From b7b40258403823c33a97a2d6ddac5c1329363e2b Mon Sep 17 00:00:00 2001 From: Marco Mosca Date: Fri, 29 Nov 2024 16:59:09 +0000 Subject: [PATCH 01/10] Add sample_uuid to Illumina annotator --- lib/WTSI/NPG/HTS/Illumina/Annotator.pm | 1 + t/lib/WTSI/NPG/HTS/Illumina/MetaUpdaterTest.pm | 1 + 2 files changed, 2 insertions(+) diff --git a/lib/WTSI/NPG/HTS/Illumina/Annotator.pm b/lib/WTSI/NPG/HTS/Illumina/Annotator.pm index 000c6da4..a11dc60c 100644 --- a/lib/WTSI/NPG/HTS/Illumina/Annotator.pm +++ b/lib/WTSI/NPG/HTS/Illumina/Annotator.pm @@ -422,6 +422,7 @@ sub make_sample_metadata { sample_public_names => $SAMPLE_PUBLIC_NAME, sample_common_names => $SAMPLE_COMMON_NAME, sample_supplier_names => $SAMPLE_SUPPLIER_NAME, + sample_uuids => $SAMPLE_UUID, sample_cohorts => $SAMPLE_COHORT, sample_donor_ids => $SAMPLE_DONOR_ID}; diff --git a/t/lib/WTSI/NPG/HTS/Illumina/MetaUpdaterTest.pm b/t/lib/WTSI/NPG/HTS/Illumina/MetaUpdaterTest.pm index 9df68c92..c764e7ea 100644 --- a/t/lib/WTSI/NPG/HTS/Illumina/MetaUpdaterTest.pm +++ b/t/lib/WTSI/NPG/HTS/Illumina/MetaUpdaterTest.pm @@ -140,6 +140,7 @@ sub update_secondary_metadata : Test(5) { value => 'Burkholderia pseudomallei' }, { attribute => $SAMPLE_ID, value => '230889' }, { attribute => $SAMPLE_PUBLIC_NAME, value => '153.0' }, + { attribute => $SAMPLE_UUID, value => 'a8b4ebaa-c628-11df-8e7f-00144f2062b0' }, { attribute => $STUDY_NAME, value => 'Burkholderia pseudomallei diversity' }, { attribute => $STUDY_ACCESSION_NUMBER, value => 'ERP000251' }, From c5603326e63ffa8028f87135fd68af9fbb69e025 Mon Sep 17 00:00:00 2001 From: Marco Mosca Date: Fri, 29 Nov 2024 16:59:42 +0000 Subject: [PATCH 02/10] Add sample uuid to Pacbio annotator --- lib/WTSI/NPG/HTS/PacBio/Annotator.pm | 1 + t/lib/WTSI/NPG/HTS/PacBio/MetaUpdaterTest.pm | 1 + 2 files changed, 2 insertions(+) diff --git a/lib/WTSI/NPG/HTS/PacBio/Annotator.pm b/lib/WTSI/NPG/HTS/PacBio/Annotator.pm index 1968e9e2..ebdcc96b 100644 --- a/lib/WTSI/NPG/HTS/PacBio/Annotator.pm +++ b/lib/WTSI/NPG/HTS/PacBio/Annotator.pm @@ -161,6 +161,7 @@ sub make_sample_metadata { my @samples = map { $_->sample } @run_records; my $method_attr = {accession_number => $SAMPLE_ACCESSION_NUMBER, id_sample_lims => $SAMPLE_ID, + uuid_sample_lims => $SAMPLE_UUID, name => $SAMPLE_NAME, public_name => $SAMPLE_PUBLIC_NAME, common_name => $SAMPLE_COMMON_NAME, diff --git a/t/lib/WTSI/NPG/HTS/PacBio/MetaUpdaterTest.pm b/t/lib/WTSI/NPG/HTS/PacBio/MetaUpdaterTest.pm index d1b5903a..ce19d654 100644 --- a/t/lib/WTSI/NPG/HTS/PacBio/MetaUpdaterTest.pm +++ b/t/lib/WTSI/NPG/HTS/PacBio/MetaUpdaterTest.pm @@ -111,6 +111,7 @@ sub update_secondary_metadata : Test(8) { {attribute => $SAMPLE_ID, value => 2567488}, {attribute => $SAMPLE_PUBLIC_NAME, value => 70628}, {attribute => $SAMPLE_SUPPLIER_NAME, value => 'AR0091-CW'}, + {attribute => $SAMPLE_UUID, value => '1ca1a900-e463-11e5-88b1-3c4a9275d6c6'}, {attribute => $STUDY_NAME, value => $study_name}, {attribute => $STUDY_ACCESSION_NUMBER, value => 'ERP002372'}, {attribute => $STUDY_ID, value => $study_id}, From dd1d09cefdf893127bcab7bccbf75cef8df77392 Mon Sep 17 00:00:00 2001 From: Marco Mosca Date: Mon, 2 Dec 2024 13:43:10 +0000 Subject: [PATCH 03/10] Update AgfDataObjectTest with sample_uuid --- t/lib/WTSI/NPG/HTS/Illumina/AgfDataObjectTest.pm | 1 + 1 file changed, 1 insertion(+) diff --git a/t/lib/WTSI/NPG/HTS/Illumina/AgfDataObjectTest.pm b/t/lib/WTSI/NPG/HTS/Illumina/AgfDataObjectTest.pm index b6dec855..ac918f6b 100644 --- a/t/lib/WTSI/NPG/HTS/Illumina/AgfDataObjectTest.pm +++ b/t/lib/WTSI/NPG/HTS/Illumina/AgfDataObjectTest.pm @@ -223,6 +223,7 @@ sub update_secondary_metadata_tag1_no_spike_human : Test(12) { {attribute => $SAMPLE_ID, value => '2376982'}, {attribute => $SAMPLE_PUBLIC_NAME, value => 'UTX_IP_UTX_GTX_A'}, {attribute => $SAMPLE_SUPPLIER_NAME, value => 'UTX_IP_UTX_GTX_A'}, + {attribute => $SAMPLE_UUID, value => '4e0f6640-40f7-11e5-998e-3c4a9275d6c6'}, {attribute => $STUDY_NAME, value => 'Analysis of the chromatin state of mouse stem and progenitor cell compartment'}, {attribute => $STUDY_ACCESSION_NUMBER, value => 'ERP004563'}, From 430dbe8f9c8a4c21d7056ef10d1f2b1046047b80 Mon Sep 17 00:00:00 2001 From: Marco Mosca Date: Mon, 2 Dec 2024 13:44:32 +0000 Subject: [PATCH 04/10] Update copyright for Illumina and PAcbio Annotators --- lib/WTSI/NPG/HTS/Illumina/Annotator.pm | 2 +- lib/WTSI/NPG/HTS/PacBio/Annotator.pm | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/lib/WTSI/NPG/HTS/Illumina/Annotator.pm b/lib/WTSI/NPG/HTS/Illumina/Annotator.pm index a11dc60c..3e8b8f74 100644 --- a/lib/WTSI/NPG/HTS/Illumina/Annotator.pm +++ b/lib/WTSI/NPG/HTS/Illumina/Annotator.pm @@ -586,7 +586,7 @@ Keith James , Iain Bancarz =head1 COPYRIGHT AND DISCLAIMER -Copyright (C) 2015, 2016, 2017, 2018, 2019 Genome Research Limited. +Copyright (C) 2015, 2016, 2017, 2018, 2019, 2024 Genome Research Limited. All Rights Reserved. This program is free software: you can redistribute it and/or modify diff --git a/lib/WTSI/NPG/HTS/PacBio/Annotator.pm b/lib/WTSI/NPG/HTS/PacBio/Annotator.pm index ebdcc96b..4acdd663 100644 --- a/lib/WTSI/NPG/HTS/PacBio/Annotator.pm +++ b/lib/WTSI/NPG/HTS/PacBio/Annotator.pm @@ -320,7 +320,7 @@ Keith James =head1 COPYRIGHT AND DISCLAIMER -Copyright (C) 2016, 2017 Genome Research Limited. All Rights Reserved. +Copyright (C) 2016, 2017, 2024 Genome Research Limited. All Rights Reserved. This program is free software: you can redistribute it and/or modify it under the terms of the Perl Artistic License or the GNU General From 2e30a0c1e5b1381247cc84d3806c659d840708a8 Mon Sep 17 00:00:00 2001 From: Marco Mosca Date: Tue, 3 Dec 2024 13:14:44 +0000 Subject: [PATCH 05/10] Add sample_lims for Pacbio Annotator --- lib/WTSI/NPG/HTS/PacBio/Annotator.pm | 1 + t/lib/WTSI/NPG/HTS/PacBio/MetaUpdaterTest.pm | 1 + 2 files changed, 2 insertions(+) diff --git a/lib/WTSI/NPG/HTS/PacBio/Annotator.pm b/lib/WTSI/NPG/HTS/PacBio/Annotator.pm index 4acdd663..4c96799d 100644 --- a/lib/WTSI/NPG/HTS/PacBio/Annotator.pm +++ b/lib/WTSI/NPG/HTS/PacBio/Annotator.pm @@ -161,6 +161,7 @@ sub make_sample_metadata { my @samples = map { $_->sample } @run_records; my $method_attr = {accession_number => $SAMPLE_ACCESSION_NUMBER, id_sample_lims => $SAMPLE_ID, + id_lims => $SAMPLE_LIMS, uuid_sample_lims => $SAMPLE_UUID, name => $SAMPLE_NAME, public_name => $SAMPLE_PUBLIC_NAME, diff --git a/t/lib/WTSI/NPG/HTS/PacBio/MetaUpdaterTest.pm b/t/lib/WTSI/NPG/HTS/PacBio/MetaUpdaterTest.pm index ce19d654..7f2c0f76 100644 --- a/t/lib/WTSI/NPG/HTS/PacBio/MetaUpdaterTest.pm +++ b/t/lib/WTSI/NPG/HTS/PacBio/MetaUpdaterTest.pm @@ -109,6 +109,7 @@ sub update_secondary_metadata : Test(8) { {attribute => $SAMPLE_COMMON_NAME, value => 'Anopheles gambiae'}, {attribute => $SAMPLE_DONOR_ID, value => '2572STDY6358500'}, {attribute => $SAMPLE_ID, value => 2567488}, + {attribute => $SAMPLE_LIMS, value => 'SQSCP'}, {attribute => $SAMPLE_PUBLIC_NAME, value => 70628}, {attribute => $SAMPLE_SUPPLIER_NAME, value => 'AR0091-CW'}, {attribute => $SAMPLE_UUID, value => '1ca1a900-e463-11e5-88b1-3c4a9275d6c6'}, From 9e610106adb48656079de162d651531e3180830d Mon Sep 17 00:00:00 2001 From: Marco Mosca Date: Tue, 10 Dec 2024 15:26:03 +0000 Subject: [PATCH 06/10] Update tests in AlnDataObjectTest with the sample_uuid --- .../NPG/HTS/Illumina/AlnDataObjectTest.pm | 81 +++++++++++++++++++ 1 file changed, 81 insertions(+) diff --git a/t/lib/WTSI/NPG/HTS/Illumina/AlnDataObjectTest.pm b/t/lib/WTSI/NPG/HTS/Illumina/AlnDataObjectTest.pm index b7db088c..57a29f70 100644 --- a/t/lib/WTSI/NPG/HTS/Illumina/AlnDataObjectTest.pm +++ b/t/lib/WTSI/NPG/HTS/Illumina/AlnDataObjectTest.pm @@ -375,6 +375,7 @@ sub nonconsented_human_access_revoked : Test(6) { value => 'Burkholderia pseudomallei'}, {attribute => $SAMPLE_ID, value => '230889'}, {attribute => $SAMPLE_PUBLIC_NAME, value => '153.0'}, + {attribute => $SAMPLE_UUID, value => 'a8b4ebaa-c628-11df-8e7f-00144f2062b0'}, {attribute => $STUDY_NAME, value => 'Burkholderia pseudomallei diversity'}, {attribute => $STUDY_ACCESSION_NUMBER, value => 'ERP000251'}, @@ -712,6 +713,39 @@ sub update_secondary_metadata_tag0_no_spike_bact : Test(12) { {attribute => $SAMPLE_PUBLIC_NAME, value => 'K11277244-293'}, {attribute => $SAMPLE_PUBLIC_NAME, value => 'P73230-3018'}, {attribute => $SAMPLE_PUBLIC_NAME, value => 'SOIL'}, + {attribute => $SAMPLE_UUID, value => 'a8b4ebaa-c628-11df-8e7f-00144f2062b0'}, + {attribute => $SAMPLE_UUID, value => 'a8b4f3ac-c628-11df-8e7f-00144f2062b0'}, + {attribute => $SAMPLE_UUID, value => 'a8b4fbae-c628-11df-8e7f-00144f2062b0'}, + {attribute => $SAMPLE_UUID, value => 'a8b503a6-c628-11df-8e7f-00144f2062b0'}, + {attribute => $SAMPLE_UUID, value => 'a8b50b9e-c628-11df-8e7f-00144f2062b0'}, + {attribute => $SAMPLE_UUID, value => 'a8b51396-c628-11df-8e7f-00144f2062b0'}, + {attribute => $SAMPLE_UUID, value => 'a8b51ba2-c628-11df-8e7f-00144f2062b0'}, + {attribute => $SAMPLE_UUID, value => 'a8b5239a-c628-11df-8e7f-00144f2062b0'}, + {attribute => $SAMPLE_UUID, value => 'a8b52b92-c628-11df-8e7f-00144f2062b0'}, + {attribute => $SAMPLE_UUID, value => 'a8b5338a-c628-11df-8e7f-00144f2062b0'}, + {attribute => $SAMPLE_UUID, value => 'a8b53b82-c628-11df-8e7f-00144f2062b0'}, + {attribute => $SAMPLE_UUID, value => 'a8b5437a-c628-11df-8e7f-00144f2062b0'}, + {attribute => $SAMPLE_UUID, value => 'a8b54b7c-c628-11df-8e7f-00144f2062b0'}, + {attribute => $SAMPLE_UUID, value => 'a8b55374-c628-11df-8e7f-00144f2062b0'}, + {attribute => $SAMPLE_UUID, value => 'a8b55b94-c628-11df-8e7f-00144f2062b0'}, + {attribute => $SAMPLE_UUID, value => 'a8b5638c-c628-11df-8e7f-00144f2062b0'}, + {attribute => $SAMPLE_UUID, value => 'a8b56bb6-c628-11df-8e7f-00144f2062b0'}, + {attribute => $SAMPLE_UUID, value => 'a8b573ae-c628-11df-8e7f-00144f2062b0'}, + {attribute => $SAMPLE_UUID, value => 'a8b57bb0-c628-11df-8e7f-00144f2062b0'}, + {attribute => $SAMPLE_UUID, value => 'a8b583a8-c628-11df-8e7f-00144f2062b0'}, + {attribute => $SAMPLE_UUID, value => 'a8b58b96-c628-11df-8e7f-00144f2062b0'}, + {attribute => $SAMPLE_UUID, value => 'a8b5938e-c628-11df-8e7f-00144f2062b0'}, + {attribute => $SAMPLE_UUID, value => 'a8b59b86-c628-11df-8e7f-00144f2062b0'}, + {attribute => $SAMPLE_UUID, value => 'a8b5a37e-c628-11df-8e7f-00144f2062b0'}, + {attribute => $SAMPLE_UUID, value => 'a8b5ab6c-c628-11df-8e7f-00144f2062b0'}, + {attribute => $SAMPLE_UUID, value => 'a8b5b364-c628-11df-8e7f-00144f2062b0'}, + {attribute => $SAMPLE_UUID, value => 'a8b5bb5c-c628-11df-8e7f-00144f2062b0'}, + {attribute => $SAMPLE_UUID, value => 'a8b5c35e-c628-11df-8e7f-00144f2062b0'}, + {attribute => $SAMPLE_UUID, value => 'a8b5cb4c-c628-11df-8e7f-00144f2062b0'}, + {attribute => $SAMPLE_UUID, value => 'a8b5d34e-c628-11df-8e7f-00144f2062b0'}, + {attribute => $SAMPLE_UUID, value => 'a8b5db46-c628-11df-8e7f-00144f2062b0'}, + {attribute => $SAMPLE_UUID, value => 'a8b5e352-c628-11df-8e7f-00144f2062b0'}, + {attribute => $SAMPLE_UUID, value => 'a8b5eb54-c628-11df-8e7f-00144f2062b0'}, {attribute => $STUDY_NAME, value => 'Burkholderia pseudomallei diversity'}, {attribute => $STUDY_ACCESSION_NUMBER, value => 'ERP000251'}, @@ -937,6 +971,40 @@ sub update_secondary_metadata_tag0_spike_bact : Test(12) { {attribute => $SAMPLE_PUBLIC_NAME, value => 'K11277244-293'}, {attribute => $SAMPLE_PUBLIC_NAME, value => 'P73230-3018'}, {attribute => $SAMPLE_PUBLIC_NAME, value => 'SOIL'}, + {attribute => $SAMPLE_UUID, value => 'a8b4ebaa-c628-11df-8e7f-00144f2062b0'}, + {attribute => $SAMPLE_UUID, value => 'a8b4f3ac-c628-11df-8e7f-00144f2062b0'}, + {attribute => $SAMPLE_UUID, value => 