Merging from FAIR Data Station

app/controllers/investigations_controller.rb

@@ -5,12 +5,13 @@ class InvestigationsController < ApplicationController
   include Seek::AssetsCommon
 
   before_action :investigations_enabled?
-  before_action :find_assets, :only=>[:index]
-  before_action :find_and_authorize_requested_item,:only=>[:edit, :manage, :update, :manage_update, :destroy, :show,:new_object_based_on_existing_one]
+  before_action :fair_data_station_enabled?, only: %i[update_from_fairdata_station submit_fairdata_station]
+  before_action :find_assets, only: [:index]
+  before_action :find_and_authorize_requested_item, only: [:edit, :manage, :update, :manage_update, :destroy, :show, :update_from_fairdata_station, :submit_fairdata_station, :new_object_based_on_existing_one]
 
   #project_membership_required_appended is an alias to project_membership_required, but is necesary to include the actions
   #defined in the application controller
-  before_action :project_membership_required_appended, :only=>[:new_object_based_on_existing_one]
+  before_action :project_membership_required_appended, only: [:new_object_based_on_existing_one]
 
   before_action :check_studies_are_for_this_investigation, only: %i[update]
 
@@ -34,6 +35,30 @@ def new_object_based_on_existing_one
 
   end
 
+  def submit_fairdata_station
+    path = params[:datastation_data].path
+    data_station_inv = Seek::FairDataStation::Reader.new.parse_graph(path).first
+
+    begin
+      Investigation.transaction do
+        @investigation = Seek::FairDataStation::Writer.new.update_isa(@investigation, data_station_inv, current_person, @investigation.projects, @investigation.policy)
+        @investigation.save!
+      end
+    rescue ActiveRecord::RecordInvalid, Seek::FairDataStation::ExternalIdMismatchException => e
+      flash.now[:error] = e.message
+    end
+
+    if flash[:error].present?
+      respond_to do |format|
+        format.html { render action: :update_from_fairdata_station, status: :unprocessable_entity }
+      end
+    else
+      respond_to do |format|
+        format.html { redirect_to(@investigation) }
+      end
+    end
+  end
+
   def export_isatab_json
     the_hash = IsaTabConverter.convert_investigation(Investigation.find(params[:id]))
     send_data JSON.pretty_generate(the_hash) , filename: 'isatab.json'

app/controllers/projects_controller.rb

@@ -203,13 +203,23 @@ def submit_fairdata_station
     path = params[:datastation_data].path
     policy = Policy.new
     policy.set_attributes_with_sharing(policy_params)
-    datadata_inv = Seek::FairDataStation::Reader.new.parse_graph(path)
-    @investigation = Seek::FairDataStation::Writer.new.construct_isa(datadata_inv.first, current_person, [@project], policy)
-    @investigation.save!
+    fair_data_station_inv = Seek::FairDataStation::Reader.new.parse_graph(path).first
+    @existing_investigation = Investigation.by_external_identifier(fair_data_station_inv.external_id,[@project])
 
-    respond_to do |format|
-      format.html { redirect_to(@investigation) }
+    if @existing_investigation
+      flash.now[:error] = "An #{t('investigation')} with that external identifier already exists for this #{t('project')}"
+      respond_to do |format|
+        format.html { render action: :import_from_fairdata_station, status: :unprocessable_entity }
+      end
+    else
+      @investigation = Seek::FairDataStation::Writer.new.construct_isa(fair_data_station_inv, current_person, [@project], policy)
+      @investigation.save!
+
+      respond_to do |format|
+        format.html { redirect_to(@investigation) }
+      end
     end
+
   end
 
   def request_create

app/helpers/investigations_helper.rb

@@ -11,6 +11,10 @@ def investigation_link(investigation)
     end
   end
 
+  def show_update_from_fair_data_station_button?(investigation)
+    Seek::Config.fair_data_station_enabled && investigation.external_identifier.present? && investigation.can_manage?
+  end
+
   def authorised_investigations(projects = nil)
     authorised_assets(Investigation, projects, 'view')
   end

app/models/concerns/has_external_identifier.rb

@@ -16,6 +16,15 @@ def has_external_identifier
         end
       end
     end
+
+    # returns an item where :external_identifier and any of the projects match
+    def by_external_identifier(external_identifier, projects)
+      self.where(external_identifier: external_identifier).each do |item|
+        return item if (item.projects & projects).any?
+      end
+      nil
+    end
+
   end
 
   module InstanceMethods

app/views/investigations/_buttons.html.erb

@@ -47,5 +47,11 @@
 
   <%= order_icon(item, current_user, order_studies_investigation_path(item), item.studies, 'study') -%>
 
