Merge pull request wtsi-npg#842 from mgcam/archive_incomplete_genotyp…

…e_results

Archive incomplete genotype results

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;
   }
 

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 +43,46 @@ END {
   }
 }
 
+subtest 'Test early exit' => sub {
+  plan tests => 6;
+
+  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 $fasta = join q[/], $ref_repos, 'references',
+    'Homo_sapiens/GRCh38_full_analysis_set_plus_decoy_hla/all/fasta',
+    'GRCh38_full_analysis_set_plus_decoy_hla.fasta';
+
+  # Set the reference_fasta path explicitly, the CI pipeline has
+  # difficulty inferring it.
+  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",
+    reference_fasta => $fasta
+  );
+  isa_ok ($check, 'npg_qc::autoqc::checks::genotype');
+  # For a check that cannot be run in full in a meaningful way we
+  # need to save enough data in the output JSON file to allow for
+  # this output to be uploaded to the database.
+  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 ($result->comments(), 'Specified reference genome may be non-human',
+    'correct reason for not running in full is captured');
+  ok ($result->snp_call_set(), 'the snp_call_set attribute is set');
+  # Testing ability to run last to avoid duplicates in comments.
+  ok (!$check->can_run(), 'the check cannot be run in full');
+};
+
 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 +94,7 @@ 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 +108,6 @@ 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 { $db_loader->load() } 'no error loading an incomplete result';
+  is ($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,