'a8b4fbae-c628-11df-8e7f-00144f2062b0'}, + {attribute => $SAMPLE_UUID, value => 'a8b503a6-c628-11df-8e7f-00144f2062b0'}, + {attribute => $SAMPLE_UUID, value => 'a8b50b9e-c628-11df-8e7f-00144f2062b0'}, + {attribute => $SAMPLE_UUID, value => 'a8b51396-c628-11df-8e7f-00144f2062b0'}, + {attribute => $SAMPLE_UUID, value => 'a8b51ba2-c628-11df-8e7f-00144f2062b0'}, + {attribute => $SAMPLE_UUID, value => 'a8b5239a-c628-11df-8e7f-00144f2062b0'}, + {attribute => $SAMPLE_UUID, value => 'a8b52b92-c628-11df-8e7f-00144f2062b0'}, + {attribute => $SAMPLE_UUID, value => 'a8b5338a-c628-11df-8e7f-00144f2062b0'}, + {attribute => $SAMPLE_UUID, value => 'a8b53b82-c628-11df-8e7f-00144f2062b0'}, + {attribute => $SAMPLE_UUID, value => 'a8b5437a-c628-11df-8e7f-00144f2062b0'}, + {attribute => $SAMPLE_UUID, value => 'a8b54b7c-c628-11df-8e7f-00144f2062b0'}, + {attribute => $SAMPLE_UUID, value => 'a8b55374-c628-11df-8e7f-00144f2062b0'}, + {attribute => $SAMPLE_UUID, value => 'a8b55b94-c628-11df-8e7f-00144f2062b0'}, + {attribute => $SAMPLE_UUID, value => 'a8b5638c-c628-11df-8e7f-00144f2062b0'}, + {attribute => $SAMPLE_UUID, value => 'a8b56bb6-c628-11df-8e7f-00144f2062b0'}, + {attribute => $SAMPLE_UUID, value => 'a8b573ae-c628-11df-8e7f-00144f2062b0'}, + {attribute => $SAMPLE_UUID, value => 'a8b57bb0-c628-11df-8e7f-00144f2062b0'}, + {attribute => $SAMPLE_UUID, value => 'a8b583a8-c628-11df-8e7f-00144f2062b0'}, + {attribute => $SAMPLE_UUID, value => 'a8b58b96-c628-11df-8e7f-00144f2062b0'}, + {attribute => $SAMPLE_UUID, value => 'a8b5938e-c628-11df-8e7f-00144f2062b0'}, + {attribute => $SAMPLE_UUID, value => 'a8b59b86-c628-11df-8e7f-00144f2062b0'}, + {attribute => $SAMPLE_UUID, value => 'a8b5a37e-c628-11df-8e7f-00144f2062b0'}, + {attribute => $SAMPLE_UUID, value => 'a8b5ab6c-c628-11df-8e7f-00144f2062b0'}, + {attribute => $SAMPLE_UUID, value => 'a8b5b364-c628-11df-8e7f-00144f2062b0'}, + {attribute => $SAMPLE_UUID, value => 'a8b5bb5c-c628-11df-8e7f-00144f2062b0'}, + {attribute => $SAMPLE_UUID, value => 'a8b5c35e-c628-11df-8e7f-00144f2062b0'}, + {attribute => $SAMPLE_UUID, value => 'a8b5cb4c-c628-11df-8e7f-00144f2062b0'}, + {attribute => $SAMPLE_UUID, value => 'a8b5d34e-c628-11df-8e7f-00144f2062b0'}, + {attribute => $SAMPLE_UUID, value => 'a8b5db46-c628-11df-8e7f-00144f2062b0'}, + {attribute => $SAMPLE_UUID, value => 'a8b5e352-c628-11df-8e7f-00144f2062b0'}, + {attribute => $SAMPLE_UUID, value => 'a8b5eb54-c628-11df-8e7f-00144f2062b0'}, + {attribute => $SAMPLE_UUID, value => 'd3a59c4c-c037-11e0-834c-00144f01a414'}, {attribute => $STUDY_NAME, value => 'Burkholderia pseudomallei diversity'}, {attribute => $STUDY_NAME, @@ -999,6 +1067,7 @@ sub update_secondary_metadata_tag1_no_spike_bact : Test(12) { value => 'Burkholderia pseudomallei'}, {attribute => $SAMPLE_ID, value => '230889'}, {attribute => $SAMPLE_PUBLIC_NAME, value => '153.0'}, + {attribute => $SAMPLE_UUID, value => 'a8b4ebaa-c628-11df-8e7f-00144f2062b0'}, {attribute => $STUDY_NAME, value => 'Burkholderia pseudomallei diversity'}, {attribute => $STUDY_ACCESSION_NUMBER, value => 'ERP000251'}, @@ -1057,6 +1126,7 @@ sub update_secondary_metadata_tag1_spike_bact : Test(12) { value => 'Burkholderia pseudomallei'}, {attribute => $SAMPLE_ID, value => '230889'}, {attribute => $SAMPLE_PUBLIC_NAME, value => '153.0'}, + {attribute => $SAMPLE_UUID, value => 'a8b4ebaa-c628-11df-8e7f-00144f2062b0'}, {attribute => $STUDY_NAME, value => 'Burkholderia pseudomallei diversity'}, {attribute => $STUDY_ACCESSION_NUMBER, value => 'ERP000251'}, @@ -1133,6 +1203,10 @@ sub update_secondary_metadata_tag0_no_spike_human : Test(12) { {attribute => $SAMPLE_SUPPLIER_NAME, value => '7R5'}, {attribute => $SAMPLE_SUPPLIER_NAME, value => '8AJ1'}, {attribute => $SAMPLE_SUPPLIER_NAME, value => '8R163'}, + {attribute => $SAMPLE_UUID, value => 'd41d4a40-a521-11e3-8055-3c4a9275d6c6'}, + {attribute => $SAMPLE_UUID, value => 'd492a150-a521-11e3-8055-3c4a9275d6c6'}, + {attribute => $SAMPLE_UUID, value => 'd4ee2ed0-a521-11e3-8055-3c4a9275d6c6'}, + {attribute => $SAMPLE_UUID, value => 'd62d8ca0-a521-11e3-8055-3c4a9275d6c6'}, {attribute => $STUDY_NAME, value => 'SEQCAP_Lebanon_LowCov-seq'}, {attribute => $STUDY_ACCESSION_NUMBER, value => 'EGAS00001002084'}, @@ -1213,6 +1287,11 @@ sub update_secondary_metadata_tag0_spike_human : Test(12) { {attribute => $SAMPLE_SUPPLIER_NAME, value => '7R5'}, {attribute => $SAMPLE_SUPPLIER_NAME, value => '8AJ1'}, {attribute => $SAMPLE_SUPPLIER_NAME, value => '8R163'}, + {attribute => $SAMPLE_UUID, value => 'd3a59c4c-c037-11e0-834c-00144f01a414'}, + {attribute => $SAMPLE_UUID, value => 'd41d4a40-a521-11e3-8055-3c4a9275d6c6'}, + {attribute => $SAMPLE_UUID, value => 'd492a150-a521-11e3-8055-3c4a9275d6c6'}, + {attribute => $SAMPLE_UUID, value => 'd4ee2ed0-a521-11e3-8055-3c4a9275d6c6'}, + {attribute => $SAMPLE_UUID, value => 'd62d8ca0-a521-11e3-8055-3c4a9275d6c6'}, {attribute => $STUDY_NAME, value => 'Illumina Controls'}, {attribute => $STUDY_NAME, value => 'SEQCAP_Lebanon_LowCov-seq'}, @@ -1274,6 +1353,7 @@ sub update_secondary_metadata_tag81_no_spike_human : Test(12) { {attribute => $SAMPLE_DONOR_ID, value => 'T19PG5759041'}, {attribute => $SAMPLE_ID, value => '1877285'}, {attribute => $SAMPLE_SUPPLIER_NAME, value => '7R5'}, + {attribute => $SAMPLE_UUID, value => 'd41d4a40-a521-11e3-8055-3c4a9275d6c6'}, {attribute => $STUDY_NAME, value => 'SEQCAP_Lebanon_LowCov-seq'}, {attribute => $STUDY_ACCESSION_NUMBER, value => 'EGAS00001002084'}, @@ -1332,6 +1412,7 @@ sub update_secondary_metadata_tag81_spike_human : Test(12) { {attribute => $SAMPLE_DONOR_ID, value => 'T19PG5759041'}, {attribute => $SAMPLE_ID, value => '1877285'}, {attribute => $SAMPLE_SUPPLIER_NAME, value => '7R5'}, + {attribute => $SAMPLE_UUID, value => 'd41d4a40-a521-11e3-8055-3c4a9275d6c6'}, {attribute => $STUDY_NAME, value => 