Merge pull request #4640 from sanger/4409-y24-379--study-setup-fields…

…-to-align-to-the-ena-database-fields Reapply "4409 y24 379 study setup fields to align to the ena databas…
sanger · Feb 5, 2025 · 8501436 · 8501436
2 parents 088dcf7 + 363ff25
commit 8501436
Show file tree

Hide file tree

Showing 20 changed files with 180 additions and 12 deletions.
diff --git a/app/api/io/study.rb b/app/api/io/study.rb
@@ -26,7 +26,7 @@ class Io::Study < Core::Io::Base
           study_metadata.commercially_available     => commercially_available
     study_metadata.data_release_study_type.name     => data_release_sort_of_study
            study_metadata.data_release_strategy     => data_release_strategy
-study_metadata.contaminated_human_data_access_group     => contaminated_human_data_access_group
+study_metadata.contaminated_human_data_access_group => contaminated_human_data_access_group
   '
   )
 end
diff --git a/app/models/api/study_io.rb b/app/models/api/study_io.rb
@@ -101,5 +101,8 @@ def render_class
     map_attribute_to_json_attribute(:data_deletion_period)
     map_attribute_to_json_attribute(:contaminated_human_data_access_group)
     with_association(:program, lookup_by: :id) { map_attribute_to_json_attribute(:name, 'programme') }
+    map_attribute_to_json_attribute(:ebi_library_strategy)
+    map_attribute_to_json_attribute(:ebi_library_source)
+    map_attribute_to_json_attribute(:ebi_library_selection)
   end
 end
diff --git a/app/models/study.rb b/app/models/study.rb
@@ -107,6 +107,10 @@ class Study < ApplicationRecord # rubocop:todo Metrics/ClassLength
 
   DATA_RELEASE_DELAY_PERIODS = ['3 months', '6 months', '9 months', '12 months', '18 months'].freeze
 
+  EBI_LIBRARY_STRATEGY_OPTIONS = Rails.configuration.ena_requirement_fields['EBI_Library_strategy']
+  EBI_LIBRARY_SOURCE_OPTIONS = Rails.configuration.ena_requirement_fields['EBI_Library_source']
+  EBI_LIBRARY_SELECTION_OPTIONS = Rails.configuration.ena_requirement_fields['EBI_Library_selection']
+
   # Class variables
   self.per_page = 500
 
@@ -214,6 +218,11 @@ class Study < ApplicationRecord # rubocop:todo Metrics/ClassLength
     custom_attribute(:commercially_available, required: true, in: YES_OR_NO)
     custom_attribute(:study_name_abbreviation)
 
+    # add ebi library strategy
+    custom_attribute(:ebi_library_strategy, required: true, in: EBI_LIBRARY_STRATEGY_OPTIONS)
+    custom_attribute(:ebi_library_source, required: true, in: EBI_LIBRARY_SOURCE_OPTIONS)
+    custom_attribute(:ebi_library_selection, required: true, in: EBI_LIBRARY_SELECTION_OPTIONS)
+
     custom_attribute(
       :data_release_strategy,
       required: true,
@@ -309,6 +318,10 @@ class Study < ApplicationRecord # rubocop:todo Metrics/ClassLength
                 allow_blank: true
               }
 
+    validates :ebi_library_strategy, inclusion: { in: EBI_LIBRARY_STRATEGY_OPTIONS }
+    validates :ebi_library_source, inclusion: { in: EBI_LIBRARY_SOURCE_OPTIONS }
+    validates :ebi_library_selection, inclusion: { in: EBI_LIBRARY_SELECTION_OPTIONS }
+
     before_validation do |record|
       record.reference_genome_id = 1 if record.reference_genome_id.blank?
 

diff --git a/app/uat_actions/uat_actions/generate_sample_manifest.rb b/app/uat_actions/uat_actions/generate_sample_manifest.rb
@@ -114,7 +114,10 @@ def study
           contaminated_human_dna: 'No',
           contains_human_dna: 'No',
           commercially_available: 'No',
-          program: UatActions::StaticRecords.program
+          program: UatActions::StaticRecords.program,
+          ebi_library_strategy: 'WGS',
+          ebi_library_source: 'GENOMIC',
+          ebi_library_selection: 'PCR'
         }
       ).find_or_create_by!(name: study_name)
   end

