Merge pull request #157 from ces/PacQC2021

add tables pac_bio_run_well_metrics and pac_bio_product_metrics
wtsi-npg · Feb 9, 2021 · b6b1a65 · b6b1a65
2 parents dfa3f91 + d26db5c
commit b6b1a65
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Showing 5 changed files with 801 additions and 2 deletions.
diff --git a/Changes b/Changes
@@ -1,6 +1,10 @@
 LIST OF CHANGES
 ---------------
 
+release 6.13.0
+ - add tables pac_bio_run_well_metrics and pac_bio_product_metrics 
+   to store metrics extracted from PacBio's SMRT Link LIMS
+
 release 6.12.0
  - a new iseq_product_ampliconstats table to store per sample
    per amplicon statistics that is generated by 'samtools

diff --git a/lib/WTSI/DNAP/Warehouse/Schema/Result/PacBioProductMetric.pm b/lib/WTSI/DNAP/Warehouse/Schema/Result/PacBioProductMetric.pm
@@ -0,0 +1,193 @@
+
+package WTSI::DNAP::Warehouse::Schema::Result::PacBioProductMetric;
+
+# Created by DBIx::Class::Schema::Loader
+# DO NOT MODIFY THE FIRST PART OF THIS FILE
+
+=head1 NAME
+
+WTSI::DNAP::Warehouse::Schema::Result::PacBioProductMetric
+
+=head1 DESCRIPTION
+
+A linking table for the pac_bio_run and pac_bio_run_well_metrics tables with a potential for adding per-product QC data
+
+=cut
+
+use strict;
+use warnings;
+
+use Moose;
+use MooseX::NonMoose;
+use MooseX::MarkAsMethods autoclean => 1;
+extends 'DBIx::Class::Core';
+
+=head1 COMPONENTS LOADED
+
+=over 4
+
+=item * L<DBIx::Class::InflateColumn::DateTime>
+
+=back
+
+=cut
+
+__PACKAGE__->load_components('InflateColumn::DateTime');
+
+=head1 TABLE: C<pac_bio_product_metrics>
+
+=cut
+
+__PACKAGE__->table('pac_bio_product_metrics');
+
+=head1 ACCESSORS
+
+=head2 id_pac_bio_pr_metrics_tmp
+
+  data_type: 'integer'
+  is_auto_increment: 1
+  is_nullable: 0
+
+=head2 id_pac_bio_rw_metrics_tmp
+
+  data_type: 'integer'
+  is_foreign_key: 1
+  is_nullable: 0
+
+PacBio run well metrics id, see 'pac_bio_run_well_metrics.id_pac_bio_rw_metrics_tmp'
+
+=head2 id_pac_bio_tmp
+
+  data_type: 'integer'
+  is_foreign_key: 1
+  is_nullable: 1
+
+PacBio run id, see 'pac_bio_run.id_pac_bio_tmp'
+
+=cut
+
+__PACKAGE__->add_columns(
+  'id_pac_bio_pr_metrics_tmp',
+  { data_type => 'integer', is_auto_increment => 1, is_nullable => 0 },
+  'id_pac_bio_rw_metrics_tmp',
+  { data_type => 'integer', is_foreign_key => 1, is_nullable => 0 },
+  'id_pac_bio_tmp',
+  { data_type => 'integer', is_foreign_key => 1, is_nullable => 1 },
+);
+
+=head1 PRIMARY KEY
+
+=over 4
+
+=item * L</id_pac_bio_pr_metrics_tmp>
+
+=back
+
+=cut
+
+__PACKAGE__->set_primary_key('id_pac_bio_pr_metrics_tmp');
+
+=head1 RELATIONS
+
+=head2 pac_bio
+
+Type: belongs_to
+
+Related object: L<WTSI::DNAP::Warehouse::Schema::Result::PacBioRun>
+
+=cut
+
+__PACKAGE__->belongs_to(
+  'pac_bio',
+  'WTSI::DNAP::Warehouse::Schema::Result::PacBioRun',
+  { id_pac_bio_tmp => 'id_pac_bio_tmp' },
+  {
+    is_deferrable => 1,
+    join_type     => 'LEFT',
+    on_delete     => 'SET NULL',
+    on_update     => 'NO ACTION',
+  },
+);
+
+=head2 pac_bio_rw_metrics
+
+Type: belongs_to
+
+Related object: L<WTSI::DNAP::Warehouse::Schema::Result::PacBioRunWellMetric>
+
+=cut
+
+__PACKAGE__->belongs_to(
+  'pac_bio_rw_metrics',
+  'WTSI::DNAP::Warehouse::Schema::Result::PacBioRunWellMetric',
+  { id_pac_bio_rw_metrics_tmp => 'id_pac_bio_rw_metrics_tmp' },
+  { is_deferrable => 1, on_delete => 'CASCADE', on_update => 'NO ACTION' },
+);
+
+
+# Created by DBIx::Class::Schema::Loader v0.07049 @ 2021-02-09 11:33:17
+# DO NOT MODIFY THIS OR ANYTHING ABOVE! md5sum:Ea+iVDOfptyUAPyi3Otvyg
+
+our $VERSION = '0';
+
+__PACKAGE__->meta->make_immutable;
+1;
+
+=head1 SYNOPSIS
+
+=head1 DESCRIPTION
+
+Result class definition in DBIx binding for the multi-lims warehouse database.
+
+=head1 DIAGNOSTICS
+
+=head1 CONFIGURATION AND ENVIRONMENT
+
+=head1 SUBROUTINES/METHODS
+
+=head1 DEPENDENCIES
+
+=over
+
+=item strict
+
+=item warnings
+
+=item Moose
+
+=item MooseX::NonMoose
+
+=item MooseX::MarkAsMethods
+
+=item DBIx::Class::Core
+
+=item DBIx::Class::InflateColumn::DateTime
+
+=back
+
+=head1 INCOMPATIBILITIES
+
+=head1 BUGS AND LIMITATIONS
+
+=head1 AUTHOR
+
+=head1 LICENSE AND COPYRIGHT
+
+Copyright (C) 2021 Genome Research Limited
+
+This file is part of the ml_warehouse package L<https://github.com/wtsi-npg/ml_warehouse>.
+
+NPG is free software: you can redistribute it and/or modify
+it under the terms of the GNU General Public License as published by
+the Free Software Foundation, either version 3 of the License, or
+(at your option) any later version.
+
+This program is distributed in the hope that it will be useful,
+but WITHOUT ANY WARRANTY; without even the implied warranty of
+MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+GNU General Public License for more details.
+
+You should have received a copy of the GNU General Public License
+along with this program.  If not, see <http://www.gnu.org/licenses/>.
+
+=cut
diff --git a/lib/WTSI/DNAP/Warehouse/Schema/Result/PacBioRun.pm b/lib/WTSI/DNAP/Warehouse/Schema/Result/PacBioRun.pm
@@ -142,6 +142,30 @@ LIMs-specific identifier of the tag set for tag
 
