Merge remote-tracking branch 'js10-remote/devel' into devel

wtsi-npg · May 29, 2015 · 2bd1c7b · 2bd1c7b
2 parents e757cdf + 051400a
commit 2bd1c7b
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Showing 5 changed files with 86 additions and 9 deletions.
diff --git a/lib/npg_qc/Schema/Result/VerifyBamId.pm b/lib/npg_qc/Schema/Result/VerifyBamId.pm
@@ -93,15 +93,13 @@ __PACKAGE__->table('verify_bam_id');
 
 =head2 freeLK0
 
-  accessor: 'free_lk0'
   data_type: 'decimal'
   default_value: 0.00
   is_nullable: 0
   size: [11,2]
 
 =head2 freeLK1
 
-  accessor: 'free_lk1'
   data_type: 'decimal'
   default_value: 0.00
   is_nullable: 0
@@ -164,15 +162,13 @@ __PACKAGE__->add_columns(
   },
   'freeLK0',
   {
-    accessor => 'free_lk0',
     data_type => 'decimal',
     default_value => '0.00',
     is_nullable => 0,
     size => [11, 2],
   },
   'freeLK1',
   {
-    accessor => 'free_lk1',
     data_type => 'decimal',
     default_value => '0.00',
     is_nullable => 0,
@@ -234,17 +230,17 @@ __PACKAGE__->add_unique_constraint('unq_run_lane_verify', ['id_run', 'position',
 with 'npg_qc::Schema::Flators', 'npg_qc::autoqc::role::verify_bam_id';
 
 
-# Created by DBIx::Class::Schema::Loader v0.07036 @ 2015-02-13 15:21:35
-# DO NOT MODIFY THIS OR ANYTHING ABOVE! md5sum:AqOkJZFkV3LvyDSgZLez2g
+# Created by DBIx::Class::Schema::Loader v0.07036 @ 2015-05-28 16:47:33
+# DO NOT MODIFY THIS OR ANYTHING ABOVE! md5sum:FK7FU+Oo6v6VCmsi3TyjqA
 
 __PACKAGE__->set_flators4non_scalar(qw( info ));
 __PACKAGE__->set_inflator4scalar('tag_index');
 
 
 our $VERSION = '0';
 
+# You can replace this text with custom code or comments, and it will be preserved on regeneration
 __PACKAGE__->meta->make_immutable;
-
 1;
 __END__
 

diff --git a/scripts/npgqc_dbix_schema_loader.pl b/scripts/npgqc_dbix_schema_loader.pl
@@ -49,7 +49,11 @@
     {
         debug               => 0,
         dump_directory      => q[lib],
-        naming              => q[current],
+        naming              => { 
+            relationships => 'current', 
+            monikers => 'current', 
+            column_accessors => 'preserve',
+        },
         skip_load_external  => 1,
         use_moose           => 1,
         preserve_case       => 1,

