Ensure snp_call_set attribute is always defined.

Previously if the genotype check failed to run and
exited early, this attribute was not defined in the
result object. This gave an error on loading the result
to the database.

lib/npg_qc/autoqc/checks/genotype.pm

@@ -100,8 +100,8 @@ has 'sequenom_plex' => (
 );
 
 # snp_call_set - this specifies the set of loci to be called. This may be
-#  the same for different sequenom_plex data sets. It is used to construct
-#  the name of some information files (positions, alleles, etc)
+# the same for different sequenom_plex data sets. It is used to construct
+# the name of some information files (positions, alleles, etc)
 has 'snp_call_set' => (
   is => 'ro',
   isa => 'Str',
@@ -426,9 +426,9 @@ override 'can_run' => sub {
   if(! any { $_ eq fileparse($self->reference_fasta); } (keys %{$self->_ref_to_snppos_suffix_map})) {
     $self->result->add_comment('Specified reference genome may be non-human');
     return 0;
-   }
+  }
 
-   return 1;
+  return 1;
 };
 
 override 'execute' => sub {
@@ -444,6 +444,9 @@ override 'execute' => sub {
   };
 
   if(!$self->can_run()) {
+    # The value has to be set in order to be able to upload the result
+    # to the database; it is a part of the unique constraint.
+    $self->result->snp_call_set($self->snp_call_set);
     return 1;
   }
 
@@ -658,7 +661,7 @@ sub _set_attrib_by_geno_refset {
   my $name   = fileparse($self->geno_refset);
 
   $self->_set_sequenom_plex($name);
-  $self->_set_snp_call_set($name);
+  $self->_set_ssnp_call_setnp_call_set($name);
   $self->_set_gt_db($self->geno_refset);
 
   if($self->alternate_sample_name) {

t/60-autoqc-checks-genotype.t

@@ -2,11 +2,15 @@ use strict;
 use warnings;
 use Cwd;
 use File::Temp qw/ tempdir /;
-use Test::More tests => 10;
+use Test::More tests => 11;
 use Test::Exception;
+use File::Copy;
+use Perl6::Slurp;
+
 use WTSI::NPG::iRODS;
 
 use_ok ('npg_qc::autoqc::checks::genotype');
+use_ok ('npg_qc::autoqc::results::genotype');
 
 my $dir = tempdir(CLEANUP => 1);
 my $pid = $$;
@@ -23,6 +27,8 @@ if ($env_file && $have_irods_execs) {
   $irods_tmp_coll = $irods->add_collection("GenotypeTest.$pid") ;
 }
 
+my $ref_repos = cwd . '/t/data/autoqc';
+
 sub exist_irods_executables {
   return 0 unless `which ienv`;
   return 0 unless `which imkdir`;
@@ -37,10 +43,35 @@ END {
   }
 }
 
+subtest 'Test early exit' => sub {
+  plan tests => 5;
+
+  local $ENV{'NPG_CACHED_SAMPLESHEET_FILE'} =
+    't/data/autoqc/samplesheets/samplesheet_47646.csv';
+  my $input_file = "$dir/47646_1#999.cram";
+  my $output_file = "$dir/47646_1#999.genotype.json";
+  copy('t/data/autoqc/alignment.bam', $input_file);
+  mkdir("$dir/genotypes");
+
+  my $check = npg_qc::autoqc::checks::genotype->new(
+    rpt_list    => '47646:1:999',
+    input_files => [$input_file],
+    qc_out      => $dir,
+    repository  => $ref_repos,
+    genotypes_repository => "$dir/genotypes"
+  );
+  isa_ok ($check, 'npg_qc::autoqc::checks::genotype');
+  lives_ok { $check->run() } 'check executed';
+  ok (-e $output_file, "output file $output_file has been generated");
+  my $result = npg_qc::autoqc::results::genotype->thaw(slurp($output_file));
+  is ($result->comments(), 'Specified reference genome may be non-human',
+    'correct comment is captured');
+  ok ($result->snp_call_set(), 'the snp_call_set attribute is set');
+};
+
 SKIP: {
-  skip 'iRODS not available', 9 unless $irods_tmp_coll;
+  skip 'iRODS not available', 8 unless $irods_tmp_coll;
 
-  my $ref_repos = cwd . '/t/data/autoqc';
   my $expected_md5 = q[a4790111996a3f1c0247d65f4998e492];
 
   my $st = join q[/], $dir, q[samtools];
@@ -52,7 +83,7 @@ SKIP: {
   local $ENV{PATH} = join q[:], $dir, $ENV{PATH};
   my $data_dir = $dir."/data";
   mkdir($data_dir);
-  `cp t/data/autoqc/alignment.bam $data_dir/2_1.bam`;
+  copy('t/data/autoqc/alignment.bam', "$data_dir/2_1.bam");
   `echo -n $expected_md5 > $data_dir/2_1.bam.md5`;
 
   # populate a temporary iRODS collection
@@ -66,7 +97,6 @@ SKIP: {
         input_files => ["$data_dir/2_1.bam"],
         repository  => $ref_repos,
   );
-  isa_ok ($r, 'npg_qc::autoqc::checks::genotype');
   lives_ok { $r->result; } 'No error creating result object';
   lives_ok {$r->samtools } 'No error calling "samtools" accessor';
   is($r->samtools, $st, 'correct samtools path');

t/60-autoqc-db_loader.t

@@ -1,6 +1,6 @@
 use strict;
 use warnings;
-use Test::More tests => 21;
+use Test::More tests => 22;
 use Test::Exception;
 use Test::Warn;
 use Moose::Meta::Class;
@@ -874,4 +874,18 @@ subtest 'loading review and other results from path' => sub {
   is( $row->criteria_md5, '27c522a795e99e3aea57162541de75b1', 'criteria_md5 column populated');
 };
 
