Additions to the observation unit UI

app/controllers/admin_controller.rb

@@ -121,6 +121,7 @@ def update_features_enabled
  Seek::Config.documents_enabled = string_to_boolean params[:documents_enabled]
  Seek::Config.events_enabled = string_to_boolean params[:events_enabled]
  Seek::Config.isa_enabled = string_to_boolean params[:isa_enabled]
+ Seek::Config.observation_units_enabled = string_to_boolean params[:observation_units_enabled]
  Seek::Config.models_enabled = string_to_boolean params[:models_enabled]
  Seek::Config.organisms_enabled = string_to_boolean params[:organisms_enabled]
  Seek::Config.programmes_enabled = string_to_boolean params[:programmes_enabled]

app/controllers/observation_units_controller.rb

@@ -10,6 +10,9 @@ class ObservationUnitsController < ApplicationController
  before_action :login_required,:except=>[:show,:index]
  before_action :find_assets, only: [:index]
 
+ include Seek::Publishing::PublishingCommon
+ include Seek::IsaGraphExtensions
+
  api_actions :index, :show, :create, :update, :destroy
 
  def show

app/views/admin/features_enabled.html.erb

@@ -58,7 +58,8 @@
 
  <%= admin_checkbox_setting(:isa_enabled, 1, Seek::Config.isa_enabled,
  "ISA enabled", "Whether the ISA framework is enabled. The ISA framework allows users to create Investigations, Studies and Assays to organize their work.") %>
-
+ <%= admin_checkbox_setting(:observation_units_enabled, 1, Seek::Config.observation_units_enabled,
+ "Observation Units enabled", "Whether the users can register Observation Units to organize their work.") %>
  <%= admin_checkbox_setting(:models_enabled, 1, Seek::Config.models_enabled,
  "Models enabled", "Whether the users can register computational models in SEEK.") %>
 

app/views/assets/_resource_preview.html.erb

@@ -11,7 +11,7 @@
 
  <%= list_item_contributors resource -%>
 
- <%= list_item_simple_list resource.creators, t('contributor').capitalize -%>
+ <%= list_item_simple_list resource.creators, t('creator').capitalize.pluralize -%>
 
  <%= list_item_description resource.description -%>
  </div>

app/views/observation_units/_form.html.erb

@@ -0,0 +1,34 @@
+<div class="asset_form">
+ <%= f.error_messages %>
+
+ <div class="form-group">
+ <label class="required">Title</label>
+ <%= f.text_field :title, class: "form-control" -%>
+ </div>
+
+ <div class="form-group">
+ <label>Description</label>
+ <%= f.text_area :description, class: "form-control rich-text-edit", rows: 5 -%>
+ </div>
+
+ <%= render partial: 'extended_metadata/extended_metadata_type_selection', locals: { f: f, resource: @observation_unit } %>
+ <%= render partial: 'extended_metadata/extended_metadata_attribute_input', locals: { f: f, resource: @observation_unit } %>
+
+ <% if action == :new %>
+ <%= render partial: "projects/project_selector", locals: { resource: @observation_unit } %>
+ <% end %>
+
+ <div class="form-group">
+ <label class="required"><%= t('study') -%></label>
+
+ <%= resource_study_selection('observation_unit[study_id]', @observation_unit.study) %>
+ </div>
+
+ <%= render partial: "assets/asset_form_bottom", locals: {show_publications:false, attribution_enable: false, f: f} %>
+ <%= f.fancy_multiselect :data_files, other_projects_checkbox: true %>
+ <%= f.fancy_multiselect :samples, other_projects_checkbox: true %>
+
+
+ <%= form_submit_buttons(@observation_unit) %>
+
+</div>

app/views/observation_units/edit.html.erb

@@ -2,27 +2,5 @@
 <h1>Editing <%= t('observation_unit') %>: <%= link_to(h(@observation_unit.title), observation_unit_path(@observation_unit)) -%></h1>
 
 <%= form_for(@observation_unit) do |f| %>
- <div class="asset_form">
- <%= f.error_messages %>
-
- <div class="form-group">
- <label class="required">Title</label>
- <%= f.text_field :title, class: "form-control" -%>
- </div>
-
- <div class="form-group">
- <label>Description</label>
- <%= f.text_area :description, class: "form-control rich-text-edit", rows: 5 -%>
- </div>
-
- <%= render partial: 'extended_metadata/extended_metadata_type_selection', locals: { f: f, resource: @observation_unit } %>
- <%= render partial: 'extended_metadata/extended_metadata_attribute_input', locals: { f: f, resource: @observation_unit } %>
-
-
- <%= render partial: "assets/asset_form_bottom", locals: {show_publications:false, attribution_enable: false, f: f}-%>
-
-
- <%= form_submit_buttons(@observation_unit) %>
-
- </div>
-<% end %>
+ <%= render partial: "form", locals: { f: f, action: :edit } -%>
+<% end %>