diff --git a/t/50-schema-result-VerifyBamId.t b/t/50-schema-result-VerifyBamId.t
@@ -0,0 +1,53 @@
+use strict;
+use warnings;
+use Test::More tests => 8;
+use Test::Exception;
+use Test::Deep;
+use Moose::Meta::Class;
+use JSON;
+use npg_testing::db;
+
+use_ok('npg_qc::Schema::Result::VerifyBamId');
+
+my $schema = Moose::Meta::Class->create_anon_class(
+          roles => [qw/npg_testing::db/])
+          ->new_object({})->create_test_db(q[npg_qc::Schema]);
+
+my $json = 
+q { 
+{
+ "avg_depth":1.41,
+ "freeLK0":815501.89,
+ "freeLK1":815501.89,
+ "freemix":0,
+ "id_run":"7321",
+ "info":{"Check":"npg_qc::autoqc::checks::verify_bam_id","Check_version":"58.0","Verifier":"verifyBamID","Verify_options":" --bam in/7321_7#5.bam --vcf /lustre/scratch110/srpipe/population_snv/Homo_sapiens/1000G_Omni25_genotypes_2141/Standard/1000Genomes/Standard-1000Genomes.vcf.gz --self --ignoreRG --minQ 20 --minAF 0.05 --maxDepth 500 --precise --out /tmp/lew2Twr019/7321_7#5.bam"},
+ "number_of_reads":1908387,
+ "number_of_snps":1351960,
+ "path":"in",
+ "position":"7",
+ "tag_index":"5"}
+};
+
+my $values = from_json($json);
+my $rs = $schema->resultset('VerifyBamId');
+isa_ok($rs->new($values), 'npg_qc::Schema::Result::VerifyBamId');
+
+{
+  my %values1 = %{$values};
+  my $v1 = \%values1;
+
+  $rs->result_class->deflate_unique_key_components($v1);
+  is($v1->{'tag_index'}, 5, 'tag index deflated');
+  lives_ok {$rs->find_or_new($v1)->set_inflated_columns($v1)->update_or_insert()} 'lane record inserted';
+  my $rs1 = $rs->search({});
+  is ($rs1->count, 1, q[one row created in the table]);
+  my $row = $rs1->next;
+  is($row->tag_index, 5, 'tag index inflated');
+  is(ref $row->info, 'HASH', 'info returned as hash ref');
+  cmp_deeply($row->info, $values->{'info'},
+    'info hash content is correct');  
+}
+1;
+
+
diff --git a/t/60-autoqc-db_loader.t b/t/60-autoqc-db_loader.t
@@ -1,6 +1,6 @@
 use strict;
 use warnings;
-use Test::More tests => 58;
+use Test::More tests => 66;
 use Test::Exception;
 use Test::Warn;
 use Moose::Meta::Class;
@@ -118,6 +118,29 @@ my $schema = Moose::Meta::Class->create_anon_class(
   is($is_rs->search({})->count, $current_count+1, 'a new records added');
 }
 
+{
+  my $is_rs = $schema->resultset('VerifyBamId');
+  my $current_count = $is_rs->search({})->count;
+  my $count_loaded;
+
+  my $db_loader = npg_qc::autoqc::db_loader->new(
+       schema => $schema,
+       json_file   => ['t/data/autoqc/7321_7#8.verify_bam_id.json'],
+       verbose => 0,
+  );
+  lives_ok {$count_loaded = $db_loader->load()} 'file loaded';
+  is($count_loaded, 1, 'reported one file loaded');
+  $current_count++;
+  is ($is_rs->search({})->count, $current_count, 'one record added to the table');
+  lives_ok {$db_loader->load()} 'reload VerifyBamId result';
+  my $rs = $is_rs->search({});
+  is($rs->count, $current_count, 'no new records added');
+  my $row = $rs->next;
+  is($row->freemix, 0.00025, 'freemix');
+  is($row->freeLK0, 823213.22, 'freeLK0');
+  is($row->freeLK1, 823213.92, 'freeLK1');
+}
+
 {
   my $is_rs = $schema->resultset('InsertSize');
   $is_rs->delete_all();

diff --git a/t/data/autoqc/7321_7#8.verify_bam_id.json b/t/data/autoqc/7321_7#8.verify_bam_id.json
@@ -0,0 +1 @@
+{"__CLASS__":"npg_qc::autoqc::results::verify_bam_id-58.0","avg_depth":1.43,"freeLK0":823213.22,"freeLK1":823213.92,"freemix":0.00025,"id_run":"7321","info":{"Check":"npg_qc::autoqc::checks::verify_bam_id","Check_version":"58.0","Verifier":"verifyBamID","Verify_options":" --bam in/7321_7#8.bam --vcf /lustre/scratch110/srpipe/population_snv/Homo_sapiens/1000G_Omni25_genotypes_2141/Standard/1000Genomes/Standard-1000Genomes.vcf.gz --self --ignoreRG --minQ 20 --minAF 0.05 --maxDepth 500 --precise --out /tmp/IxVQiyJg_W/7321_7#8.bam"},"number_of_reads":1930480,"number_of_snps":1351960,"path":"in","position":"7","tag_index":"8"}