Y24-481 - Study setup page changes

app/models/study.rb

@@ -82,11 +82,24 @@ 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
+  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',
+    'Other (please specify)'
+  ].freeze
+
+  DATA_RELEASE_DELAY_FOR_OTHER = 'Other (with free text box)'
+  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', *DATA_RELEASE_DELAY_REASONS_STANDARD].freeze
 
   DATA_RELEASE_DELAY_PERIODS = ['3 months', '6 months', '9 months', '12 months', '18 months'].freeze
 
@@ -217,6 +230,7 @@ class Study < ApplicationRecord # rubocop:todo Metrics/ClassLength
       in: DATA_RELEASE_DELAY_REASONS_ASSAY,
       if: :delayed_release?
     )
+
     custom_attribute(:data_release_delay_period, required: true, in: DATA_RELEASE_DELAY_PERIODS, if: :delayed_release?)
     custom_attribute(:bam, default: true)
 
@@ -231,14 +245,10 @@ 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, required: true)
+      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

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

@@ -59,13 +59,13 @@
       %>
 
       <% 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_REASONS) %>
+        <%= 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_REASONS_STANDARD) %>
           <%
             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,
@@ -74,9 +74,6 @@
           %>
 
           <%= 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 %>
             <%= group.text_area(:data_release_delay_other_comment) %>
             <% metadata_fields.related_fields(to: :data_release_delay_period, in: Study::DATA_RELEASE_DELAY_PERIODS) do %>

config/locales/metadata/en.yml

@@ -422,7 +422,7 @@ 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?"
@@ -432,21 +432,20 @@ 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?
+          label: If reason for exemption requires DAC approval, what is the approval number?
           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 />"
 
         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

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>

features/studies/8447221_data_release_help_text.feature

@@ -22,31 +22,27 @@ Feature: Update the data release fields for creating a study
   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 (with free text box)" 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 choose "Not Applicable" 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:
+    Then the help text for "If reason for exemption requires DAC approval, what is the approval number?" 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 (with free text box)" 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:

features/studies/data_release_timings.feature

@@ -28,7 +28,7 @@ Feature: Studies have timings for release of their data
 
   Scenario: When the data release is delayed for PhD study
     Given I select "delayed" from "How is the data release to be timed?"
-      And I select "phd study" from "Reason for delaying release"
+      And I select "PhD study" from "Reason for delaying release"
     Then the "Comment regarding data release timing and approval" field is hidden
     When I select "6 months" from "Delay for"
       And I press "Create"
@@ -37,7 +37,7 @@ Feature: Studies have timings for release of their data
 
   Scenario Outline: When the data release is delayed but no reasons are provided
     Given 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 (with free text box)" from "Reason for delaying release"
     And I fill in "Please explain the reason for delaying release" with "Some reason"
     And I select "<period>" from "Delay for"
     When I press "Create"
@@ -54,7 +54,7 @@ Feature: Studies have timings for release of their data
 
   Scenario Outline: When the data release is delayed and the reasons are provided
     Given 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 (with free text box)" from "Reason for delaying release"
     And I fill in "Please explain the reason for delaying release" with "Some reason"
     And I select "<period>" from "Delay for"
     And I fill in "Comment regarding data release timing and approval" with "Because it is ok?"
@@ -70,19 +70,21 @@ Feature: Studies have timings for release of their data
       | 12 months |
 
   Scenario: When the data release is never but the comment is not supplied
-    When I choose "Not Applicable (Contact Datasharing)" from "What is the data release strategy for this study?"
+    When I choose "Not Applicable" from "What is the data release strategy for this study?"
     And I select "never" from "How is the data release to be timed?"
-    And I choose "Yes" from "Has this been approved?"
+    And I select "Protecting IP - DAC approval required" from "What is the reason for preventing data release?"
+    And I fill in "If reason for exemption requires DAC approval, what is the approval number?" with "12345"
     When I press "Create"
     Then I should be on the studies page
     # Again, ideally without study metadata
     And I should see "Study metadata data release prevention reason comment can't be blank"
 
   Scenario: When the data release is never and the comment is supplied
-    When I choose "Not Applicable (Contact Datasharing)" from "What is the data release strategy for this study?"
+    When I choose "Not Applicable" from "What is the data release strategy for this study?"
     And I select "never" from "How is the data release to be timed?"
+    And I select "Protecting IP - DAC approval required" from "What is the reason for preventing data release?"
     And I fill in "Comment regarding prevention of data release and approval" with "Some reason"
-    And I choose "Yes" from "Has this been approved?"
+    And I fill in "If reason for exemption requires DAC approval, what is the approval number?" with "12345"
     When I press "Create"
     Then I should be on the study information page for "Testing data release strategies"
     And I should see "Your study has been created"

features/support/step_definitions/study_steps.rb

@@ -159,10 +159,9 @@ def given_study_metadata(attribute, regexp)
   study.update!(
     study_metadata_attributes: {
       data_release_timing: 'delayed',
-      data_release_delay_reason: 'other',
+      data_release_delay_reason: 'Other (with free text box)',
       data_release_delay_other_comment: reason,
       data_release_delay_period: "#{period} months",
-      data_release_delay_approval: 'Yes',
       data_release_delay_reason_comment: reason
     }
   )