app/views/observation_units/new.html.erb

@@ -1,35 +1,21 @@
-
-<h1>New <%= t('observation_unit') %></h1>
-
-<%= form_for(@observation_unit) do |f| %>
- <div class="asset_form">
- <%= f.error_messages %>
-
- <div class="form-group">
- <label class="required">Title</label>
- <%= f.text_field :title, class: "form-control" -%>
+<% if Investigation.authorized_for('view').none? %>
+ <%= alert_box('info') do %>
+ <%= "No #{t('study')} and #{t('investigation')} available, you have to create a new #{t('investigation')} first before creating your #{t('study')} and #{t('observation_unit')}!" %>
+ <% end %>
+ <div class="text-center">
+ <%= button_link_to("New #{t('investigation')}", 'arrow_right', new_investigation_path) -%>
  </div>
-
- <div class="form-group">
- <label>Description</label>
- <%= f.text_area :description, class: "form-control rich-text-edit", rows: 5 -%>
+<% elsif Study.authorized_for('view').none? %>
+ <%= alert_box('info') do %>
+ <%= "No #{t('study')} available, you have to create a new #{t('study')} before creating your #{t('observation_unit')}!" %>
+ <% end %>
+ <div class="text-center">
+ <%= button_link_to("New #{t('study')}", 'arrow_right', new_study_path) -%>
  </div>
-
- <%= render partial: 'extended_metadata/extended_metadata_type_selection', locals: { f: f, resource: @observation_unit } %>
- <%= render partial: 'extended_metadata/extended_metadata_attribute_input', locals: { f: f, resource: @observation_unit } %>
-
- <%= render partial: "projects/project_selector", locals: { resource: @observation_unit } %>
-
- <div class="form-group">
- <label class="required"><%= t('study') -%></label>
-
- <%= resource_study_selection('observation_unit[study_id]', @observation_unit.study) %>
- </div>
-
- <%= render partial: "assets/asset_form_bottom", locals: {show_publications:false, attribution_enable: false, f: f}-%>
-
-
- <%= form_submit_buttons(@observation_unit) %>
-
- </div>
-<% end %>
+<% else %>
+ <h1>New <%= t('observation_unit') %></h1>
+ <%= index_and_new_help_icon controller_name %>
+ <%= form_for @observation_unit do |f| %>
+ <%= render partial: "form", locals: { f: f, action: :new } -%>
+ <% end %>
+<% end %>

app/views/samples/_resource_preview.html.erb

@@ -1 +1,16 @@
-<strong>Preview Not Yet Implemented</strong>
+<% unless resource.nil? -%>
+
+ <div data-tooltip='<%= tooltip(h(resource.title)) %>'>
+ <p class="title">
+ <%= list_item_title resource -%>
+ </p>
+
+ <%= render :partial => 'projects/show_project_relationship', :locals => {:resource => resource, :list_item => false} -%>
+
+ <%= list_item_contributors resource -%>
+
+ <%= list_item_simple_list resource.creators, t('creator').capitalize.pluralize -%>
+ <%= sample_type_list_item_attribute(t('sample_type'),resource) %>
+ </div>
+
+<% end -%>

config/initializers/seek_configuration.rb

@@ -82,6 +82,7 @@ def load_seek_config_defaults!
  Seek::Config.default :data_files_enabled,true
  Seek::Config.default :events_enabled,true
  Seek::Config.default :isa_enabled, true
+ Seek::Config.default :observation_units_enabled,true
  Seek::Config.default :models_enabled,true
  Seek::Config.default :organisms_enabled,true
  Seek::Config.default :programmes_enabled, false

config/initializers/seek_testing.rb

@@ -37,6 +37,7 @@ def load_seek_testing_defaults!
  Settings.defaults[:file_templates_enabled] = true
  Settings.defaults[:human_diseases_enabled] = true
  Settings.defaults[:isa_enabled] = true
+ Settings.defaults[:observation_units_enabled] = true
  Settings.defaults[:models_enabled] = true
  Settings.defaults[:organisms_enabled] = true
  Settings.defaults[:programmes_enabled] = true

config/locales/en.yml

@@ -16,6 +16,7 @@ en:
  investigation: &investigation "Investigation"
  study: &study "Study"
  assay: &assay "Assay"
+ observation_unit: &observation_unit "Observation Unit"
  assays:
  assay: "Assay"
  experimental_assay: "Experimental assay"

lib/seek/add_buttons.rb

@@ -21,7 +21,8 @@ class AddButtons
  [Workflow, 'workflow[project_ids][]']
  ],
  'Investigation' => [[Study, 'study[investigation_id]']],
- 'Study' => [[Assay, 'assay[study_id]']],
+ 'Study' => [[Assay, 'assay[study_id]'],
+ [ObservationUnit, 'observation_unit[study_id]']],
  'Modelling Analysis' => [[DataFile, 'data_file[assay_assets_attributes[][assay_id]]'],
  [Document, 'document[assay_assets_attributes[][assay_id]]'],
  [Sop, 'sop[assay_assets_attributes[][assay_id]]'],

