Merge remote-tracking branch 'origin/develop' into refactor-configs-f…

…or-mq-vol-tracking
sanger · Oct 22, 2024 · b8dfddc · b8dfddc
2 parents 05e57d1 + ae7f96c
commit b8dfddc
Show file tree

Hide file tree

Showing 6 changed files with 78 additions and 21 deletions.
diff --git 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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -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" \