'SEQCAP_Lebanon_LowCov-seq'}, {attribute => $STUDY_ACCESSION_NUMBER, value => 'EGAS00001002084'}, From 9d943069cc811a2326797f444f979e02b5e165e3 Mon Sep 17 00:00:00 2001 From: Marco Mosca Date: Tue, 10 Dec 2024 15:48:23 +0000 Subject: [PATCH 07/10] Fix indentation in AlnDataObjectTest --- .../NPG/HTS/Illumina/AlnDataObjectTest.pm | 156 +++++++++--------- 1 file changed, 78 insertions(+), 78 deletions(-) diff --git a/t/lib/WTSI/NPG/HTS/Illumina/AlnDataObjectTest.pm b/t/lib/WTSI/NPG/HTS/Illumina/AlnDataObjectTest.pm index 57a29f70..88bc3523 100644 --- a/t/lib/WTSI/NPG/HTS/Illumina/AlnDataObjectTest.pm +++ b/t/lib/WTSI/NPG/HTS/Illumina/AlnDataObjectTest.pm @@ -714,38 +714,38 @@ sub update_secondary_metadata_tag0_no_spike_bact : Test(12) { {attribute => $SAMPLE_PUBLIC_NAME, value => 'P73230-3018'}, {attribute => $SAMPLE_PUBLIC_NAME, value => 'SOIL'}, {attribute => $SAMPLE_UUID, value => 'a8b4ebaa-c628-11df-8e7f-00144f2062b0'}, - {attribute => $SAMPLE_UUID, value => 'a8b4f3ac-c628-11df-8e7f-00144f2062b0'}, - {attribute => $SAMPLE_UUID, value => 'a8b4fbae-c628-11df-8e7f-00144f2062b0'}, - {attribute => $SAMPLE_UUID, value => 'a8b503a6-c628-11df-8e7f-00144f2062b0'}, - {attribute => $SAMPLE_UUID, value => 'a8b50b9e-c628-11df-8e7f-00144f2062b0'}, - {attribute => $SAMPLE_UUID, value => 'a8b51396-c628-11df-8e7f-00144f2062b0'}, - {attribute => $SAMPLE_UUID, value => 'a8b51ba2-c628-11df-8e7f-00144f2062b0'}, - {attribute => $SAMPLE_UUID, value => 'a8b5239a-c628-11df-8e7f-00144f2062b0'}, - {attribute => $SAMPLE_UUID, value => 'a8b52b92-c628-11df-8e7f-00144f2062b0'}, - {attribute => $SAMPLE_UUID, value => 'a8b5338a-c628-11df-8e7f-00144f2062b0'}, - {attribute => $SAMPLE_UUID, value => 'a8b53b82-c628-11df-8e7f-00144f2062b0'}, - {attribute => $SAMPLE_UUID, value => 'a8b5437a-c628-11df-8e7f-00144f2062b0'}, - {attribute => $SAMPLE_UUID, value => 'a8b54b7c-c628-11df-8e7f-00144f2062b0'}, - {attribute => $SAMPLE_UUID, value => 'a8b55374-c628-11df-8e7f-00144f2062b0'}, - {attribute => $SAMPLE_UUID, value => 'a8b55b94-c628-11df-8e7f-00144f2062b0'}, - {attribute => $SAMPLE_UUID, value => 'a8b5638c-c628-11df-8e7f-00144f2062b0'}, - {attribute => $SAMPLE_UUID, value => 'a8b56bb6-c628-11df-8e7f-00144f2062b0'}, - {attribute => $SAMPLE_UUID, value => 'a8b573ae-c628-11df-8e7f-00144f2062b0'}, - {attribute => $SAMPLE_UUID, value => 'a8b57bb0-c628-11df-8e7f-00144f2062b0'}, - {attribute => $SAMPLE_UUID, value => 'a8b583a8-c628-11df-8e7f-00144f2062b0'}, - {attribute => $SAMPLE_UUID, value => 'a8b58b96-c628-11df-8e7f-00144f2062b0'}, - {attribute => $SAMPLE_UUID, value => 'a8b5938e-c628-11df-8e7f-00144f2062b0'}, - {attribute => $SAMPLE_UUID, value => 'a8b59b86-c628-11df-8e7f-00144f2062b0'}, - {attribute => $SAMPLE_UUID, value => 'a8b5a37e-c628-11df-8e7f-00144f2062b0'}, - {attribute => $SAMPLE_UUID, value => 'a8b5ab6c-c628-11df-8e7f-00144f2062b0'}, - {attribute => $SAMPLE_UUID, value => 'a8b5b364-c628-11df-8e7f-00144f2062b0'}, - {attribute => $SAMPLE_UUID, value => 'a8b5bb5c-c628-11df-8e7f-00144f2062b0'}, - {attribute => $SAMPLE_UUID, value => 'a8b5c35e-c628-11df-8e7f-00144f2062b0'}, - {attribute => $SAMPLE_UUID, value => 'a8b5cb4c-c628-11df-8e7f-00144f2062b0'}, - {attribute => $SAMPLE_UUID, value => 'a8b5d34e-c628-11df-8e7f-00144f2062b0'}, - {attribute => $SAMPLE_UUID, value => 'a8b5db46-c628-11df-8e7f-00144f2062b0'}, - {attribute => $SAMPLE_UUID, value => 'a8b5e352-c628-11df-8e7f-00144f2062b0'}, - {attribute => $SAMPLE_UUID, value => 'a8b5eb54-c628-11df-8e7f-00144f2062b0'}, + {attribute => $SAMPLE_UUID, value => 'a8b4f3ac-c628-11df-8e7f-00144f2062b0'}, + {attribute => $SAMPLE_UUID, value => 'a8b4fbae-c628-11df-8e7f-00144f2062b0'}, + {attribute => $SAMPLE_UUID, value => 'a8b503a6-c628-11df-8e7f-00144f2062b0'}, + {attribute => $SAMPLE_UUID, value => 'a8b50b9e-c628-11df-8e7f-00144f2062b0'}, + {attribute => $SAMPLE_UUID, value => 'a8b51396-c628-11df-8e7f-00144f2062b0'}, + {attribute => $SAMPLE_UUID, value => 'a8b51ba2-c628-11df-8e7f-00144f2062b0'}, + {attribute => $SAMPLE_UUID, value => 'a8b5239a-c628-11df-8e7f-00144f2062b0'}, + {attribute => $SAMPLE_UUID, value => 'a8b52b92-c628-11df-8e7f-00144f2062b0'}, + {attribute => $SAMPLE_UUID, value => 'a8b5338a-c628-11df-8e7f-00144f2062b0'}, + {attribute => $SAMPLE_UUID, value => 'a8b53b82-c628-11df-8e7f-00144f2062b0'}, + {attribute => $SAMPLE_UUID, value => 'a8b5437a-c628-11df-8e7f-00144f2062b0'}, + {attribute => $SAMPLE_UUID, value => 'a8b54b7c-c628-11df-8e7f-00144f2062b0'}, + {attribute => $SAMPLE_UUID, value => 'a8b55374-c628-11df-8e7f-00144f2062b0'}, + {attribute => $SAMPLE_UUID, value => 'a8b55b94-c628-11df-8e7f-00144f2062b0'}, + {attribute => $SAMPLE_UUID, value => 'a8b5638c-c628-11df-8e7f-00144f2062b0'}, + {attribute => $SAMPLE_UUID, value => 'a8b56bb6-c628-11df-8e7f-00144f2062b0'}, + {attribute => $SAMPLE_UUID, value => 'a8b573ae-c628-11df-8e7f-00144f2062b0'}, + {attribute => $SAMPLE_UUID, value => 'a8b57bb0-c628-11df-8e7f-00144f2062b0'}, + {attribute => $SAMPLE_UUID, value => 'a8b583a8-c628-11df-8e7f-00144f2062b0'}, + {attribute => $SAMPLE_UUID, value => 'a8b58b96-c628-11df-8e7f-00144f2062b0'}, + {attribute => $SAMPLE_UUID, value => 'a8b5938e-c628-11df-8e7f-00144f2062b0'}, + {attribute => $SAMPLE_UUID, value => 'a8b59b86-c628-11df-8e7f-00144f2062b0'}, + {attribute => $SAMPLE_UUID, value => 'a8b5a37e-c628-11df-8e7f-00144f2062b0'}, + {attribute => $SAMPLE_UUID, value => 'a8b5ab6c-c628-11df-8e7f-00144f2062b0'}, + {attribute => $SAMPLE_UUID, value => 'a8b5b364-c628-11df-8e7f-00144f2062b0'}, + {attribute => $SAMPLE_UUID, value => 'a8b5bb5c-c628-11df-8e7f-00144f2062b0'}, + {attribute => $SAMPLE_UUID, value => 'a8b5c35e-c628-11df-8e7f-00144f2062b0'}, + {attribute => $SAMPLE_UUID, value => 'a8b5cb4c-c628-11df-8e7f-00144f2062b0'}, + {attribute => $SAMPLE_UUID, value => 