns a DBIx row object representing the library QC outcome.
-  Returns an undefined value if the library QC outcome is
-  not available for this product.
-
-  npg_qc::Schema object argument is required.
-
-    my $lib_qc_obj = $p->libqc_obj($schema);
-
-=cut
-
-sub libqc_obj {
-  my ($self, $schema) = @_;
-
-  $schema or croak 'qc schema argument is required';
-
-  return $schema->resultset('MqcLibraryOutcomeEnt')
-                ->search_via_composition([$self->composition])->next;
-}
-
-
-
 __PACKAGE__->meta->make_immutable;
 
 1;

lib/npg_pipeline/validation.pm

@@ -405,9 +405,11 @@ a database connection.
 
 =cut
 
-has '+qc_schema' => (
-  lazy       => 1,
-  builder    => '_build_qc_schema',
+has 'qc_schema' => (
+  isa        => 'npg_qc::Schema',
+  is         => 'ro',
+  required   => 0,
+  lazy_build => 1,
 );
 sub _build_qc_schema {
   return npg_qc::Schema->connect();

t/15-product-release.t

@@ -24,11 +24,6 @@ Log::Log4perl->easy_init({level  => $INFO,
   with 'npg_testing::db';
 }
 
-# See README in fixtures for a description of the test data.
-my $qc = TestDB->new (
-  sqlite_utf8_enabled => 1,
-  verbose             => 0)->create_test_db('npg_qc::Schema');
-
 local $ENV{NPG_CACHED_SAMPLESHEET_FILE} =
   't/data/novaseq/180709_A00538_0010_BH3FCMDRXX/' .
   'Data/Intensities/BAM_basecalls_20180805-013153/' .
@@ -49,8 +44,7 @@ subtest 'expected_files' => sub {
     (conf_path      => "t/data/release/config/archive_on",
      runfolder_path => $runfolder_path,
      id_run         => 26291,
-     timestamp      => $timestamp,
-     qc_schema      => $qc);
+     timestamp      => $timestamp);
 
   my $path = "$runfolder_path/Data/Intensities/" .
              'BAM_basecalls_20180805-013153/no_cal/archive/plex1';
@@ -86,8 +80,7 @@ subtest 'expected_unaligned_files' => sub {
       (conf_path      => "t/data/release/config/archive_on",
        runfolder_path => $runfolder_path,
        id_run         => 26291,
-       timestamp      => $timestamp,
-       qc_schema      => $qc);
+       timestamp      => $timestamp);
 
   my $product = $archiver->products->{data_products}->[4];
   my $path = "$runfolder_path/Data/Intensities/" .