+	<% if show_update_from_fair_data_station_button?(item) %>
+		<li>
+			<%= image_tag_for_key('import', update_from_fairdata_station_investigation_path(item), "Update from FAIR Data Station", nil, "Update from FAIR Data Station") -%>
+		</li>
+	<% end %>
+
   <%= delete_icon item, current_user -%>
 <% end -%>

app/views/investigations/update_from_fairdata_station.html.erb

@@ -0,0 +1,14 @@
+<%= render partial: "general/page_title",locals: {title: "Update from FAIR Data Station for #{ t('investigation') } #{link_to(@investigation.title, @investigation)}".html_safe} %>
+
+<%= form_tag submit_fairdata_station_investigation_path(@investigation), multipart: true do %>
+
+  <%= panel('FAIR Data Station turtle (ttl) metadata file') do %>
+
+    <%= file_field_tag "datastation_data", accept: '.ttl' -%>
+
+  <% end %>
+
+  <div>
+    <%= submit_tag("Submit", class: 'btn btn-primary') %>
+  </div>
+<% end %>

app/views/projects/_buttons.html.erb

@@ -62,14 +62,16 @@
       <%= order_icon(item,current_user, order_investigations_project_path(item), item.investigations, 'investigation') %>
     <% end %>
 
-    <% if admin_logged_in? || item.can_manage? -%>
-      <%= delete_icon(item,current_user,"Any members will also be removed from the #{t('project')}, are you sure?") %>
-    <% end -%>
     <% if Seek::Config.fair_data_station_enabled %>
       <li>
-        <%= image_tag_for_key('import', import_from_fairdata_station_project_path(item), "Import from FAIRData Station", nil, "Import from FAIRData Station") -%>
+        <%= image_tag_for_key('import', import_from_fairdata_station_project_path(item), "Import from FAIR Data Station", nil, "Import from FAIR Data Station") -%>
       </li>
     <% end %>
 
+    <% if admin_logged_in? || item.can_manage? -%>
+      <%= delete_icon(item,current_user,"Any members will also be removed from the #{t('project')}, are you sure?") %>
+    <% end -%>
+
+
   <% end -%>
 <% end -%>

app/views/projects/import_from_fairdata_station.html.erb

@@ -1,4 +1,24 @@
-<%= render :partial => "general/page_title",:locals=>{:title=>"Import ISA from FAIRData Station for #{ t('Project') } #{link_to(@project.title, @project)}".html_safe} %>
+<%= render partial: "general/page_title",locals: {title: "Import ISA from FAIR Data Station for #{ t('Project') } #{link_to(@project.title, @project)}".html_safe} %>
+
+<% if @existing_investigation %>
+  <%= panel("#{image("warning")} Existing #{t('investigation')}", id: 'existing-investigation') do %>
+
+    <p>
+      A matching <%= t('investigation') %> already
+      exists: <%= link_to(@existing_investigation.title, @existing_investigation) %>
+    </p>
+    <p>
+      You can update this <%= t('investigation') %> by going
+      to <%= link_to('Update from FAIR Data Station', update_from_fairdata_station_investigation_path(@existing_investigation)) %>
+    </p>
+
+  <% end %>
+
+  <p>
+    Otherwise you can try importing a different file ...
+  </p>
+
+<% end %>
 
 <%= form_tag submit_fairdata_station_project_path(@project), multipart: true do %>
 
@@ -24,4 +44,5 @@
   <div>
     <%= submit_tag("Submit", class: 'btn btn-primary') %>
   </div>
-<% end %>
+<% end %>
+

config/routes.rb

@@ -420,6 +420,8 @@
       get :manage
       get :order_studies
       patch :manage_update
+      get :update_from_fairdata_station
+      post :submit_fairdata_station
     end
     resources :people, :programmes, :projects, :assays, :studies, :models, :sops, :workflows, :data_files, :publications, :documents, :observation_units, :samples, only: [:index]
   end

