Y24-481 - Study setup page changes

app/models/study.rb

@@ -82,11 +82,28 @@ class Study < ApplicationRecord # rubocop:todo Metrics/ClassLength
     DATA_RELEASE_TIMING_IMMEDIATE,
     DATA_RELEASE_TIMING_DELAYED
   ].freeze
-  DATA_RELEASE_PREVENTION_REASONS = ['data validity', 'legal', 'replication of data subset'].freeze
 
-  DATA_RELEASE_DELAY_FOR_OTHER = 'other'
-  DATA_RELEASE_DELAY_REASONS_STANDARD = ['phd study', DATA_RELEASE_DELAY_FOR_OTHER].freeze
-  DATA_RELEASE_DELAY_REASONS_ASSAY = ['phd study', 'assay of no other use', DATA_RELEASE_DELAY_FOR_OTHER].freeze
+  OLD_DATA_RELEASE_PREVENTION_REASONS = ['data validity', 'legal', 'replication of data subset'].freeze
+  DATA_RELEASE_PREVENTION_REASON_OTHER = 'Other (please specify)'
+  DATA_RELEASE_PREVENTION_REASONS = [
+    'Pilot or validation studies - DAC approval not required',
+    'Collaborators will share data in a research repository - DAC approval not required',
+    'Prevent harm (e.g sensitive studies or biosecurity) - DAC approval required',
+    'Protecting IP - DAC approval required',
+    DATA_RELEASE_PREVENTION_REASON_OTHER
+  ].freeze
+
+  OLD_DATA_RELEASE_DELAY_FOR_OTHER = 'other'
+  DATA_RELEASE_DELAY_FOR_OTHER = 'Other (please specify below)'
+  OLD_DATA_RELEASE_DELAY_REASONS = ['other', 'phd study'].freeze
+  DATA_RELEASE_DELAY_REASONS_STANDARD = [
+    'PhD study',
+    'Capacity building',
+    'Intellectual property protection',
+    'Additional time to make data FAIR',
+    DATA_RELEASE_DELAY_FOR_OTHER
+  ].freeze
+  DATA_RELEASE_DELAY_REASONS_ASSAY = ['assay of no other use'].freeze
 
   DATA_RELEASE_DELAY_PERIODS = ['3 months', '6 months', '9 months', '12 months', '18 months'].freeze
 
@@ -214,14 +231,15 @@ class Study < ApplicationRecord # rubocop:todo Metrics/ClassLength
     custom_attribute(
       :data_release_delay_reason,
       required: true,
-      in: DATA_RELEASE_DELAY_REASONS_ASSAY,
+      in: [*DATA_RELEASE_DELAY_REASONS_STANDARD, *DATA_RELEASE_DELAY_REASONS_ASSAY, *OLD_DATA_RELEASE_DELAY_REASONS],
       if: :delayed_release?
     )
+
     custom_attribute(:data_release_delay_period, required: true, in: DATA_RELEASE_DELAY_PERIODS, if: :delayed_release?)
     custom_attribute(:bam, default: true)
 
-    with_options(required: true, if: :delayed_for_other_reasons?) do
-      custom_attribute(:data_release_delay_other_comment)
+    with_options(if: :delayed_for_other_reasons?) do
+      custom_attribute(:data_release_delay_other_comment, required: true)
       custom_attribute(:data_release_delay_reason_comment)
     end
 
@@ -231,14 +249,19 @@ class Study < ApplicationRecord # rubocop:todo Metrics/ClassLength
     custom_attribute(:ega_policy_accession_number)
     custom_attribute(:array_express_accession_number)
 
