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Feature: sample lims and sample UUID #481

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merged 10 commits into from
Dec 13, 2024
Merged

Feature: sample lims and sample UUID #481

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b7b4025
Add sample_uuid to Illumina annotator
marcomoscasgr Nov 29, 2024
c560332
Add sample uuid to Pacbio annotator
marcomoscasgr Nov 29, 2024
dd1d09c
Update AgfDataObjectTest with sample_uuid
marcomoscasgr Dec 2, 2024
430dbe8
Update copyright for Illumina and PAcbio Annotators
marcomoscasgr Dec 2, 2024
2e30a0c
Add sample_lims for Pacbio Annotator
marcomoscasgr Dec 3, 2024
9e61010
Update tests in AlnDataObjectTest with the sample_uuid
marcomoscasgr Dec 10, 2024
9d94306
Fix indentation in AlnDataObjectTest
marcomoscasgr Dec 10, 2024
e69637c
Add sample_lims for Illumina Annotator
marcomoscasgr Dec 11, 2024
4b74b78
Update tests in AgfDataObjectTest for sample_lims
marcomoscasgr Dec 11, 2024
fcbff2d
Fix indentation in AlnDataObjectTest for sample_uuid attributes
marcomoscasgr Dec 11, 2024
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4 changes: 3 additions & 1 deletion lib/WTSI/NPG/HTS/Illumina/Annotator.pm
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Original file line number Diff line number Diff line change
Expand Up @@ -418,10 +418,12 @@ 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,
sample_supplier_names => $SAMPLE_SUPPLIER_NAME,
sample_uuids => $SAMPLE_UUID,
sample_cohorts => $SAMPLE_COHORT,
sample_donor_ids => $SAMPLE_DONOR_ID};

Expand Down Expand Up @@ -585,7 +587,7 @@ Keith James <[email protected]>, Iain Bancarz <[email protected]>

=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
Expand Down
4 changes: 3 additions & 1 deletion lib/WTSI/NPG/HTS/PacBio/Annotator.pm
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Expand Up @@ -161,6 +161,8 @@ 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,
common_name => $SAMPLE_COMMON_NAME,
Expand Down Expand Up @@ -319,7 +321,7 @@ Keith James <[email protected]>

=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
Expand Down
2 changes: 2 additions & 0 deletions t/lib/WTSI/NPG/HTS/Illumina/AgfDataObjectTest.pm
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Expand Up @@ -221,8 +221,10 @@ 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'},
{attribute => $STUDY_NAME,
value => 'Analysis of the chromatin state of mouse stem and progenitor cell compartment'},
{attribute => $STUDY_ACCESSION_NUMBER, value => 'ERP004563'},
Expand Down
90 changes: 90 additions & 0 deletions t/lib/WTSI/NPG/HTS/Illumina/AlnDataObjectTest.pm
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Original file line number Diff line number Diff line change
Expand Up @@ -374,7 +374,9 @@ 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,
value => 'Burkholderia pseudomallei diversity'},
{attribute => $STUDY_ACCESSION_NUMBER, value => 'ERP000251'},
Expand Down Expand Up @@ -679,6 +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'},
Expand Down Expand Up @@ -712,6 +715,39 @@ 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'},
Expand Down Expand Up @@ -904,6 +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'},
Expand Down Expand Up @@ -937,6 +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 => $STUDY_NAME,
value => 'Burkholderia pseudomallei diversity'},
{attribute => $STUDY_NAME,
Expand Down Expand Up @@ -998,7 +1069,9 @@ 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,
value => 'Burkholderia pseudomallei diversity'},
{attribute => $STUDY_ACCESSION_NUMBER, value => 'ERP000251'},
Expand Down Expand Up @@ -1056,7 +1129,9 @@ 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,
value => 'Burkholderia pseudomallei diversity'},
{attribute => $STUDY_ACCESSION_NUMBER, value => 'ERP000251'},
Expand Down Expand Up @@ -1129,10 +1204,15 @@ 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'},
{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'},
Expand Down Expand Up @@ -1209,10 +1289,16 @@ 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'},
{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'},
Expand Down Expand Up @@ -1273,7 +1359,9 @@ 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,
value => 'SEQCAP_Lebanon_LowCov-seq'},
{attribute => $STUDY_ACCESSION_NUMBER, value => 'EGAS00001002084'},
Expand Down Expand Up @@ -1331,7 +1419,9 @@ 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,
value => 'SEQCAP_Lebanon_LowCov-seq'},
{attribute => $STUDY_ACCESSION_NUMBER, value => 'EGAS00001002084'},
Expand Down
2 changes: 2 additions & 0 deletions t/lib/WTSI/NPG/HTS/Illumina/MetaUpdaterTest.pm
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Original file line number Diff line number Diff line change
Expand Up @@ -139,7 +139,9 @@ 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,
value => 'Burkholderia pseudomallei diversity' },
{ attribute => $STUDY_ACCESSION_NUMBER, value => 'ERP000251' },
Expand Down
2 changes: 2 additions & 0 deletions t/lib/WTSI/NPG/HTS/PacBio/MetaUpdaterTest.pm
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Original file line number Diff line number Diff line change
Expand Up @@ -109,8 +109,10 @@ 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'},
{attribute => $STUDY_NAME, value => $study_name},
{attribute => $STUDY_ACCESSION_NUMBER, value => 'ERP002372'},
{attribute => $STUDY_ID, value => $study_id},
Expand Down
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