lib/seek/config.rb

@@ -340,10 +340,6 @@ def strains_enabled
  organisms_enabled
  end
 
- def observation_units_enabled
- fair_data_station_enabled
- end
-
  def omniauth_elixir_aai_config
  if omniauth_elixir_aai_legacy_mode
  {

lib/seek/config_setting_attributes.yml

@@ -205,6 +205,7 @@ data_files_enabled:
 documents_enabled:
 events_enabled:
 isa_enabled:
+observation_units_enabled:
 models_enabled:
 organisms_enabled:
 programmes_enabled:

test/functional/observation_units_controller_test.rb

@@ -36,13 +36,19 @@ def rdf_test_object
  login_as(unit.contributor)
  get :edit, params: { id: unit.id}
  assert_response :success
+ assert_select 'form.edit_observation_unit' do
+ assert_select 'div#project-selector', count: 0
+ end
  end
 
  test 'manage' do
  unit = FactoryBot.create(:max_observation_unit)
  login_as(unit.contributor)
  get :manage, params: { id: unit.id}
  assert_response :success
+ assert_select 'form.edit_observation_unit' do
+ assert_select 'div#project-selector'
+ end
  end
 
  test 'manage update' do
@@ -83,12 +89,16 @@ def rdf_test_object
  test 'update' do
  obs_unit = FactoryBot.create(:observation_unit)
  emt = FactoryBot.create(:simple_observation_unit_extended_metadata_type)
+ datafile = FactoryBot.create(:data_file, contributor: obs_unit.contributor)
+ sample = FactoryBot.create(:sample, contributor: obs_unit.contributor)
  login_as(obs_unit.contributor)
 
  patch :update, params: { id: obs_unit,
  observation_unit:{
  title: 'updated title',
  description: 'updated description',
+ data_file_ids: [datafile.id],
+ sample_ids: [sample.id],
  extended_metadata_attributes: {
  extended_metadata_type_id: emt.id,
  data: {
@@ -109,20 +119,27 @@ def rdf_test_object
  assert_equal 'updated name', obs_unit.extended_metadata.get_attribute_value('name')
  assert_equal 'updated strain', obs_unit.extended_metadata.get_attribute_value('strain')
  assert_equal %w[fish soup], obs_unit.tags.sort
+ assert_equal [datafile], obs_unit.data_files
+ assert_equal [sample], obs_unit.samples
  end
 
  test 'new' do
  person = FactoryBot.create(:person)
+ FactoryBot.create(:study, contributor: person)
  login_as(person)
  get :new
  assert_response :success
- assert_select 'form.new_observation_unit'
+ assert_select 'form.new_observation_unit' do
+ assert_select 'div#project-selector'
+ end
  end
 
  test 'create' do
  emt = FactoryBot.create(:simple_observation_unit_extended_metadata_type)
  contributor = FactoryBot.create(:person)
  study = FactoryBot.create(:study, contributor: contributor)
+ datafile = FactoryBot.create(:data_file, contributor: contributor)
+ sample = FactoryBot.create(:sample, contributor: contributor)
  project = contributor.projects.first
  other_person = FactoryBot.create(:person)
  creator = FactoryBot.create(:person)
@@ -132,7 +149,9 @@ def rdf_test_object
  title: 'new title',
  description: 'new description',
  creator_ids: [creator.id],
- project_ids: [project],
+ project_ids: [project.id],
+ data_file_ids: [datafile.id],
+ sample_ids: [sample.id],
  study_id: study,
  extended_metadata_attributes: {
  extended_metadata_type_id: emt.id,
@@ -158,18 +177,20 @@ def rdf_test_object
  assert_equal 'new strain', obs_unit.extended_metadata.get_attribute_value('strain')
  assert_equal %w[fish soup], obs_unit.tags.sort
  assert_equal contributor, obs_unit.contributor
- assert_equal [project],obs_unit.projects.sort_by(&:id)
+ assert_equal [project],obs_unit.projects
  assert_equal [creator],obs_unit.creators
+ assert_equal [datafile],obs_unit.data_files
+ assert_equal [sample],obs_unit.samples
  assert_equal Policy::VISIBLE,obs_unit.policy.access_type
  assert_equal 1,obs_unit.policy.permissions.count
  assert_equal other_person,obs_unit.policy.permissions.first.contributor
  assert_equal Policy::MANAGING,obs_unit.policy.permissions.first.access_type
  end
 
- test 'no access if fair data station disabled' do
+ test 'no access if observation units disabled' do
  unit = FactoryBot.create(:max_observation_unit)
  login_as(unit.contributor)
- with_config_value(:fair_data_station_enabled, false) do
+ with_config_value(:observation_units_enabled, false) do
  get :show, params: { id: unit.id }
  assert_redirected_to :root
  refute_nil flash[:error]