diff --git a/app/uat_actions/uat_actions/generate_study.rb b/app/uat_actions/uat_actions/generate_study.rb
@@ -31,7 +31,10 @@ def create_study
         contaminated_human_dna: 'No',
         contains_human_dna: 'No',
         commercially_available: 'No',
-        program: UatActions::StaticRecords.program
+        program: UatActions::StaticRecords.program,
+        ebi_library_strategy: 'WGS',
+        ebi_library_source: 'GENOMIC',
+        ebi_library_selection: 'PCR'
       }
     ).find_or_create_by!(name: study_name)
   end

diff --git a/app/uat_actions/uat_actions/static_records.rb b/app/uat_actions/uat_actions/static_records.rb
@@ -33,7 +33,10 @@ def self.study
         contaminated_human_dna: 'No',
         contains_human_dna: 'No',
         commercially_available: 'No',
-        program: program
+        program: program,
+        ebi_library_strategy: 'WGS',
+        ebi_library_source: 'GENOMIC',
+        ebi_library_selection: 'PCR'
       }
     ).find_or_create_by!(name: 'UAT Study')
   end

diff --git a/app/views/shared/metadata/edit/_study.html.erb b/app/views/shared/metadata/edit/_study.html.erb
@@ -9,14 +9,17 @@
     <%= metadata_fields.text_field(:prelim_id) %>
 
     <%= metadata_fields.select_by_association(:reference_genome, {}, { class: 'select2' }) %>
+    <%= metadata_fields.select_by_association(:study_type)%>
 
     <% metadata_fields.with_options(grouping: 'ENA requirement') do |group| %>
       <%= group.text_field(:study_study_title) %>
-      <%= group.select_by_association(:study_type)%>
       <%= group.text_area(:study_description) %>
       <%= group.text_area(:study_abstract) %>
       <%= group.radio_select(:study_sra_hold, Study::STUDY_SRA_HOLDS) %>
-    <% end %>
+      <%= metadata_fields.select(:ebi_library_strategy, Study::EBI_LIBRARY_STRATEGY_OPTIONS) %> 
+      <%= metadata_fields.select(:ebi_library_source, Study::EBI_LIBRARY_SOURCE_OPTIONS) %> 
+      <%= metadata_fields.select(:ebi_library_selection, Study::EBI_LIBRARY_SELECTION_OPTIONS) %> 
+    <% end %>    
 
     <%= metadata_fields.radio_select(:contains_human_dna, Study::YES_OR_NO) %>
     <%= metadata_fields.radio_select(:contaminated_human_dna, Study::YES_OR_NO) %>

diff --git a/app/views/shared/metadata/show/_study.html.erb b/app/views/shared/metadata/show/_study.html.erb
@@ -14,6 +14,10 @@
       <%= group.plain_value(:study_sra_hold) %>
     <% end %>
 
+    <%= metadata_fields.plain_value(:ebi_library_strategy) %>
+    <%= metadata_fields.plain_value(:ebi_library_source) %>
+    <%= metadata_fields.plain_value(:ebi_library_selection) %>
+
     <%= metadata_fields.plain_value(:contains_human_dna) %>
     <%= metadata_fields.plain_value(:contaminated_human_dna) %>
     <%= metadata_fields.plain_value(:commercially_available) %>

diff --git a/config/application.rb b/config/application.rb
@@ -91,6 +91,9 @@ class Application < Rails::Application
 
     config.phi_x = config_for(:phi_x).with_indifferent_access
 
+    # add ena requirement fields here
+    config.ena_requirement_fields = config_for(:ena_requirement_fields)
+
     config.generators do |g|
       g.test_framework :rspec,
                        fixtures: true,