 WTSI-wide tag set name for tag
 
+=head2 tag2_sequence
+
+  data_type: 'varchar'
+  is_nullable: 1
+  size: 30
+
+=head2 tag2_set_id_lims
+
+  data_type: 'varchar'
+  is_nullable: 1
+  size: 20
+
+=head2 tag2_set_name
+
+  data_type: 'varchar'
+  is_nullable: 1
+  size: 100
+
+=head2 tag2_identifier
+
+  data_type: 'varchar'
+  is_nullable: 1
+  size: 30
+
 =head2 plate_barcode
 
   data_type: 'varchar'
@@ -268,6 +292,14 @@ __PACKAGE__->add_columns(
   { data_type => 'varchar', is_nullable => 1, size => 20 },
   'tag_set_name',
   { data_type => 'varchar', is_nullable => 1, size => 100 },
+  'tag2_sequence',
+  { data_type => 'varchar', is_nullable => 1, size => 30 },
+  'tag2_set_id_lims',
+  { data_type => 'varchar', is_nullable => 1, size => 20 },
+  'tag2_set_name',
+  { data_type => 'varchar', is_nullable => 1, size => 100 },
+  'tag2_identifier',
+  { data_type => 'varchar', is_nullable => 1, size => 30 },
   'plate_barcode',
   { data_type => 'varchar', is_nullable => 0, size => 255 },
   'plate_uuid_lims',
@@ -308,6 +340,21 @@ __PACKAGE__->set_primary_key('id_pac_bio_tmp');
 
 =head1 RELATIONS
 
+=head2 pac_bio_product_metrics
+
+Type: has_many
+
+Related object: L<WTSI::DNAP::Warehouse::Schema::Result::PacBioProductMetric>
+
+=cut
+
+__PACKAGE__->has_many(
+  'pac_bio_product_metrics',
+  'WTSI::DNAP::Warehouse::Schema::Result::PacBioProductMetric',
+  { 'foreign.id_pac_bio_tmp' => 'self.id_pac_bio_tmp' },
+  { cascade_copy => 0, cascade_delete => 0 },
+);
+
 =head2 sample
 
 Type: belongs_to
@@ -339,8 +386,9 @@ __PACKAGE__->belongs_to(
 );
 
 
-# Created by DBIx::Class::Schema::Loader v0.07049 @ 2020-02-10 15:05:13
-# DO NOT MODIFY THIS OR ANYTHING ABOVE! md5sum:dkAFMFOOZ7+MTrEn5sI6nQ
+# Created by DBIx::Class::Schema::Loader v0.07049 @ 2021-01-24 15:45:02
+# DO NOT MODIFY THIS OR ANYTHING ABOVE! md5sum:eVqS5iL7i47o9VqosVsjTg
+
 
 our $VERSION = '0';