crude controller action and views for investigation to support updati…

…ng from FDS #1981

for testing out

app/controllers/investigations_controller.rb

@@ -6,7 +6,7 @@ class InvestigationsController < ApplicationController
 
   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 :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
@@ -34,6 +34,18 @@ def new_object_based_on_existing_one
 
   end
 
+  def submit_fairdata_station
+    path = params[:datastation_data].path
+    datastation_inv = Seek::FairDataStation::Reader.new.parse_graph(path).first
+    raise 'identifiers dont match' if datastation_inv.external_id != @investigation.external_identifier
+    @investigation = Seek::FairDataStation::Writer.new.update_isa(@investigation, datastation_inv, current_person, @investigation.projects, @investigation.policy)
+    @investigation.save!
+
+    respond_to do |format|
+      format.html { redirect_to(@investigation) }
+    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/views/investigations/_buttons.html.erb

@@ -47,5 +47,11 @@
 
   <%= order_icon(item, current_user, order_studies_investigation_path(item), item.studies, 'study') -%>
 
+	<% if Seek::Config.fair_data_station_enabled && item.can_manage? %>
+		<li>
+			<%= image_tag_for_key('import', update_from_fairdata_station_investigation_path(item), "Update from FAIRData Station", nil, "Update from FAIRData 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 FAIRData 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") -%>
       </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 -%>

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

lib/seek/permissions/translator.rb

@@ -30,6 +30,7 @@ class Translator
                           manage manage_update notification read_interaction write_interaction report_problem storage_report
                           select_sample_type extraction_status persistence_status extract_samples confirm_extraction cancel_extraction
                           upload_fulltext upload_pdf soft_delete_fulltext has_matching_sample_type unzip unzip_status confirm_unzip unzip_persistence_status cancel_unzip
+                          update_from_fairdata_station submit_fairdata_station
                         ]).freeze
       }.freeze