diff --git a/config/ena_requirement_fields.yml b/config/ena_requirement_fields.yml
@@ -0,0 +1,64 @@
+default: &DEFAULT
+  EBI_Library_strategy:
+    - "RNA-Seq"
+    - "ChIP-Seq"
+    - "WGS"
+    - "WXS"
+    - "AMPLICON"
+    - "CLONE"
+    - "POOLCLONE"
+    - "CLONEEND"
+    - "Bisulfite-Seq"
+    - "MNase-Seq"
+    - "DNase-Hypersensitivity"
+    - "FAIRE-seq"
+    - "SELEX"
+    - "RIP-Seq"
+    - "ChIA-PET"
+    - "OTHER"
+  EBI_Library_source:
+    - "GENOMIC"
+    - "TRANSCRIPTOMIC"
+    - "METAGENOMIC"
+    - "METATRANSCRIPTOMIC"
+    - "SYNTHETIC"
+    - "VIRAL RNA"
+    - "OTHER"
+  EBI_Library_selection:
+    - "RANDOM"
+    - "PCR"
+    - "RANDOM PCR"
+    - "RT-PCR"
+    - "HMPR"
+    - "MF"
+    - "CF-S"
+    - "CF-M"
+    - "CF-T"
+    - "MDA"
+    - "MSLL"
+    - "cDNA"
+    - "ChIP"
+    - "MNase"
+    - "DNAse"
+    - "Hybrid Selection"
+    - "Reduced Representation"
+    - "Restriction Digest"
+    - "5-methylcytidine antibody"
+    - "MBD2 protein methyl-CpG binding domain"
+
+development:
+  <<: *DEFAULT
+next_release:
+  <<: *DEFAULT
+test:
+  <<: *DEFAULT
+cucumber:
+  <<: *DEFAULT
+production:
+  <<: *DEFAULT
+staging:
+  <<: *DEFAULT
+staging_2:
+  <<: *DEFAULT
+training:
+  <<: *DEFAULT
diff --git a/config/locales/metadata/en.yml b/config/locales/metadata/en.yml
@@ -384,7 +384,6 @@ en:
 
         study_type_id:
           label: Study Type
-          edit_info: "ENA requirement"
 
         study_ebi_accession_number:
           label: ENA Study Accession Number
@@ -522,6 +521,19 @@ en:
         contaminated_human_data_access_group:
           label: Contaminated Human Data Access Group
           help: "Allows specified Unix groups and users access to data segregated from the main data product, which is potentially contaminated with human data. This access is typically rarely used and is primarily for validating the separation process, as we may not have the ethical or legal clearance."
+
+        ebi_library_strategy:
+          label: EBI Library Strategy
+          edit_info: "ENA requirement"
+
+        ebi_library_source:
+          label: EBI Library Source
+          edit_info: "ENA requirement"
+
+        ebi_library_selection:
+          label: EBI Library Selection
+          edit_info: "ENA requirement"
+
     project:
       metadata:
         project_manager_id:

diff --git a/db/migrate/20250108172249_add_ebi_requirement_fields_to_study_metadata.rb b/db/migrate/20250108172249_add_ebi_requirement_fields_to_study_metadata.rb
@@ -0,0 +1,8 @@
+# frozen_string_literal: true
+class AddEbiRequirementFieldsToStudyMetadata < ActiveRecord::Migration[6.1]
+  def change
+    add_column :study_metadata, :ebi_library_strategy, :string, default: nil
+    add_column :study_metadata, :ebi_library_source, :string, default: nil
+    add_column :study_metadata, :ebi_library_selection, :string, default: nil
+  end
+end
diff --git a/db/schema.rb b/db/schema.rb
@@ -1548,6 +1548,9 @@
     t.string "s3_email_list"
     t.string "data_deletion_period"
     t.string "contaminated_human_data_access_group"
+    t.string "ebi_library_strategy"
+    t.string "ebi_library_source"
+    t.string "ebi_library_selection"
     t.string "data_release_prevention_other_comment"
     t.index ["faculty_sponsor_id"], name: "index_study_metadata_on_faculty_sponsor_id"
     t.index ["study_id"], name: "index_study_metadata_on_study_id"

diff --git a/features/studies/4295391_study_xml_needs_to_be_reverted_to_old_version.feature b/features/studies/4295391_study_xml_needs_to_be_reverted_to_old_version.feature
@@ -205,6 +205,18 @@ Feature: The XML for the sequencescape API
           <descriptor><name>Policy Url</name></descriptor>
           <descriptor><name>Policy title</name></descriptor>
           <descriptor><name>ArrayExpress Accession Number</name></descriptor>
+          <descriptor>
+            <name>EBI Library Strategy</name>
+            <value>WGS</value>
+          </descriptor>
+          <descriptor>
+            <name>EBI Library Source</name>
+            <value>GENOMIC</value>
+          </descriptor>
+          <descriptor>
+            <name>EBI Library Selection</name>
+            <value>PCR</value>
+          </descriptor>
         </descriptors>
       </study>
       """