-    with_options(if: :delayed_for_long_time?, required: true) do
-      custom_attribute(:data_release_delay_approval, in: YES_OR_NO, default: NO)
-    end
-
-    with_options(if: :never_release?, required: true) do
-      custom_attribute(:data_release_prevention_reason, in: DATA_RELEASE_PREVENTION_REASONS)
-      custom_attribute(:data_release_prevention_approval, in: YES_OR_NO)
-      custom_attribute(:data_release_prevention_reason_comment)
+    with_options(if: :never_release?) do
+      custom_attribute(
+        :data_release_prevention_reason,
+        in: [*DATA_RELEASE_PREVENTION_REASONS, *OLD_DATA_RELEASE_PREVENTION_REASONS],
+        required: true
+      )
+      custom_attribute(
+        :data_release_prevention_other_comment,
+        required: true,
+        if: :data_release_prevention_reason_other?
+      )
+      custom_attribute(:data_release_prevention_reason_comment, required: true)
+      custom_attribute(:data_release_prevention_approval)
     end
 
     # NOTE: Additional validation in Study::Metadata Class to validate_presence_of :data_access_group, if: :managed
@@ -567,6 +590,33 @@ def poly_metadatum_by_key(key)
     poly_metadata.find { |pm| pm.key == key.to_s }
   end
 
+  # Helper method for edit dropdowns to support backwards compatibility with old options.
+  #
+  # @return [Array<String>] the list of options for the data release prevention reason dropdown
+  def data_release_prevention_options
+    additional_options = []
+    if OLD_DATA_RELEASE_PREVENTION_REASONS.include? study_metadata.data_release_prevention_reason
+      additional_options << study_metadata.data_release_prevention_reason
+    end
+
+    DATA_RELEASE_PREVENTION_REASONS + additional_options
+  end
+
+  # Helper method for edit dropdowns to support backwards compatibility with old options.
+  #
+  # @param [Boolean] assay_option - whether to include assay-specific options
+  # @return [Array<String>] the list of options for the data release delay reason dropdown
+  def data_release_delay_options(assay_option: false)
+    # If the current value is an old one, then we need to include it in the list of options
+    additional_options = []
+    if OLD_DATA_RELEASE_DELAY_REASONS.include? study_metadata.data_release_delay_reason
+      additional_options << study_metadata.data_release_delay_reason
+    end
+
+    additional_options.concat(DATA_RELEASE_DELAY_REASONS_ASSAY) if assay_option
+    DATA_RELEASE_DELAY_REASONS_STANDARD + additional_options
+  end
+
   private
 
   def valid_ethically_approved?
@@ -601,7 +651,11 @@ def never_release?
     end
 
     def delayed_for_other_reasons?
-      data_release_delay_reason == DATA_RELEASE_DELAY_FOR_OTHER
+      [DATA_RELEASE_DELAY_FOR_OTHER, OLD_DATA_RELEASE_DELAY_FOR_OTHER].include?(data_release_delay_reason)
+    end
+
+    def data_release_prevention_reason_other?
+      data_release_prevention_reason == DATA_RELEASE_PREVENTION_REASON_OTHER
     end
 
     def delayed_for_long_time?

app/views/shared/metadata/_related_fields.html.erb

@@ -23,7 +23,7 @@
 
       var valueFrom = function(element) {
         if (element === null) { return null }
-        var value = element.value.toLowerCase().replace(/[^a-z0-9]+/, '_');
+        var value = element.value.toLowerCase().replaceAll(/[^a-z0-9]+/g, '_');
         return (value.length == 0) ? 'blank' : value;
       };
 