'a8b5d34e-c628-11df-8e7f-00144f2062b0'}, + {attribute => $SAMPLE_UUID, value => 'a8b5db46-c628-11df-8e7f-00144f2062b0'}, + {attribute => $SAMPLE_UUID, value => 'a8b5e352-c628-11df-8e7f-00144f2062b0'}, + {attribute => $SAMPLE_UUID, value => 'a8b5eb54-c628-11df-8e7f-00144f2062b0'}, {attribute => $STUDY_NAME, value => 'Burkholderia pseudomallei diversity'}, {attribute => $STUDY_ACCESSION_NUMBER, value => 'ERP000251'}, @@ -971,40 +971,40 @@ sub update_secondary_metadata_tag0_spike_bact : Test(12) { {attribute => $SAMPLE_PUBLIC_NAME, value => 'K11277244-293'}, {attribute => $SAMPLE_PUBLIC_NAME, value => 'P73230-3018'}, {attribute => $SAMPLE_PUBLIC_NAME, value => 'SOIL'}, - {attribute => $SAMPLE_UUID, value => 'a8b4ebaa-c628-11df-8e7f-00144f2062b0'}, - {attribute => $SAMPLE_UUID, value => 'a8b4f3ac-c628-11df-8e7f-00144f2062b0'}, - {attribute => $SAMPLE_UUID, value => 'a8b4fbae-c628-11df-8e7f-00144f2062b0'}, - {attribute => $SAMPLE_UUID, value => 'a8b503a6-c628-11df-8e7f-00144f2062b0'}, - {attribute => $SAMPLE_UUID, value => 'a8b50b9e-c628-11df-8e7f-00144f2062b0'}, - {attribute => $SAMPLE_UUID, value => 'a8b51396-c628-11df-8e7f-00144f2062b0'}, - {attribute => $SAMPLE_UUID, value => 'a8b51ba2-c628-11df-8e7f-00144f2062b0'}, - {attribute => $SAMPLE_UUID, value => 'a8b5239a-c628-11df-8e7f-00144f2062b0'}, - {attribute => $SAMPLE_UUID, value => 'a8b52b92-c628-11df-8e7f-00144f2062b0'}, - {attribute => $SAMPLE_UUID, value => 'a8b5338a-c628-11df-8e7f-00144f2062b0'}, - {attribute => $SAMPLE_UUID, value => 'a8b53b82-c628-11df-8e7f-00144f2062b0'}, - {attribute => $SAMPLE_UUID, value => 'a8b5437a-c628-11df-8e7f-00144f2062b0'}, - {attribute => $SAMPLE_UUID, value => 'a8b54b7c-c628-11df-8e7f-00144f2062b0'}, - {attribute => $SAMPLE_UUID, value => 'a8b55374-c628-11df-8e7f-00144f2062b0'}, - {attribute => $SAMPLE_UUID, value => 'a8b55b94-c628-11df-8e7f-00144f2062b0'}, - {attribute => $SAMPLE_UUID, value => 'a8b5638c-c628-11df-8e7f-00144f2062b0'}, - {attribute => $SAMPLE_UUID, value => 'a8b56bb6-c628-11df-8e7f-00144f2062b0'}, - {attribute => $SAMPLE_UUID, value => 'a8b573ae-c628-11df-8e7f-00144f2062b0'}, - {attribute => $SAMPLE_UUID, value => 'a8b57bb0-c628-11df-8e7f-00144f2062b0'}, - {attribute => $SAMPLE_UUID, value => 'a8b583a8-c628-11df-8e7f-00144f2062b0'}, - {attribute => $SAMPLE_UUID, value => 'a8b58b96-c628-11df-8e7f-00144f2062b0'}, - {attribute => $SAMPLE_UUID, value => 'a8b5938e-c628-11df-8e7f-00144f2062b0'}, - {attribute => $SAMPLE_UUID, value => 'a8b59b86-c628-11df-8e7f-00144f2062b0'}, - {attribute => $SAMPLE_UUID, value => 'a8b5a37e-c628-11df-8e7f-00144f2062b0'}, - {attribute => $SAMPLE_UUID, value => 'a8b5ab6c-c628-11df-8e7f-00144f2062b0'}, - {attribute => $SAMPLE_UUID, value => 'a8b5b364-c628-11df-8e7f-00144f2062b0'}, - {attribute => $SAMPLE_UUID, value => 'a8b5bb5c-c628-11df-8e7f-00144f2062b0'}, - {attribute => $SAMPLE_UUID, value => 'a8b5c35e-c628-11df-8e7f-00144f2062b0'}, - {attribute => $SAMPLE_UUID, value => 'a8b5cb4c-c628-11df-8e7f-00144f2062b0'}, - {attribute => $SAMPLE_UUID, value => 'a8b5d34e-c628-11df-8e7f-00144f2062b0'}, - {attribute => $SAMPLE_UUID, value => 'a8b5db46-c628-11df-8e7f-00144f2062b0'}, - {attribute => $SAMPLE_UUID, value => 'a8b5e352-c628-11df-8e7f-00144f2062b0'}, - {attribute => $SAMPLE_UUID, value => 'a8b5eb54-c628-11df-8e7f-00144f2062b0'}, - {attribute => $SAMPLE_UUID, value => 'd3a59c4c-c037-11e0-834c-00144f01a414'}, + {attribute => $SAMPLE_UUID, value => 'a8b4ebaa-c628-11df-8e7f-00144f2062b0'}, + {attribute => $SAMPLE_UUID, value => 'a8b4f3ac-c628-11df-8e7f-00144f2062b0'}, + {attribute => $SAMPLE_UUID, value => 'a8b4fbae-c628-11df-8e7f-00144f2062b0'}, + {attribute => $SAMPLE_UUID, value => 'a8b503a6-c628-11df-8e7f-00144f2062b0'}, + {attribute => $SAMPLE_UUID, value => 'a8b50b9e-c628-11df-8e7f-00144f2062b0'}, + {attribute => $SAMPLE_UUID, value => 'a8b51396-c628-11df-8e7f-00144f2062b0'}, + {attribute => $SAMPLE_UUID, value => 'a8b51ba2-c628-11df-8e7f-00144f2062b0'}, + {attribute => $SAMPLE_UUID, value => 'a8b5239a-c628-11df-8e7f-00144f2062b0'}, + {attribute => $SAMPLE_UUID, value => 'a8b52b92-c628-11df-8e7f-00144f2062b0'}, + {attribute => $SAMPLE_UUID, value => 'a8b5338a-c628-11df-8e7f-00144f2062b0'}, + {attribute => $SAMPLE_UUID, value => 'a8b53b82-c628-11df-8e7f-00144f2062b0'}, + {attribute => $SAMPLE_UUID, value => 'a8b5437a-c628-11df-8e7f-00144f2062b0'}, + {attribute => $SAMPLE_UUID, value => 'a8b54b7c-c628-11df-8e7f-00144f2062b0'}, + {attribute => $SAMPLE_UUID, value => 'a8b55374-c628-11df-8e7f-00144f2062b0'}, + {attribute => $SAMPLE_UUID, value => 'a8b55b94-c628-11df-8e7f-00144f2062b0'}, + {attribute => $SAMPLE_UUID, value => 'a8b5638c-c628-11df-8e7f-00144f2062b0'}, + {attribute => $SAMPLE_UUID, value => 'a8b56bb6-c628-11df-8e7f-00144f2062b0'}, + {attribute => $SAMPLE_UUID, value => 'a8b573ae-c628-11df-8e7f-00144f2062b0'}, + {attribute => $SAMPLE_UUID, value => 'a8b57bb0-c628-11df-8e7f-00144f2062b0'}, + {attribute => $SAMPLE_UUID, value => 'a8b583a8-c628-11df-8e7f-00144f2062b0'}, + {attribute => $SAMPLE_UUID, value => 'a8b58b96-c628-11df-8e7f-00144f2062b0'}, + {attribute => $SAMPLE_UUID, value => 'a8b5938e-c628-11df-8e7f-00144f2062b0'}, + {attribute => $SAMPLE_UUID, value => 'a8b59b86-c628-11df-8e7f-00144f2062b0'}, + {attribute => $SAMPLE_UUID, value => 'a8b5a37e-c628-11df-8e7f-00144f2062b0'}, + {attribute => $SAMPLE_UUID, value => 'a8b5ab6c-c628-11df-8e7f-00144f2062b0'}, + {attribute => $SAMPLE_UUID, value => 'a8b5b364-c628-11df-8e7f-00144f2062b0'}, + {attribute => $SAMPLE_UUID, value => 'a8b5bb5c-c628-11df-8e7f-00144f2062b0'}, + {attribute => $SAMPLE_UUID, value => 'a8b5c35e-c628-11df-8e7f-00144f2062b0'}, + {attribute => $SAMPLE_UUID, value => 'a8b5cb4c-c628-11df-8e7f-00144f2062b0'}, + {attribute => $SAMPLE_UUID, value => 'a8b5d34e-c628-11df-8e7f-00144f2062b0'}, + {attribute => $SAMPLE_UUID, value => 'a8b5db46-c628-11df-8e7f-00144f2062b0'}, + {attribute => $SAMPLE_UUID, value => 'a8b5e352-c628-11df-8e7f-00144f2062b0'}, + {attribute => $SAMPLE_UUID, value => 'a8b5eb54-c628-11df-8e7f-00144f2062b0'}, + {attribute => $SAMPLE_UUID, value => 'd3a59c4c-c037-11e0-834c-00144f01a414'}, {attribute => $STUDY_NAME, value => 'Burkholderia pseudomallei diversity'}, {attribute => $STUDY_NAME, @@ -1126,7 +1126,7 @@ sub update_secondary_metadata_tag1_spike_bact : Test(12) { value => 'Burkholderia pseudomallei'}, {attribute => $SAMPLE_ID, value => '230889'}, {attribute => $SAMPLE_PUBLIC_NAME, value => '153.0'}, - {attribute => $SAMPLE_UUID, value => 'a8b4ebaa-c628-11df-8e7f-00144f2062b0'}, + {attribute => $SAMPLE_UUID, value => 'a8b4ebaa-c628-11df-8e7f-00144f2062b0'}, {attribute => $STUDY_NAME, value => 'Burkholderia pseudomallei diversity'}, {attribute => $STUDY_ACCESSION_NUMBER, value => 'ERP000251'}, @@ -1203,10 +1203,10 @@ sub update_secondary_metadata_tag0_no_spike_human : Test(12) { {attribute => $SAMPLE_SUPPLIER_NAME, value => '7R5'}, {attribute => $SAMPLE_SUPPLIER_NAME, value => '8AJ1'}, {attribute => $SAMPLE_SUPPLIER_NAME, value => '8R163'}, - {attribute => $SAMPLE_UUID, value => 'd41d4a40-a521-11e3-8055-3c4a9275d6c6'}, - {attribute => $SAMPLE_UUID, value => 'd492a150-a521-11e3-8055-3c4a9275d6c6'}, - {attribute => $SAMPLE_UUID, value => 'd4ee2ed0-a521-11e3-8055-3c4a9275d6c6'}, - {attribute => $SAMPLE_UUID, value => 'd62d8ca0-a521-11e3-8055-3c4a9275d6c6'}, + {attribute => $SAMPLE_UUID, value => 'd41d4a40-a521-11e3-8055-3c4a9275d6c6'}, + {attribute => $SAMPLE_UUID, value => 'd492a150-a521-11e3-8055-3c4a9275d6c6'}, + {attribute => $SAMPLE_UUID, value => 'd4ee2ed0-a521-11e3-8055-3c4a9275d6c6'}, + {attribute => $SAMPLE_UUID, value => 'd62d8ca0-a521-11e3-8055-3c4a9275d6c6'}, {attribute => $STUDY_NAME, value => 'SEQCAP_Lebanon_LowCov-seq'}, {attribute => $STUDY_ACCESSION_NUMBER, value => 'EGAS00001002084'}, @@ -1287,11 +1287,11 @@ sub update_secondary_metadata_tag0_spike_human : Test(12) { {attribute => $SAMPLE_SUPPLIER_NAME, value => '7R5'}, {attribute => $SAMPLE_SUPPLIER_NAME, value => '8AJ1'}, {attribute => $SAMPLE_SUPPLIER_NAME, value => '8R163'}, - {attribute => $SAMPLE_UUID, value => 'd3a59c4c-c037-11e0-834c-00144f01a414'}, - {attribute => $SAMPLE_UUID, value => 'd41d4a40-a521-11e3-8055-3c4a9275d6c6'}, - {attribute => $SAMPLE_UUID, value => 'd492a150-a521-11e3-8055-3c4a9275d6c6'}, - {attribute => $SAMPLE_UUID, value => 'd4ee2ed0-a521-11e3-8055-3c4a9275d6c6'}, - {attribute => $SAMPLE_UUID, value => 'd62d8ca0-a521-11e3-8055-3c4a9275d6c6'}, + {attribute => $SAMPLE_UUID, value => 'd3a59c4c-c037-11e0-834c-00144f01a414'}, + {attribute => $SAMPLE_UUID, value => 'd41d4a40-a521-11e3-8055-3c4a9275d6c6'}, + {attribute => $SAMPLE_UUID, value => 'd492a150-a521-11e3-8055-3c4a9275d6c6'}, + {attribute => $SAMPLE_UUID, value => 'd4ee2ed0-a521-11e3-8055-3c4a9275d6c6'}, + {attribute => $SAMPLE_UUID, value => 'd62d8ca0-a521-11e3-8055-3c4a9275d6c6'}, {attribute => $STUDY_NAME, value => 'Illumina Controls'}, {attribute => $STUDY_NAME, value => 'SEQCAP_Lebanon_LowCov-seq'}, @@ -1353,7 +1353,7 @@ sub update_secondary_metadata_tag81_no_spike_human : Test(12) { {attribute => $SAMPLE_DONOR_ID, value => 'T19PG5759041'}, {attribute => $SAMPLE_ID, value => '1877285'}, {attribute => $SAMPLE_SUPPLIER_NAME, value => '7R5'}, - {attribute => $SAMPLE_UUID, value => 'd41d4a40-a521-11e3-8055-3c4a9275d6c6'}, + {attribute => $SAMPLE_UUID, value => 'd41d4a40-a521-11e3-8055-3c4a9275d6c6'}, {attribute => $STUDY_NAME, value => 'SEQCAP_Lebanon_LowCov-seq'}, {attribute => $STUDY_ACCESSION_NUMBER, value => 'EGAS00001002084'}, @@ -1412,7 +1412,7 @@ sub update_secondary_metadata_tag81_spike_human : Test(12) { {attribute => $SAMPLE_DONOR_ID, value => 'T19PG5759041'}, {attribute => $SAMPLE_ID, value => '1877285'}, {attribute => $SAMPLE_SUPPLIER_NAME, value => '7R5'}, - {attribute => $SAMPLE_UUID, value => 'd41d4a40-a521-11e3-8055-3c4a9275d6c6'}, + {attribute => $SAMPLE_UUID, value => 'd41d4a40-a521-11e3-8055-3c4a9275d6c6'}, {attribute => $STUDY_NAME, value => 'SEQCAP_Lebanon_LowCov-seq'}, {attribute => $STUDY_ACCESSION_NUMBER, value => 'EGAS00001002084'}, From e69637c7c7ececabb014c02b73bb0f72ab7d5efa Mon Sep 17 00:00:00 2001 From: Marco Mosca Date: Wed, 11 Dec 2024 12:35:52 +0000 Subject: [PATCH 08/10] Add sample_lims for Illumina Annotator --- lib/WTSI/NPG/HTS/Illumina/Annotator.pm | 1 + t/lib/WTSI/NPG/HTS/Illumina/AlnDataObjectTest.pm | 9 +++++++++ t/lib/WTSI/NPG/HTS/Illumina/MetaUpdaterTest.pm | 1 + 3 files changed, 11 insertions(+) diff --git a/lib/WTSI/NPG/HTS/Illumina/Annotator.pm b/lib/WTSI/NPG/HTS/Illumina/Annotator.pm index 3e8b8f74..1da049dd 100644 --- a/lib/WTSI/NPG/HTS/Illumina/Annotator.pm +++ b/lib/WTSI/NPG/HTS/Illumina/Annotator.pm @@ -418,6 +418,7 @@ sub make_sample_metadata { my $method_attr = {sample_accession_numbers => $SAMPLE_ACCESSION_NUMBER, sample_ids => $SAMPLE_ID, + sample_lims => $SAMPLE_LIMS, sample_names => $SAMPLE_NAME, sample_public_names => $SAMPLE_PUBLIC_NAME, sample_common_names => $SAMPLE_COMMON_NAME, diff --git a/t/lib/WTSI/NPG/HTS/Illumina/AlnDataObjectTest.pm b/t/lib/WTSI/NPG/HTS/Illumina/AlnDataObjectTest.pm index 88bc3523..9a254db2 100644 --- a/t/lib/WTSI/NPG/HTS/Illumina/AlnDataObjectTest.pm +++ b/t/lib/WTSI/NPG/HTS/Illumina/AlnDataObjectTest.pm @@ -374,6 +374,7 @@ sub nonconsented_human_access_revoked : Test(6) { {attribute => $SAMPLE_COMMON_NAME, value => 'Burkholderia pseudomallei'}, {attribute => $SAMPLE_ID, value => '230889'}, + {attribute => $SAMPLE_LIMS, value => 'SQSCP'}, {attribute => $SAMPLE_PUBLIC_NAME, value => '153.0'}, {attribute => $SAMPLE_UUID, value => 'a8b4ebaa-c628-11df-8e7f-00144f2062b0'}, {attribute => $STUDY_NAME, @@ -680,6 +681,7 @@ sub update_secondary_metadata_tag0_no_spike_bact : Test(12) { {attribute => $SAMPLE_ID, value => '230919'}, {attribute => $SAMPLE_ID, value => '230920'}, {attribute => $SAMPLE_ID, value => '230921'}, + {attribute => $SAMPLE_LIMS, value => 'SQSCP'}, {attribute => $SAMPLE_PUBLIC_NAME, value => '10/96'}, {attribute => $SAMPLE_PUBLIC_NAME, value => '109/96'}, {attribute => $SAMPLE_PUBLIC_NAME, value => '15/96'}, @@ -938,6 +940,7 @@ sub update_secondary_metadata_tag0_spike_bact : Test(12) { {attribute => $SAMPLE_ID, value => '230919'}, {attribute => $SAMPLE_ID, value => '230920'}, {attribute => $SAMPLE_ID, value => '230921'}, + {attribute => $SAMPLE_LIMS, value => 'SQSCP'}, {attribute => $SAMPLE_PUBLIC_NAME, value => '10/96'}, {attribute => $SAMPLE_PUBLIC_NAME, value => '109/96'}, {attribute => $SAMPLE_PUBLIC_NAME, value => '15/96'}, @@ -1066,6 +1069,7 @@ sub update_secondary_metadata_tag1_no_spike_bact : Test(12) { {attribute => $SAMPLE_COMMON_NAME, value => 'Burkholderia pseudomallei'}, {attribute => $SAMPLE_ID, value => '230889'}, + {attribute => $SAMPLE_LIMS, value => 'SQSCP'}, {attribute => $SAMPLE_PUBLIC_NAME, value => '153.0'}, {attribute => $SAMPLE_UUID, value => 'a8b4ebaa-c628-11df-8e7f-00144f2062b0'}, {attribute => $STUDY_NAME, @@ -1125,6 +1129,7 @@ sub update_secondary_metadata_tag1_spike_bact : Test(12) { {attribute => $SAMPLE_COMMON_NAME, value => 'Burkholderia pseudomallei'}, {attribute => $SAMPLE_ID, value => '230889'}, + {attribute => $SAMPLE_LIMS, value => 'SQSCP'}, {attribute => $SAMPLE_PUBLIC_NAME, value => '153.0'}, {attribute => $SAMPLE_UUID, value => 'a8b4ebaa-c628-11df-8e7f-00144f2062b0'}, {attribute => $STUDY_NAME, @@ -1199,6 +1204,7 @@ sub update_secondary_metadata_tag0_no_spike_human : Test(12) { {attribute => $SAMPLE_ID, value => '1877289'}, {attribute => $SAMPLE_ID, value => '1877292'}, {attribute => $SAMPLE_ID, value => '1877306'}, + {attribute => $SAMPLE_LIMS, value => 'SQSCP'}, {attribute => $SAMPLE_SUPPLIER_NAME, value => '6AJ182'}, {attribute => $SAMPLE_SUPPLIER_NAME, value => '7R5'}, {attribute => $SAMPLE_SUPPLIER_NAME, value => '8AJ1'}, @@ -1283,6 +1289,7 @@ sub update_secondary_metadata_tag0_spike_human : Test(12) { {attribute => $SAMPLE_ID, value => '1877289'}, {attribute => $SAMPLE_ID, value => '1877292'}, {attribute => $SAMPLE_ID, value => '1877306'}, + {attribute => $SAMPLE_LIMS, value => 'SQSCP'}, {attribute => $SAMPLE_SUPPLIER_NAME, value => '6AJ182'}, {attribute => $SAMPLE_SUPPLIER_NAME, value => '7R5'}, {attribute => $SAMPLE_SUPPLIER_NAME, value => '8AJ1'}, @@ -1352,6 +1359,7 @@ sub update_secondary_metadata_tag81_no_spike_human : Test(12) { {attribute => $SAMPLE_COMMON_NAME, value => 'Homo Sapien'}, {attribute => $SAMPLE_DONOR_ID, value => 'T19PG5759041'}, {attribute => $SAMPLE_ID, value => '1877285'}, + {attribute => $SAMPLE_LIMS, value => 'SQSCP'}, {attribute => $SAMPLE_SUPPLIER_NAME, value => '7R5'}, {attribute => $SAMPLE_UUID, value => 'd41d4a40-a521-11e3-8055-3c4a9275d6c6'}, {attribute => $STUDY_NAME, @@ -1411,6 +1419,7 @@ sub update_secondary_metadata_tag81_spike_human : Test(12) { {attribute => $SAMPLE_COMMON_NAME, value => 'Homo Sapien'}, {attribute => $SAMPLE_DONOR_ID, value => 'T19PG5759041'}, {attribute => $SAMPLE_ID, value => '1877285'}, + {attribute => $SAMPLE_LIMS, value => 'SQSCP'}, {attribute => $SAMPLE_SUPPLIER_NAME, value => '7R5'}, {attribute => $SAMPLE_UUID, value => 'd41d4a40-a521-11e3-8055-3c4a9275d6c6'}, {attribute => $STUDY_NAME, diff --git a/t/lib/WTSI/NPG/HTS/Illumina/MetaUpdaterTest.pm b/t/lib/WTSI/NPG/HTS/Illumina/MetaUpdaterTest.pm index c764e7ea..defc14e1 100644 --- a/t/lib/WTSI/NPG/HTS/Illumina/MetaUpdaterTest.pm +++ b/t/lib/WTSI/NPG/HTS/Illumina/MetaUpdaterTest.pm @@ -139,6 +139,7 @@ sub update_secondary_metadata : Test(5) { { attribute => $SAMPLE_COMMON_NAME, value => 'Burkholderia pseudomallei' }, { attribute => $SAMPLE_ID, value => '230889' }, + { attribute => $SAMPLE_LIMS, value => 'SQSCP' }, { attribute => $SAMPLE_PUBLIC_NAME, value => '153.0' }, { attribute => $SAMPLE_UUID, value => 'a8b4ebaa-c628-11df-8e7f-00144f2062b0' }, { attribute => $STUDY_NAME, From 4b74b780ed16a361d38a169e8946d6104b7a3e73 Mon Sep 17 00:00:00 2001 From: Marco Mosca Date: Wed, 11 Dec 2024 13:06:14 +0000 Subject: [PATCH 09/10] Update tests in AgfDataObjectTest for sample_lims --- t/lib/WTSI/NPG/HTS/Illumina/AgfDataObjectTest.pm | 1 + 1 file changed, 1 insertion(+) diff --git a/t/lib/WTSI/NPG/HTS/Illumina/AgfDataObjectTest.pm b/t/lib/WTSI/NPG/HTS/Illumina/AgfDataObjectTest.pm index ac918f6b..0c3c66bd 100644 --- a/t/lib/WTSI/NPG/HTS/Illumina/AgfDataObjectTest.pm +++ b/t/lib/WTSI/NPG/HTS/Illumina/AgfDataObjectTest.pm @@ -221,6 +221,7 @@ sub update_secondary_metadata_tag1_no_spike_human : Test(12) { {attribute => $SAMPLE_COMMON_NAME, value => 'Mus musculus'}, {attribute => $SAMPLE_DONOR_ID, value => '2905STDY6178180'}, {attribute => $SAMPLE_ID, value => '2376982'}, + {attribute => $SAMPLE_LIMS, value => 'SQSCP'}, {attribute => $SAMPLE_PUBLIC_NAME, value => 'UTX_IP_UTX_GTX_A'}, {attribute => $SAMPLE_SUPPLIER_NAME, value => 'UTX_IP_UTX_GTX_A'}, {attribute => $SAMPLE_UUID, value => '4e0f6640-40f7-11e5-998e-3c4a9275d6c6'}, From fcbff2d718e7fab21e742a55cf66813bbb6c51d2 Mon Sep 17 00:00:00 2001 From: Marco Mosca Date: Wed, 11 Dec 2024 13:07:49 +0000 Subject: [PATCH 10/10] Fix indentation in AlnDataObjectTest for sample_uuid attributes --- .../NPG/HTS/Illumina/AlnDataObjectTest.pm | 68 +++++++++---------- 1 file changed, 34 insertions(+), 34 deletions(-) diff --git a/t/lib/WTSI/NPG/HTS/Illumina/AlnDataObjectTest.pm b/t/lib/WTSI/NPG/HTS/Illumina/AlnDataObjectTest.pm index 9a254db2..971449a7 100644 --- a/t/lib/WTSI/NPG/HTS/Illumina/AlnDataObjectTest.pm +++ b/t/lib/WTSI/NPG/HTS/Illumina/AlnDataObjectTest.pm @@ -974,40 +974,40 @@ sub update_secondary_metadata_tag0_spike_bact : Test(12) { {attribute => $SAMPLE_PUBLIC_NAME, value => 'K11277244-293'}, {attribute => $SAMPLE_PUBLIC_NAME, value => 'P73230-3018'}, {attribute => $SAMPLE_PUBLIC_NAME, value => 'SOIL'}, - {attribute => $SAMPLE_UUID, value => 'a8b4ebaa-c628-11df-8e7f-00144f2062b0'}, - {attribute => $SAMPLE_UUID, value => 'a8b4f3ac-c628-11df-8e7f-00144f2062b0'}, - {attribute => $SAMPLE_UUID, value => 'a8b4fbae-c628-11df-8e7f-00144f2062b0'}, - {attribute => $SAMPLE_UUID, value => 'a8b503a6-c628-11df-8e7f-00144f2062b0'}, - {attribute => $SAMPLE_UUID, value => 'a8b50b9e-c628-11df-8e7f-00144f2062b0'}, - {attribute => $SAMPLE_UUID, value => 'a8b51396-c628-11df-8e7f-00144f2062b0'}, - {attribute => $SAMPLE_UUID, value => 'a8b51ba2-c628-11df-8e7f-00144f2062b0'}, - {attribute => $SAMPLE_UUID, value => 'a8b5239a-c628-11df-8e7f-00144f2062b0'}, - {attribute => $SAMPLE_UUID, value => 'a8b52b92-c628-11df-8e7f-00144f2062b0'}, - {attribute => $SAMPLE_UUID, value => 'a8b5338a-c628-11df-8e7f-00144f2062b0'}, - {attribute => $SAMPLE_UUID, value => 'a8b53b82-c628-11df-8e7f-00144f2062b0'}, - {attribute => $SAMPLE_UUID, value => 'a8b5437a-c628-11df-8e7f-00144f2062b0'}, - {attribute => $SAMPLE_UUID, value => 'a8b54b7c-c628-11df-8e7f-00144f2062b0'}, - {attribute => $SAMPLE_UUID, value => 'a8b55374-c628-11df-8e7f-00144f2062b0'}, - {attribute => $SAMPLE_UUID, value => 'a8b55b94-c628-11df-8e7f-00144f2062b0'}, - {attribute => $SAMPLE_UUID, value => 'a8b5638c-c628-11df-8e7f-00144f2062b0'}, - {attribute => $SAMPLE_UUID, value => 'a8b56bb6-c628-11df-8e7f-00144f2062b0'}, - {attribute => $SAMPLE_UUID, value => 'a8b573ae-c628-11df-8e7f-00144f2062b0'}, - {attribute => $SAMPLE_UUID, value => 'a8b57bb0-c628-11df-8e7f-00144f2062b0'}, - {attribute => $SAMPLE_UUID, value => 'a8b583a8-c628-11df-8e7f-00144f2062b0'}, - {attribute => $SAMPLE_UUID, value => 'a8b58b96-c628-11df-8e7f-00144f2062b0'}, - {attribute => $SAMPLE_UUID, value => 'a8b5938e-c628-11df-8e7f-00144f2062b0'}, - {attribute => $SAMPLE_UUID, value => 'a8b59b86-c628-11df-8e7f-00144f2062b0'}, - {attribute => $SAMPLE_UUID, value => 'a8b5a37e-c628-11df-8e7f-00144f2062b0'}, - {attribute => $SAMPLE_UUID, value => 'a8b5ab6c-c628-11df-8e7f-00144f2062b0'}, - {attribute => $SAMPLE_UUID, value => 'a8b5b364-c628-11df-8e7f-00144f2062b0'}, - {attribute => $SAMPLE_UUID, value => 'a8b5bb5c-c628-11df-8e7f-00144f2062b0'}, - {attribute => $SAMPLE_UUID, value => 'a8b5c35e-c628-11df-8e7f-00144f2062b0'}, - {attribute => $SAMPLE_UUID, value => 'a8b5cb4c-c628-11df-8e7f-00144f2062b0'}, - {attribute => $SAMPLE_UUID, value => 'a8b5d34e-c628-11df-8e7f-00144f2062b0'}, - {attribute => $SAMPLE_UUID, value => 'a8b5db46-c628-11df-8e7f-00144f2062b0'}, - {attribute => $SAMPLE_UUID, value => 'a8b5e352-c628-11df-8e7f-00144f2062b0'}, - {attribute => $SAMPLE_UUID, value => 'a8b5eb54-c628-11df-8e7f-00144f2062b0'}, - {attribute => $SAMPLE_UUID, value => 'd3a59c4c-c037-11e0-834c-00144f01a414'}, + {attribute => $SAMPLE_UUID, value => 'a8b4ebaa-c628-11df-8e7f-00144f2062b0'}, + {attribute => $SAMPLE_UUID, value => 'a8b4f3ac-c628-11df-8e7f-00144f2062b0'}, + {attribute => $SAMPLE_UUID, value => 'a8b4fbae-c628-11df-8e7f-00144f2062b0'}, + {attribute => $SAMPLE_UUID, value => 'a8b503a6-c628-11df-8e7f-00144f2062b0'}, + {attribute => $SAMPLE_UUID, value => 'a8b50b9e-c628-11df-8e7f-00144f2062b0'}, + {attribute => $SAMPLE_UUID, value => 'a8b51396-c628-11df-8e7f-00144f2062b0'}, + {attribute => $SAMPLE_UUID, value => 'a8b51ba2-c628-11df-8e7f-00144f2062b0'}, + {attribute => $SAMPLE_UUID, value => 'a8b5239a-c628-11df-8e7f-00144f2062b0'}, + {attribute => $SAMPLE_UUID, value => 'a8b52b92-c628-11df-8e7f-00144f2062b0'}, + {attribute => $SAMPLE_UUID, value => 'a8b5338a-c628-11df-8e7f-00144f2062b0'}, + {attribute => $SAMPLE_UUID, value => 'a8b53b82-c628-11df-8e7f-00144f2062b0'}, + {attribute => $SAMPLE_UUID, value => 'a8b5437a-c628-11df-8e7f-00144f2062b0'}, + {attribute => $SAMPLE_UUID, value => 'a8b54b7c-c628-11df-8e7f-00144f2062b0'}, + {attribute => $SAMPLE_UUID, value => 'a8b55374-c628-11df-8e7f-00144f2062b0'}, + {attribute => $SAMPLE_UUID, value => 'a8b55b94-c628-11df-8e7f-00144f2062b0'}, + {attribute => $SAMPLE_UUID, value => 'a8b5638c-c628-11df-8e7f-00144f2062b0'}, + {attribute => $SAMPLE_UUID, value => 'a8b56bb6-c628-11df-8e7f-00144f2062b0'}, + {attribute => $SAMPLE_UUID, value => 'a8b573ae-c628-11df-8e7f-00144f2062b0'}, + {attribute => $SAMPLE_UUID, value => 'a8b57bb0-c628-11df-8e7f-00144f2062b0'}, + {attribute => $SAMPLE_UUID, value => 'a8b583a8-c628-11df-8e7f-00144f2062b0'}, + {attribute => $SAMPLE_UUID, value => 'a8b58b96-c628-11df-8e7f-00144f2062b0'}, + {attribute => $SAMPLE_UUID, value => 'a8b5938e-c628-11df-8e7f-00144f2062b0'}, + {attribute => $SAMPLE_UUID, value => 'a8b59b86-c628-11df-8e7f-00144f2062b0'}, + {attribute => $SAMPLE_UUID, value => 'a8b5a37e-c628-11df-8e7f-00144f2062b0'}, + {attribute => $SAMPLE_UUID, value => 'a8b5ab6c-c628-11df-8e7f-00144f2062b0'}, + {attribute => $SAMPLE_UUID, value => 'a8b5b364-c628-11df-8e7f-00144f2062b0'}, + {attribute => $SAMPLE_UUID, value => 'a8b5bb5c-c628-11df-8e7f-00144f2062b0'}, + {attribute => $SAMPLE_UUID, value => 'a8b5c35e-c628-11df-8e7f-00144f2062b0'}, + {attribute => $SAMPLE_UUID, value => 'a8b5cb4c-c628-11df-8e7f-00144f2062b0'}, + {attribute => $SAMPLE_UUID, value => 'a8b5d34e-c628-11df-8e7f-00144f2062b0'}, + {attribute => $SAMPLE_UUID, value => 'a8b5db46-c628-11df-8e7f-00144f2062b0'}, + {attribute => $SAMPLE_UUID, value => 'a8b5e352-c628-11df-8e7f-00144f2062b0'}, + {attribute => $SAMPLE_UUID, value => 'a8b5eb54-c628-11df-8e7f-00144f2062b0'}, + {attribute => $SAMPLE_UUID, value => 'd3a59c4c-c037-11e0-834c-00144f01a414'}, {attribute => $STUDY_NAME, value => 'Burkholderia pseudomallei diversity'}, {attribute => $STUDY_NAME,