diff --git a/features/support/step_definitions/study_steps.rb b/features/support/step_definitions/study_steps.rb
@@ -332,7 +332,10 @@ def assign_asset_to_study(asset, study_name)
       data_release_study_type: DataReleaseStudyType.first,
       contaminated_human_dna: 'No',
       contains_human_dna: 'Yes',
-      commercially_available: 'No'
+      commercially_available: 'No',
+      ebi_library_strategy: 'WGS',
+      ebi_library_source: 'GENOMIC',
+      ebi_library_selection: 'PCR'
     }
   )
 end

diff --git a/lib/working_setup/standard_seeder.rb b/lib/working_setup/standard_seeder.rb
@@ -140,7 +140,10 @@ def create_study(name)
           contaminated_human_dna: 'No',
           contains_human_dna: 'No',
           commercially_available: 'No',
-          program_id: program.id
+          program_id: program.id,
+          ebi_library_strategy: 'WGS',
+          ebi_library_source: 'GENOMIC',
+          ebi_library_selection: 'PCR'
         }
       ) do |study|
         study.activate!

diff --git a/spec/controllers/studies_controller_spec.rb b/spec/controllers/studies_controller_spec.rb
@@ -23,7 +23,10 @@
           'commercially_available' => 'No',
           'data_release_study_type_id' => data_release_study_type,
           'data_release_strategy' => 'open',
-          'study_type_id' => StudyType.find_or_create_by(name: 'Not specified').id
+          'study_type_id' => StudyType.find_or_create_by(name: 'Not specified').id,
+          'ebi_library_strategy' => 'WGS',
+          'ebi_library_source' => 'GENOMIC',
+          'ebi_library_selection' => 'PCR'
         }
       }
     }

diff --git a/spec/factories/study_metadata_factories.rb b/spec/factories/study_metadata_factories.rb
@@ -22,6 +22,10 @@
     s3_email_list { '[email protected];[email protected]' }
     data_deletion_period { '3 months' }
 
+    ebi_library_strategy { 'WGS' }
+    ebi_library_source { 'GENOMIC' }
+    ebi_library_selection { 'PCR' }
+
     transient { contaminated_human_data_access_group { nil } }
 
     after(:build) do |study_metadata, evaluator|

diff --git a/spec/models/api/study_io_spec.rb b/spec/models/api/study_io_spec.rb
@@ -16,7 +16,10 @@
         ega_policy_accession_number: 'EGA222',
         ega_dac_accession_number: 'DAC333',
         program: create(:program, name: 'General'),
-        contaminated_human_data_access_group: 'contaminated human data access group test'
+        contaminated_human_data_access_group: 'contaminated human data access group test',
+        ebi_library_strategy: 'WGS',
+        ebi_library_source: 'GENOMIC',
+        ebi_library_selection: 'PCR'
       }
     )
   end
@@ -57,6 +60,9 @@
       'data_deletion_period' => '3 months',
       'contaminated_human_data_access_group' => 'contaminated human data access group test',
       'programme' => 'General',
+      'ebi_library_strategy' => 'WGS',
+      'ebi_library_source' => 'GENOMIC',
+      'ebi_library_selection' => 'PCR',
       'manager' => [
         { login: manager.login, email: manager.email, name: manager.name },
         { login: manager2.login, email: manager2.email, name: manager2.name }

diff --git a/spec/models/study_spec.rb b/spec/models/study_spec.rb
@@ -518,7 +518,10 @@
         number_of_gigabases_per_sample: 6,
         hmdmc_approval_number: 'HDMC123456',
         s3_email_list: '[email protected];[email protected]',
-        data_deletion_period: '3 months'
+        data_deletion_period: '3 months',
+        ebi_library_strategy: 'WGS',
+        ebi_library_source: 'GENOMIC',
+        ebi_library_selection: 'PCR'
       }
     end
 
@@ -645,6 +648,18 @@
         expect(study.study_metadata.faculty_sponsor).not_to be_nil
       end
 
+      it 'must have a ebi library strategy' do
+        expect(study.study_metadata.ebi_library_strategy).not_to be_nil
+      end
+
+      it 'must have a ebi library source' do
+        expect(study.study_metadata.ebi_library_source).not_to be_nil
+      end
+
+      it 'must have a ebi library selection' do
+        expect(study.study_metadata.ebi_library_selection).not_to be_nil
+      end
+
       context 'contaminated human data access group' do
         it 'defaults to null when not specified' do
           expect(study.study_metadata.contaminated_human_data_access_group).to be_nil