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

@@ -59,29 +59,26 @@
       %>
 
       <% metadata_fields.related_fields(to: :data_release_strategy, when: Study::DATA_RELEASE_STRATEGY_NOT_APPLICABLE) do %>
-        <%= group.select(:data_release_prevention_reason, Study::DATA_RELEASE_PREVENTION_REASONS) %>
-        <%= group.radio_select(:data_release_prevention_approval, Study::YES_OR_NO) %>
+        <%= group.select(:data_release_prevention_reason, study.data_release_prevention_options) %>
+        <% metadata_fields.related_fields(to: :data_release_prevention_reason, in: [Study::DATA_RELEASE_PREVENTION_REASON_OTHER]) do %>
+          <%= group.text_area(:data_release_prevention_other_comment) %>
+        <% end %>
+        <%= group.text_area(:data_release_prevention_approval) %>
         <%= group.text_area(:data_release_prevention_reason_comment) %>
       <% end %>
       <% metadata_fields.related_fields(to: :data_release_strategy, in: Study::DATA_RELEASE_STRATEGIES, not: Study::DATA_RELEASE_STRATEGY_NOT_APPLICABLE) do %>
         <% metadata_fields.related_fields(to: :data_release_timing, when: Study::DATA_RELEASE_TIMING_DELAYED) do %>
-          <%= group.select(:data_release_delay_reason, Study::DATA_RELEASE_DELAY_REASONS_STANDARD) %>
+          <%= group.select(:data_release_delay_reason, study.data_release_delay_options) %>
           <%
             group.change_select_options_for(:data_release_delay_reason, when: :data_release_study_type_id, values: {
-              DataReleaseStudyType.assay_types.map(&:id)     => [ '' ] + Study::DATA_RELEASE_DELAY_REASONS_ASSAY,
-              DataReleaseStudyType.non_assay_types.map(&:id) => [ '' ] + Study::DATA_RELEASE_DELAY_REASONS_STANDARD
+              DataReleaseStudyType.assay_types.map(&:id)     => [ '' ] + study.data_release_delay_options(assay_option: true),
+              DataReleaseStudyType.non_assay_types.map(&:id) => [ '' ] + study.data_release_delay_options
             })
           %>
 
           <%= group.select(:data_release_delay_period, Study::DATA_RELEASE_DELAY_PERIODS) %>
-          <% metadata_fields.related_fields(to: :data_release_delay_period, in: Study::DATA_RELEASE_DELAY_PERIODS) do %>
-              <%= group.radio_select(:data_release_delay_approval, Study::YES_OR_NO) %>
-            <% end %>
-          <% metadata_fields.related_fields(to: :data_release_delay_reason, when: Study::DATA_RELEASE_DELAY_FOR_OTHER) do %>
+          <% metadata_fields.related_fields(to: :data_release_delay_reason, in: [Study::DATA_RELEASE_DELAY_FOR_OTHER, Study::OLD_DATA_RELEASE_DELAY_FOR_OTHER]) do %>
             <%= group.text_area(:data_release_delay_other_comment) %>
-            <% metadata_fields.related_fields(to: :data_release_delay_period, in: Study::DATA_RELEASE_DELAY_PERIODS) do %>
-              <%= group.text_area(:data_release_delay_reason_comment) %>
-            <% end %>
           <% end %>
         <% end %>
       <% end %>

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

@@ -57,6 +57,7 @@
         <%= group.plain_value(:data_release_prevention_reason) %>
         <%= group.plain_value(:data_release_prevention_approval) %>
         <%= group.plain_value(:data_release_prevention_reason_comment) %>
+        <%= group.plain_value(:data_release_prevention_other_comment) %>
       <% end %>
       <%= metadata_fields.plain_value(:dac_policy_title) %>
       <%= metadata_fields.plain_value(:dac_policy) %>

config/locales/metadata/en.yml

@@ -351,7 +351,6 @@ en:
         study_description:
           label: Study description
           edit_info: "ENA requirement"
-          help: Please choose one of the following 2 standard statements to be included with your data submissions (one or the other, depending on the study). <b>If you use the second statement, replace [doi or ref] by a reference or doi for your publication:</b><br /><br />This data is part of a pre-publication release. For information on the proper use of pre-publication data shared by the Wellcome Trust Sanger Institute (including details of any publication moratoria), please see http://www.sanger.ac.uk/datasharing/<br /><br />OR<br /><br />This data has been described in the following article [doi or ref] and its further analysis can be freely submitted for publication. For information on the proper use of data shared by the Wellcome Trust Sanger Institute (including information on acknowledgement), please see http://www.sanger.ac.uk/datasharing/<br/><p>If applicable, include a brief description of any restrictions on data usage, e.g. 'For AIDS-related research only'</p>
 
