4409 y24 379 study setup fields to align to the ena database fields improvement

app/models/metadata/builder_base.rb

@@ -24,7 +24,10 @@ def sanitized_object_name
 
   def localised_sections(field)
     sections = @object.class.localised_sections(field).dup
-    sections.label_options = { class: 'required' } if @object.required?(field)
+    required_fields = %i[ebi_library_strategy ebi_library_source ebi_library_selection]
+    if @object.required?(field) || (@object.new_record? && required_fields.include?(field))
+      sections.label_options = { class: 'required' }
+    end
     sections
   end
 

app/models/study.rb

@@ -218,10 +218,10 @@ 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)
+    # add ebi library strategy, ebi library source, ebi library selection
+    custom_attribute(:ebi_library_strategy, in: EBI_LIBRARY_STRATEGY_OPTIONS)
+    custom_attribute(:ebi_library_source, in: EBI_LIBRARY_SOURCE_OPTIONS)
+    custom_attribute(:ebi_library_selection, in: EBI_LIBRARY_SELECTION_OPTIONS)
 
     custom_attribute(
       :data_release_strategy,
@@ -318,9 +318,9 @@ 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 }
+    validates :ebi_library_strategy, presence: true, on: :create
+    validates :ebi_library_source, presence: true, on: :create
+    validates :ebi_library_selection, presence: true, on: :create
 
     before_validation do |record|
       record.reference_genome_id = 1 if record.reference_genome_id.blank?

app/views/shared/metadata/edit/_study.html.erb

@@ -16,9 +16,10 @@
       <%= group.text_area(:study_description) %>
       <%= group.text_area(:study_abstract) %>
       <%= group.radio_select(:study_sra_hold, Study::STUDY_SRA_HOLDS) %>
-      <%= 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) %> 
+
+      <%= metadata_fields.select(:ebi_library_strategy, options_for_select([['Please select...', nil]] + Study::EBI_LIBRARY_STRATEGY_OPTIONS, metadata_fields.object.ebi_library_strategy), (metadata_fields.object.new_record? ? { required: true } : {})) %>
+      <%= metadata_fields.select(:ebi_library_source,  options_for_select([['Please select...', nil]] + Study::EBI_LIBRARY_SOURCE_OPTIONS, metadata_fields.object.ebi_library_source), (metadata_fields.object.new_record? ? { required: true } : {})) %> 
+      <%= metadata_fields.select(:ebi_library_selection, options_for_select([['Please select...', nil]] + Study::EBI_LIBRARY_SELECTION_OPTIONS, metadata_fields.object.ebi_library_selection), (metadata_fields.object.new_record? ? { required: true } : {})) %> 
     <% end %>    
 
     <%= metadata_fields.radio_select(:contains_human_dna, Study::YES_OR_NO) %>

config/ena_requirement_fields.yml

@@ -1,50 +1,91 @@
 default: &DEFAULT
   EBI_Library_strategy:
-    - "RNA-Seq"
-    - "ChIP-Seq"
     - "WGS"
+    - "WGA"
     - "WXS"
-    - "AMPLICON"
+    - "RNA-Seq"
+    - "ssRNA-seq"
+    - "snRNA-seq"
+    - "miRNA-Seq"
+    - "ncRNA-Seq"
+    - "FL-cDNA"
+    - "EST"
+    - "Hi-C"
+    - "ATAC-seq"
+    - "WCS"
+    - "RAD-Seq"
     - "CLONE"
     - "POOLCLONE"
+    - "AMPLICON"
     - "CLONEEND"
-    - "Bisulfite-Seq"
+    - "FINISHING"
+    - "ChIP-Seq"
     - "MNase-Seq"
     - "DNase-Hypersensitivity"
+    - "Bisulfite-Seq"
+    - "CTS"
+    - "MRE-Seq"
+    - "MeDIP-Seq"
+    - "MBD-Seq"
+    - "Tn-Seq"
+    - "VALIDATION"
     - "FAIRE-seq"
     - "SELEX"
     - "RIP-Seq"
     - "ChIA-PET"
+    - "Synthetic-Long-Read"
+    - "Targeted-Capture"
+    - "Tethered Chromatin Conformation Capture"
+    - "NOMe-seq"
+    - "ChM-Seq"
+    - "GBS"
+    - "Ribo-seq"
     - "OTHER"
+
   EBI_Library_source:
     - "GENOMIC"
+    - "GENOMIC SINGLE CELL"
     - "TRANSCRIPTOMIC"
+    - "TRANSCRIPTOMIC SINGLE CELL"
     - "METAGENOMIC"
     - "METATRANSCRIPTOMIC"
     - "SYNTHETIC"
     - "VIRAL RNA"
     - "OTHER"
+
   EBI_Library_selection:
     - "RANDOM"
     - "PCR"
     - "RANDOM PCR"
     - "RT-PCR"
     - "HMPR"
     - "MF"
-    - "CF-S"
-    - "CF-M"
-    - "CF-T"
-    - "MDA"
+    - "repeat fractionation"
+    - "size fractionation"
+    - "MSLL"
     - "MSLL"
     - "cDNA"
-    - "ChIP"
+    - "cDNA_randomPriming"
+    - "cDNA_oligo_dT"
+    - "PolyA"
+    - "Oligo-dT"
+    - "Inverse rRNA"
+    - "Inverse rRNA selection"
+    - "CHIP"
+    - "CHIP-Seq"
     - "MNase"
     - "DNAse"
     - "Hybrid Selection"
     - "Reduced Representation"
     - "Restriction Digest"
     - "5-methylcytidine antibody"
     - "MBD2 protein methyl-CpG binding domain"
+    - "CAGE"
+    - "RACE"
+    - "MDA"
+    - "padlock probes capture method"
+    - "other"
+    - "unspecified"
 
