diff --git a/Gemfile.lock b/Gemfile.lock index 866ed57ba..37686e5c0 100644 --- a/Gemfile.lock +++ b/Gemfile.lock @@ -129,7 +129,7 @@ GEM sanitize (< 7) globalid (1.2.1) activesupport (>= 6.1) - hashdiff (1.1.0) + hashdiff (1.1.1) i18n (1.14.6) concurrent-ruby (~> 1.0) io-console (0.7.2) @@ -186,7 +186,7 @@ GEM pry (>= 0.13.0) psych (5.1.2) stringio - public_suffix (6.0.0) + public_suffix (6.0.1) puma (6.4.3) nio4r (~> 2.0) racc (1.8.1) @@ -247,7 +247,7 @@ GEM regexp_parser (2.9.2) reline (0.5.10) io-console (~> 0.5) - rexml (3.3.7) + rexml (3.3.8) rspec-core (3.13.1) rspec-support (~> 3.13.0) rspec-expectations (3.13.3) @@ -284,7 +284,7 @@ GEM rack (>= 1.1) rubocop (>= 1.52.0, < 2.0) rubocop-ast (>= 1.31.1, < 2.0) - rubocop-rspec (3.0.5) + rubocop-rspec (3.1.0) rubocop (~> 1.61) ruby-graphviz (1.2.5) rexml @@ -317,7 +317,7 @@ GEM concurrent-ruby (~> 1.0) unicode-display_width (2.6.0) useragent (0.16.10) - webmock (3.23.1) + webmock (3.24.0) addressable (>= 2.8.0) crack (>= 0.3.2) hashdiff (>= 0.4.0, < 2.0.0) diff --git a/lib/tasks/create_enzymes.rake b/lib/tasks/create_enzymes.rake index 5653c1d04..c78d110ca 100644 --- a/lib/tasks/create_enzymes.rake +++ b/lib/tasks/create_enzymes.rake @@ -2,16 +2,18 @@ namespace :enzymes do task create: :environment do - Saphyr::Enzyme.create!( - [ - { name: 'Nb.BbvCI' }, - { name: 'Nb.BsmI' }, - { name: 'Nb.BsrDI' }, - { name: 'Nt.BspQI' }, - { name: 'Nb.BssSI' }, - { name: 'DLE-1' } - ] - ) + enzymes = [ + { name: 'Nb.BbvCI' }, + { name: 'Nb.BsmI' }, + { name: 'Nb.BsrDI' }, + { name: 'Nt.BspQI' }, + { name: 'Nb.BssSI' }, + { name: 'DLE-1' } + ] + + enzymes.each do |enzyme| + Saphyr::Enzyme.find_or_create_by!(enzyme) + end puts '-> Enzymes succesfully created' end diff --git a/lib/tasks/create_tags.rake b/lib/tasks/create_tags.rake index 57da01dde..c6c93bac3 100644 --- a/lib/tasks/create_tags.rake +++ b/lib/tasks/create_tags.rake @@ -28,6 +28,7 @@ namespace :tags do task ont_all: :environment do Rake::Task['tags:create:SQK-NBD114.96'].invoke Rake::Task['tags:create:SQK-RBK114.96'].invoke + Rake::Task['tags:create:SQK-PCB114.24'].invoke end desc 'Create pacbio sequel tags' @@ -786,6 +787,42 @@ namespace :tags do end puts '-> SQK-RBK114.96 tags successfully created' end + + task 'SQK-PCB114.24': :environment do + puts '-> Creating SQK-PCB114.24 tag set and tags' + set = TagSet.ont_pipeline + .find_or_create_by!(name: 'SQK-PCB114.24') + puts '-> Tag Set successfully created' + [ + { group_id: 'BP01', oligo: 'AAGAAAGTTGTCGGTGTCTTTGTG' }, + { group_id: 'BP02', oligo: 'TCGATTCCGTTTGTAGTCGTCTGT' }, + { group_id: 'BP03', oligo: 'GAGTCTTGTGTCCCAGTTACCAGG' }, + { group_id: 'BP04', oligo: 'TTCGGATTCTATCGTGTTTCCCTA' }, + { group_id: 'BP05', oligo: 'CTTGTCCAGGGTTTGTGTAACCTT' }, + { group_id: 'BP06', oligo: 'TTCTCGCAAAGGCAGAAAGTAGTC' }, + { group_id: 'BP07', oligo: 'GTGTTACCGTGGGAATGAATCCTT' }, + { group_id: 'BP08', oligo: 'TTCAGGGAACAAACCAAGTTACGT' }, + { group_id: 'BP09', oligo: 'AACTAGGCACAGCGAGTCTTGGTT' }, + { group_id: 'BP10', oligo: 'AAGCGTTGAAACCTTTGTCCTCTC' }, + { group_id: 'BP11', oligo: 'GTTTCATCTATCGGAGGGAATGGA' }, + { group_id: 'BP12', oligo: 'CAGGTAGAAAGAAGCAGAATCGGA' }, + { group_id: 'BP13', oligo: 'AGAACGACTTCCATACTCGTGTGA' }, + { group_id: 'BP14', oligo: 