         contaminated_human_dna:
           label: Does this study contain samples that are contaminated with human DNA which must be removed prior to analysis?
@@ -424,7 +423,7 @@ en:
           values:
             open: "Open (ENA)"
             managed: "Managed (EGA)"
-            not_applicable: "Not Applicable (Contact Datasharing)"
+            not_applicable: "Not Applicable"
 
         data_release_standard_agreement:
           label: "Will you be using WTSI's standard access agreement?"
@@ -434,21 +433,22 @@ en:
 
         data_release_timing:
           label: How is the data release to be timed?
-          help: "Choose from:<p><strong>Immediate:</strong> To be released as soon as possible.</p><p><strong>Standard:</strong> To be released:<ul><li>For managed (EGA) studies: 6 months</li><li>For open (ENA) studies: 12 months</li><li>Transcriptomics studies: on request only</li></ul></p><p><strong>Delayed:</strong><ul><li>For managed (EGA) studies: 6 months plus delay for period</li><li>For open (ENA) studies: 12 months plus delay for period.</li></ul></p><p><strong>Never:</strong> This option is only available if the data release strategy is set to 'Not applicable.'</p>"
+          help: "Choose from:<p><strong>Immediate:</strong> To be released as soon as possible.</p><p><strong>Standard:</strong> To be released:<ul><li>For managed (EGA) studies: 12 months</li><li>For open (ENA) studies: 12 months</li><li>Transcriptomics studies: 12 months</li></ul></p><p><strong>Delayed:</strong><ul><li>For managed (EGA) studies: 12 months plus delay for period</li><li>For open (ENA) studies: 12 months plus delay for period.</li></ul></p><p><strong>Never:</strong> This option is only available if the data release strategy is set to 'Not applicable.'</p>"
 
         data_release_prevention_reason:
           label: What is the reason for preventing data release?
 
         data_release_prevention_approval:
-          label: Has this been approved?
-          help: "If this is for data validity reasons: approval from the sponsor is required<br />If this is for legal reasons: approval from the Data Sharing Committee is required (please contact sd4)<br />"
+          label: If reason for exemption requires DAC approval, what is the approval number?
+
+        data_release_prevention_other_comment:
+          label: Please explain the reason for preventing data release
 
         data_release_prevention_reason_comment:
           label: Comment regarding prevention of data release and approval
 
         data_release_delay_reason:
           label: Reason for delaying release
-          help: 'To apply for a delay, please contact <a title="<%= configatron.data_sharing_contact.name %>" href="mailto:<%= configatron.data_sharing_contact.email %>"><%= configatron.data_sharing_contact.email %></a>'
 
         data_release_delay_other_comment:
           label: Please explain the reason for delaying release

db/migrate/20250114135342_add_data_release_prevention_other_comment_to_study_metadata.rb

@@ -0,0 +1,6 @@
+# frozen_string_literal: true
+class AddDataReleasePreventionOtherCommentToStudyMetadata < ActiveRecord::Migration[7.0]
+  def change
+    add_column :study_metadata, :data_release_prevention_other_comment, :string, default: nil
+  end
+end

db/schema.rb

@@ -10,7 +10,7 @@
 #
 # It's strongly recommended that you check this file into your version control system.
 
-ActiveRecord::Schema[7.0].define(version: 2024_12_11_143636) do
+ActiveRecord::Schema[7.0].define(version: 2025_01_14_135342) do
   create_table "aliquot_indices", id: :integer, charset: "utf8mb4", collation: "utf8mb4_unicode_ci", options: "ENGINE=InnoDB ROW_FORMAT=DYNAMIC", force: :cascade do |t|
     t.integer "aliquot_id", null: false
     t.integer "lane_id", null: false
@@ -1548,6 +1548,7 @@
     t.string "s3_email_list"
     t.string "data_deletion_period"
     t.string "contaminated_human_data_access_group"
+    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"
   end