db/seeds/extended_metadata_drafts/test_and_demo_extended_metadata.seeds.rb

@@ -11,4 +11,67 @@
 
   emt.save!
   puts 'Test linking registered resources'
-end
+end
+
+
+# fair data station simple seek test case
+
+unless ExtendedMetadataType.where(title: 'FAIR Data Station Investigation Test Case', supported_type: 'Investigation').any?
+  emt = ExtendedMetadataType.new(title: 'FAIR Data Station Investigation Test Case', supported_type: 'Investigation',
+                                 extended_metadata_attributes_attributes: [
+                                   { title: 'Associated publication', pid: 'http://fairbydesign.nl/ontology/associated_publication', sample_attribute_type: string_attribute_type }
+                                 ])
+  emt.save!
+  puts "Created #{emt.title}"
+end
+
+unless ExtendedMetadataType.where(title: 'FAIR Data Station Study Test Case', supported_type: 'Study').any?
+  emt = ExtendedMetadataType.new(title: 'FAIR Data Station Study Test Case', supported_type: 'Study',
+                                 extended_metadata_attributes_attributes: [
+                                   { title: 'End date of Study', pid: 'http://fairbydesign.nl/ontology/end_date_of_study', sample_attribute_type: string_attribute_type },
+                                   { title: 'Start date of Study', pid: 'http://fairbydesign.nl/ontology/start_date_of_study', sample_attribute_type: string_attribute_type },
+                                   { title: 'Experimental site name', pid: 'http://fairbydesign.nl/ontology/experimental_site_name', sample_attribute_type: string_attribute_type }
+                                 ])
+  emt.save!
+  puts "Created #{emt.title}"
+end
+
+unless ExtendedMetadataType.where(title: 'FAIR Data Station ObservationUnit Test Case', supported_type: 'ObservationUnit').any?
+  emt = ExtendedMetadataType.new(title: 'FAIR Data Station ObservationUnit Test Case', supported_type: 'ObservationUnit',
+                                 extended_metadata_attributes_attributes: [
+                                   { title: 'Birth weight', pid: 'http://fairbydesign.nl/ontology/birth_weight', sample_attribute_type: string_attribute_type },
+                                   { title: 'Date of birth', pid: 'http://fairbydesign.nl/ontology/date_of_birth', sample_attribute_type: string_attribute_type },
+                                   { title: 'Gender', pid: 'https://w3id.org/mixs/0000811', sample_attribute_type: string_attribute_type }
+                                 ])
+  emt.save!
+  puts "Created #{emt.title}"
+end
+
+unless ExtendedMetadataType.where(title: 'FAIR Data Station Assay Test Case', supported_type: 'Assay').any?
+  emt = ExtendedMetadataType.new(title: 'FAIR Data Station Assay Test Case', supported_type: 'Assay',
+                                 extended_metadata_attributes_attributes: [
+                                   { title: 'Facility', pid: 'http://fairbydesign.nl/ontology/facility', sample_attribute_type: string_attribute_type },
+                                   { title: 'Protocol', pid: 'http://fairbydesign.nl/ontology/protocol', sample_attribute_type: string_attribute_type }
+                                 ])
+  emt.save!
+  puts "Created #{emt.title}"
+end
+
+unless SampleType.where(title: 'Fair Data Station SampleType Test Case').any?
+  sample_type = SampleType.new(title: 'Fair Data Station SampleType Test Case',
+                               project_ids: [Project.first.id],
+                               contributor: Person.first,
+                               sample_attributes_attributes: [
+                                 { title: 'Title', sample_attribute_type: string_attribute_type, required: true, is_title: true },
+                                 { title: 'Description', sample_attribute_type: string_attribute_type },
+                                 { title: 'Bio safety level', pid: 'http://fairbydesign.nl/ontology/biosafety_level', sample_attribute_type: string_attribute_type },
+                                 { title: 'Scientific name', pid: 'http://gbol.life/0.1/scientificName', sample_attribute_type: string_attribute_type },
+                                 { title: 'Organism ncbi id', pid: 'http://purl.uniprot.org/core/organism', sample_attribute_type: string_attribute_type },
+                                 { title: 'Collection date', pid: 'https://w3id.org/mixs/0000011', sample_attribute_type: string_attribute_type }
+                               ])
+  disable_authorization_checks do
+    sample_type.save!
+    puts "Created #{sample_type.title}"
+  end
+end
+

lib/seek/fair_data_station/base.rb

@@ -87,8 +87,12 @@ def fetch_children
         query.execute.collect(&:child)
       end
 
+      def external_id
+        identifier
+      end
+
       def seek_attributes
-        { title: title, description: description, external_identifier: identifier }
+        { title: title, description: description, external_identifier: external_id }
       end
 
       def populate_extended_metadata(seek_resource)