'AACGAGTCTCTTGGGACCCATAGA' }, + { group_id: 'BP15', oligo: 'AGGTCTACCTCGCTAACACCACTG' }, + { group_id: 'BP16', oligo: 'CGTCAACTGACAGTGGTTCGTACT' }, + { group_id: 'BP17', oligo: 'ACCCTCCAGGAAAGTACCTCTGAT' }, + { group_id: 'BP18', oligo: 'CCAAACCCAACAACCTAGATAGGC' }, + { group_id: 'BP19', oligo: 'GTTCCTCGTGCAGTGTCAAGAGAT' }, + { group_id: 'BP20', oligo: 'TTGCGTCCTGTTACGAGAACTCAT' }, + { group_id: 'BP21', oligo: 'GAGCCTCTCATTGTCCGTTCTCTA' }, + { group_id: 'BP22', oligo: 'ACCACTGCCATGTATCAAAGTACG' }, + { group_id: 'BP23', oligo: 'CTTACTACCCAGTGAACCTCCTCG' }, + { group_id: 'BP24', oligo: 'GCATAGTTCTGCATGATGGGTTAG' } + ].each do |tag_attributes| + set.tags.find_or_create_by!(tag_attributes) + end + puts '-> SQK-PCB114.24 tags successfully created' + end end task destroy: :environment do diff --git a/lib/tasks/saphyr_runs.rake b/lib/tasks/saphyr_runs.rake index 7de770151..4dd932e50 100644 --- a/lib/tasks/saphyr_runs.rake +++ b/lib/tasks/saphyr_runs.rake @@ -11,10 +11,19 @@ namespace :saphyr_runs do { sample: { name: "SaphyrSample#{i}", external_id: SecureRandom.uuid, species: "Species#{i}" }, request: { external_study_id: } } end - factory = Saphyr::RequestFactory.new(attributes) - factory.save - - # binding.pry + Sample.transaction do + attributes.each do |attr| + sample = Sample.create!(attr[:sample]) + req = Saphyr.request_factory( + sample:, + container: nil, + request_attributes: attr[:request], + resource_factory: nil, + reception: nil + ) + req.save! + end + end Saphyr::Request.find_each do |request| library = Saphyr::Library.create!(request:, saphyr_enzyme_id: 1) diff --git a/spec/lib/tasks/create_tags.rake_spec.rb b/spec/lib/tasks/create_tags.rake_spec.rb index 31b3fb285..19031c1cf 100644 --- a/spec/lib/tasks/create_tags.rake_spec.rb +++ b/spec/lib/tasks/create_tags.rake_spec.rb @@ -52,9 +52,12 @@ -> Creating SQK-RBK114.96 tag set and tags -> Tag Set successfully created -> SQK-RBK114.96 tags successfully created + -> Creating SQK-PCB114.24 tag set and tags + -> Tag Set successfully created + -> SQK-PCB114.24 tags successfully created HEREDOC ).to_stdout - expect(TagSet.count).to eq(2) + expect(TagSet.count).to eq(3) end it 'creates all of the tag sets' do @@ -95,9 +98,12 @@ -> Creating SQK-RBK114.96 tag set and tags -> Tag Set successfully created -> SQK-RBK114.96 tags successfully created + -> Creating SQK-PCB114.24 tag set and tags + -> Tag Set successfully created + -> SQK-PCB114.24 tags successfully created HEREDOC ).to_stdout - expect(TagSet.count).to eq(11) + expect(TagSet.count).to eq(12) end end end diff --git a/spec/lib/tasks/ont_data.rake_spec.rb b/spec/lib/tasks/ont_data.rake_spec.rb index d7fb03f27..64b38ef6d 100644 --- a/spec/lib/tasks/ont_data.rake_spec.rb +++ b/spec/lib/tasks/ont_data.rake_spec.rb @@ -52,6 +52,9 @@ "-> Creating SQK-RBK114.96 tag set and tags\n" \ "-> Tag Set successfully created\n" \ "-> SQK-RBK114.96 tags successfully created\n" \ + "-> Creating SQK-PCB114.24 tag set and tags\n" \ + "-> Tag Set successfully created\n" \ + "-> SQK-PCB114.24 tags successfully created\n" \ "-> Created #{expected_single_plexed_pools} single plexed pools\n" \ "-> Created #{expected_multi_plexed_pools} multiplexed pools\n" \ "-> ONT Instruments successfully created\n" \