features/studies/4295391_study_xml_needs_to_be_reverted_to_old_version.feature

@@ -115,7 +115,7 @@ Feature: The XML for the sequencescape API
             <value>Not specified</value>
           </descriptor>
           <descriptor>
-            <name>Has this been approved?</name>
+            <name>If reason for exemption requires DAC approval, what is the approval number?</name>
             <value></value>
           </descriptor>
           <descriptor>
@@ -150,10 +150,6 @@ Feature: The XML for the sequencescape API
           <name>Are all the samples to be used in this study commercially available, unlinked anonymised cell-lines?</name>
           <value>No</value>
           </descriptor>
-          <descriptor>
-            <name>Has the delay period been approved by the data sharing committee for this project?</name>
-            <value></value>
-          </descriptor>
           <descriptor>
             <name>ENA Project ID</name>
             <value></value>
@@ -178,6 +174,10 @@ Feature: The XML for the sequencescape API
             <name>Please explain the reason for delaying release</name>
             <value></value>
           </descriptor>
+          <descriptor>
+            <name>Please explain the reason for preventing data release</name>
+            <value></value>
+          </descriptor>
           <descriptor>
             <name>SNP parent study ID</name>
             <value></value>

features/studies/8447221_data_release_help_text.feature

@@ -6,54 +6,26 @@ Feature: Update the data release fields for creating a study
     Given a faculty sponsor called "Jack Sponsor" exists
     And I am on the new study page
 
-  Scenario: Add help text to study description (8348119)
-    Then the help text for "Study description" should contain:
-      """
-      Please choose one of the following 2 standard statements to be included with your data submissions (one or the other, depending on the study). If you use the second statement, replace [doi or ref] by a reference or doi for your publication:
-
-      This data is part of a pre-publication release. For information on the proper use of pre-publication data shared by the Wellcome Trust Sanger Institute (including details of any publication moratoria), please see http://www.sanger.ac.uk/datasharing/
-
-      OR
-
-      This data has been described in the following article [doi or ref] and its further analysis can be freely submitted for publication. For information on the proper use of data shared by the Wellcome Trust Sanger Institute (including information on acknowledgement), please see http://www.sanger.ac.uk/datasharing/
-      If applicable, include a brief description of any restrictions on data usage, e.g. 'For AIDS-related research only'
-      """
-
   Scenario Outline: Add help text opposite delay drop down (4044305)
     When I choose "<release strategy>" from "What is the data release strategy for this study?"
     When I select "delayed" from "How is the data release to be timed?"
-    When I select "other" from "Reason for delaying release"
-    Then the help text for "Reason for delaying release" should contain:
-      """
-      To apply for a delay, please contact [email protected]
-      """
+    When I select "Other (please specify below)" from "Reason for delaying release"
+    Then I should exactly see "Reason for delaying release"
 
     Examples:
       | release strategy |
       | Managed (EGA)    |
       | Open (ENA)       |
 
-  Scenario: Add help text to has this been approved for never release (4044343)
-    When I choose "Not Applicable (Contact Datasharing)" from "What is the data release strategy for this study?"
-    When I select "never" from "How is the data release to be timed?"
-    Then the help text for "Has this been approved?" should contain:
-      """
-      If this is for data validity reasons: approval from the sponsor is required
-      If this is for legal reasons: approval from the Data Sharing Committee is required (please contact sd4)
-      """
-
   Scenario Outline: Delaying for 3 months should have the same questions as all other delays (4044273)
     When I select "delayed" from "How is the data release to be timed?"
-    And I select "other" from "Reason for delaying release"
+    And I select "Other (please specify below)" from "Reason for delaying release"
     And I select "<delay_period>" from "Delay for"
-    Then I should exactly see "Has the delay period been approved by the data sharing committee for this project?"
-    And I should exactly see "Comment regarding data release timing and approval"
 
     When I fill in the following:
       | Study name                                         | new study       |
       | Study description                                  | writing cukes   |
       | Please explain the reason for delaying release     | some comment    |
-      | Comment regarding data release timing and approval | another comment |
 
     And I select "Jack Sponsor" from "Faculty Sponsor"
     And I choose "Yes" from "Do any of the samples in this study contain human DNA?"