+subtest 'loading partially defined results' => sub {
+  plan tests => 2;
+
+  my $db = $db_helper->create_test_db(q[npg_qc::Schema], 't/data/fixtures');
+  my $db_loader = npg_qc::autoqc::db_loader->new(
+    path    => ['t/data/autoqc/dbix_loader/short_results'],
+    schema  => $db,
+    verbose => 0,
+  );
+  lives_ok { $db_loader->load() } 'no error loading an ncomplete result';
+  is ($db->resultset('Genotype')->search({})->count(), 1,
+    'one genotype record is created');
+};
+
 1;

t/data/autoqc/dbix_loader/short_results/47646_1#999.genotype.json

@@ -0,0 +1 @@
+{"__CLASS__":"npg_qc::autoqc::results::genotype","comments":"Specified reference genome may be non-human","composition":{"__CLASS__":"npg_tracking::glossary::composition-96.0.0","components":[{"__CLASS__":"npg_tracking::glossary::composition::component::illumina-96.0.0","id_run":47646,"position":1,"tag_index":999}]},"id_run":47646,"info":{"Check":"npg_qc::autoqc::checks::genotype","Check_version":"0"},"position":1,"snp_call_set":"W30467","tag_index":999}

t/data/autoqc/samplesheets/samplesheet_47646.csv

@@ -0,0 +1,6 @@
+[Data],,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,
+Sample_ID,Sample_Name,GenomeFolder,Index,Index2,bait_name,default_library_type,default_tag_sequence,default_tagtwo_sequence,email_addresses,email_addresses_of_followers,email_addresses_of_managers,email_addresses_of_owners,gbs_plex_name,is_control,is_pool,lane_id,lane_priority,library_name,organism,organism_taxon_id,project_cost_code,project_id,project_name,purpose,qc_state,request_id,required_insert_size_range,sample_accession_number,sample_cohort,sample_common_name,sample_consent_withdrawn,sample_control_type,sample_description,sample_donor_id,sample_id,sample_is_control,sample_name,sample_public_name,sample_reference_genome,sample_supplier_name,spiked_phix_tag_index,study_accession_number,study_alignments_in_bam,study_contains_nonconsented_human,study_contains_nonconsented_xahuman,study_description,study_id,study_name,study_reference_genome,study_separate_y_chromosome_data,study_title,tag_index,
+67859722,3073STDY13850377,,TGAACTGG,AGAGTAGA,,GBS,TGAACTGG,AGAGTAGA,[email protected] [email protected] [email protected] [email protected],,[email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected],,PFA_GRC1_v1.0,0,0,68525973,0,67859722,,5833,S0910,,,standard,,,from:450 to:450,,,Plasmodium falciparum,0,,,3073STDY13850377,8762888,0,3073STDY13850377,,,110723_negative36,,,1,0,0,Development of sequencing and library prep protocols using Human DNA ,3073,Team51_Development,Homo_sapiens (GRCh38_full_analysis_set_plus_decoy_hla),0,Team51_Development,997,
+67859770,3073STDY13850378,,TACTTCGG,AGAGTAGA,,GBS,TACTTCGG,AGAGTAGA,[email protected] [email protected] [email protected] [email protected],,[email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected],,PFA_GRC1_v1.0,0,0,68525973,0,67859770,,5833,S0910,,,standard,,,from:450 to:450,,,Plasmodium falciparum,0,,,3073STDY13850378,8762889,0,3073STDY13850378,,,110723_negative37,,,1,0,0,Development of sequencing and library prep protocols using Human DNA ,3073,Team51_Development,Homo_sapiens (GRCh38_full_analysis_set_plus_decoy_hla),0,Team51_Development,998,
+67859818,3073STDY13850379,,TCTCACGG,AGAGTAGA,,GBS,TCTCACGG,AGAGTAGA,[email protected] [email protected] [email protected] [email protected],,[email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected],,PFA_GRC1_v1.0,0,0,68525973,0,67859818,,5833,S0910,,,standard,,,from:450 to:450,,,Plasmodium falciparum,0,,,3073STDY13850379,8762890,0,3073STDY13850379,,,110723_negative38,,,1,0,0,Development of sequencing and library prep protocols using Human DNA ,3073,Team51_Development,Homo_sapiens (GRCh38_full_analysis_set_plus_decoy_hla),0,Team51_Development,999,
+67859866,3073STDY13850380,,TCAGGAGG,AGAGTAGA,,GBS,TCAGGAGG,AGAGTAGA,[email protected] [email protected] [email protected] [email protected],,[email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected],,PFA_GRC1_v1.0,0,0,68525973,0,67859866,,5833,S0910,,,standard,,,from:450 to:450,,,Plasmodium falciparum,0,,,3073STDY13850380,8762891,0,3073STDY13850380,,,110723_negative39,,,1,0,0,Development of sequencing and library prep protocols using Human DNA ,3073,Team51_Development,Homo_sapiens (GRCh38_full_analysis_set_plus_decoy_hla),0,Team51_Development,1000,