spec/factories/study_factories.rb

@@ -54,7 +54,7 @@
       new_field_values = {
         data_release_strategy: 'not applicable',
         data_release_timing: 'never',
-        data_release_prevention_reason: 'data validity',
+        data_release_prevention_reason: 'Protecting IP - DAC approval required',
         data_release_prevention_approval: 'Yes',
         data_release_prevention_reason_comment: 'This is the reason context'
       }

spec/features/studies/create_study_spec.rb

@@ -40,7 +40,7 @@
     within_fieldset('What is the data release strategy for this study?') do
       expect(page).to have_field('Open (ENA)', type: :radio)
       expect(page).to have_field('Managed (EGA)', type: :radio)
-      expect(page).to have_field('Not Applicable (Contact Datasharing)', type: :radio)
+      expect(page).to have_field('Not Applicable', type: :radio)
     end
 
     within_fieldset('Study Visibility') do
@@ -132,8 +132,8 @@
       expect(page).to have_field('HuMFre approval number', type: :text)
     end
 
-    it 'displays HuMFre approval number when Not Applicable (Contact Datasharing) is clicked' do
-      choose('Not Applicable (Contact Datasharing)', allow_label_click: true)
+    it 'displays HuMFre approval number when Not Applicable is clicked' do
+      choose('Not Applicable', allow_label_click: true)
       expect(page).to have_field('HuMFre approval number', type: :text)
     end
   end

spec/features/studies/edit_study_spec.rb

@@ -69,8 +69,8 @@
       expect(page).to have_field('HuMFre approval number', type: :text)
     end
 
-    it 'displays HuMFre approval number when Not Applicable (Contact Datasharing) is clicked' do
-      choose('Not Applicable (Contact Datasharing)', allow_label_click: true)
+    it 'displays HuMFre approval number when Not Applicable is clicked' do
+      choose('Not Applicable', allow_label_click: true)
       expect(page).to have_field('HuMFre approval number', type: :text)
     end
   end

spec/features/studies/manage_study_spec.rb

@@ -34,8 +34,8 @@
       expect(page).to have_field('HuMFre approval number', type: :text)
     end
 
-    it 'displays HuMFre approval number when Not Applicable (Contact Datasharing) is clicked' do
-      choose('Not Applicable (Contact Datasharing)', allow_label_click: true)
+    it 'displays HuMFre approval number when Not Applicable is clicked' do
+      choose('Not Applicable', allow_label_click: true)
       expect(page).to have_field('HuMFre approval number', type: :text)
     end
   end

spec/features/studies/view_study_properties_spec.rb

@@ -52,7 +52,7 @@
       expect(page).to have_content('HuMFre approval number: 12345')
     end
 
-    it 'displays HuMFre approval number for Not Applicable (Contact Datasharing) data release strategy' do
+    it 'displays HuMFre approval number for Not Applicable data release strategy' do
       study.study_metadata.data_release_strategy = Study::DATA_RELEASE_STRATEGY_NOT_APPLICABLE
       study.study_metadata.data_release_timing = Study::DATA_RELEASE_TIMING_NEVER
       study.study_metadata.data_release_prevention_reason = Study::DATA_RELEASE_PREVENTION_REASONS[0]

spec/models/study_spec.rb

@@ -445,7 +445,7 @@
         data_release_strategy: 'open',
         data_release_standard_agreement: 'Yes',
         data_release_timing: 'standard',
-        data_release_delay_reason: 'phd study',
+        data_release_delay_reason: 'PhD study',
         data_release_delay_period: '3 months',
         bam: true,
         data_release_delay_other_comment: 'Data Release delay other comment',
@@ -456,7 +456,7 @@
         ega_policy_accession_number: 'POL123456',
         array_express_accession_number: 'ARR123456',
         data_release_delay_approval: 'Yes',
-        data_release_prevention_reason: 'data validity',
+        data_release_prevention_reason: 'Protecting IP - DAC approval required',
         data_release_prevention_approval: 'Yes',
         data_release_prevention_reason_comment: 'Data Release prevention reason comment',
         data_access_group: 'something',
@@ -713,7 +713,10 @@
         create(
           :study,
           study_metadata:
-            create(:study_metadata, metadata.merge(data_release_timing: 'delayed', data_release_delay_reason: 'other'))
+            create(
+              :study_metadata,
+              metadata.merge(data_release_timing: 'delayed', data_release_delay_reason: 'Other (with free text box)')
+            )
         )
       end
 
@@ -739,23 +742,6 @@
       end
     end
 
-    context 'delayed for long time' do
-      let(:study) do
-        create(
-          :study,
-          study_metadata:
-            create(
-              :study_metadata,
-              metadata.merge(data_release_timing: 'delayed', data_release_delay_period: '6 months')
-            )
-        )
-      end
-
-      it 'will have a data_release_delay_approval' do
-        expect(study.study_metadata.data_release_delay_approval).to eq(metadata[:data_release_delay_approval])
-      end
-    end
-
     context 'never released' do
       let(:never_release_fields) do
         {