 development:
   <<: *DEFAULT

features/administration/11184645_faculty_sponsor_management.feature

@@ -41,7 +41,7 @@
       And I create study "Another Big study" with faculty sponsor "Barry Ball"
       And I create study "Small study" with faculty sponsor "Conor Cone"
       And I am on the faculty sponsor homepage
     Then the faculty sponsor index page should include:
       | Name       | Number of Studies |
       | Adam Apple | 0                 |
       | Barry Ball | 2                 |
@@ -65,6 +65,11 @@
       And I fill in "Study name" with "Study name"
       And I select "Not suitable for alignment" from "Reference genome"
       And I fill in "Study description" with "some description"
+      And I select "General" from "Program"
+      And I select "Clone Sequencing" from "Study Type"
+      And I select "WGS" from "EBI Library Strategy"
+      And I select "GENOMIC" from "EBI Library Source"
+      And I select "PCR" from "EBI Library Selection"
       And I fill in "Data access group" with "dag"
       And I select "John Doe" from "Faculty Sponsor"
       And I choose "Yes" from "Do any of the samples in this study contain human DNA?"

features/studies/data_release_timings.feature

@@ -6,6 +6,11 @@ Feature: Studies have timings for release of their data
     Given I am on the study creation page
     And I fill in "Study name" with "Testing data release strategies"
     And I select "Jack Sponsor" from "Faculty Sponsor"
+    And I select "General" from "Program"
+    And I select "Clone Sequencing" from "Study Type"
+    And I select "WGS" from "EBI Library Strategy"
+    And I select "GENOMIC" from "EBI Library Source"
+    And I select "PCR" from "EBI Library Selection"
     And I fill in "Study description" with "Checking that the data release strategies behave appropriately"
     And I choose "No" from "Do any of the samples in this study contain human DNA?"
     And I choose "No" from "Does this study contain samples that are contaminated with human DNA which must be removed prior to analysis?"

features/studies/release_agreement.feature

@@ -6,6 +6,11 @@ Feature: Studies have a release agreement
     Given I am on the study creation page
     And I fill in "Study name" with "Testing release agreements"
     And I select "Jack Sponsor" from "Faculty Sponsor"
+    And I select "General" from "Program"
+    And I select "Clone Sequencing" from "Study Type"
+    And I select "WGS" from "EBI Library Strategy"
+    And I select "GENOMIC" from "EBI Library Source"
+    And I select "PCR" from "EBI Library Selection"
     And I fill in "Study description" with "Checking that release agreements behave properly"
     And I fill in "Data access group" with "mygroup"
     And I choose "No" from "Do any of the samples in this study contain human DNA?"

spec/features/studies/create_study_spec.rb

@@ -48,6 +48,10 @@
       expect(page).to have_field('Public', type: :radio)
     end
 
+    expect(page).to have_field('EBI Library Strategy', type: :select)
+    expect(page).to have_field('EBI Library Source', type: :select)
+    expect(page).to have_field('EBI Library Selection', type: :select)
+
     expect(page).to have_field('What sort of study is this?', type: :select)
     expect(page).to have_field('How is the data release to be timed?', type: :select)
     expect(page).to have_field('Prelim ID', type: :text)
@@ -56,6 +60,9 @@
 
     expect(page).to have_content "Name can't be blank"
     expect(page).to have_content "Study description can't be blank"
+    expect(page).to have_content "Study metadata ebi library strategy can't be blank"
+    expect(page).to have_content "Study metadata ebi library source can't be blank"
+    expect(page).to have_content "Study metadata ebi library selection can't be blank"
   end
 
   it 'create managed study', :js do
@@ -83,6 +90,9 @@
     fill_in 'ENA Study Accession Number', with: '12345'
     fill_in 'Study name abbreviation', with: 'CCC3'
     select('Jack Sponsor', from: 'Faculty Sponsor')
+    select('RNA-Seq', from: 'EBI Library Strategy')
+    select('GENOMIC', from: 'EBI Library Source')
+    select('PCR', from: 'EBI Library Selection')
 
     within_fieldset 'Do any of the samples in this study contain human DNA?' do
       choose('Yes', allow_label_click: true)