refactor investigation controller, and handle external id mismatch th…

…rough an exception #1981
seek4science · Sep 24, 2024 · e54eb13 · e54eb13
1 parent da8e381
commit e54eb13
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Showing 4 changed files with 35 additions and 17 deletions.
diff --git a/app/controllers/investigations_controller.rb b/app/controllers/investigations_controller.rb
@@ -37,23 +37,18 @@ def new_object_based_on_existing_one
 
   def submit_fairdata_station
     path = params[:datastation_data].path
-    datastation_inv = Seek::FairDataStation::Reader.new.parse_graph(path).first
-    error = false
-    if datastation_inv.external_id != @investigation.external_identifier
-      flash[:error] = "This #{t('investigation')} does not match the identifier provided in the FAIR Data Station metadata"
-      error = true
-    else
-      begin
-        Investigation.transaction do
-          @investigation = Seek::FairDataStation::Writer.new.update_isa(@investigation, datastation_inv, current_person, @investigation.projects, @investigation.policy)
-          @investigation.save!
-        end
-      rescue ActiveRecord::RecordInvalid => e
-        flash[:error] = e.message
-        error = true
+    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[:error] = e.message
     end
-    if error
+
+    if flash[:error].present?
       respond_to do |format|
         format.html { render action: :update_from_fairdata_station, status: :unprocessable_entity }
       end

diff --git a/lib/seek/fair_data_station/writer.rb b/lib/seek/fair_data_station/writer.rb
@@ -1,5 +1,6 @@
 module Seek
   module FairDataStation
+    class ExternalIdMismatchException < RuntimeError; end;
     class Writer
       def construct_isa(datastation_inv, contributor, projects, policy)
         reset_data_file_cache
@@ -23,6 +24,10 @@ def construct_isa(datastation_inv, contributor, projects, policy)
       end
 
       def update_isa(investigation, datastation_inv, contributor, projects, policy)
+        unless investigation.external_identifier == datastation_inv.external_id
+          raise ExternalIdMismatchException.new('Investigation external identifiers do not match')
+        end
+
         preload_data_file_cache(investigation.related_data_files)
         update_entity(investigation, datastation_inv, contributor, projects, policy)
         datastation_inv.studies.each do |datastation_study|

diff --git a/test/functional/investigations_controller_test.rb b/test/functional/investigations_controller_test.rb
@@ -1378,8 +1378,8 @@ def test_title
             assert_no_difference('Assay.count') do
               post :submit_fairdata_station, params: {id: investigation, datastation_data: ttl_file }
               assert_response :unprocessable_entity
-              assert_match /This Investigation does not match the identifier provided in the FAIR Data Station metadata/, flash[:error]
-              assert_select 'div#error_flash', text: /This Investigation does not match the identifier provided in the FAIR Data Station metadata/
+              assert_match /Investigation external identifiers do not match/, flash[:error]
+              assert_select 'div#error_flash', text: /Investigation external identifiers do not match/
             end
           end
         end

diff --git a/test/unit/fair_data_station/fair_data_station_writer_test.rb b/test/unit/fair_data_station/fair_data_station_writer_test.rb
@@ -406,6 +406,24 @@ class FairDataStationWriterTest < ActiveSupport::TestCase
     assert_equal 'seek-test-study-1', assay.study.external_identifier
   end
 
+  test 'update_isa id mis match' do
+    investigation = setup_test_case_investigation
+    policy = investigation.policy
+    projects = investigation.projects
+    contributor = investigation.contributor
+
+    path = "#{Rails.root}/test/fixtures/files/fairdatastation/demo.ttl"
+    inv = Seek::FairDataStation::Reader.new.parse_graph(path).first
+
+    refute_equal investigation.external_identifier, inv.external_id
+
+    assert_raises(Seek::FairDataStation::ExternalIdMismatchException) do
+      investigation = Seek::FairDataStation::Writer.new.update_isa(investigation, inv, contributor,
+                                                                   projects, policy)
+    end
+
+  end
+
   private
 
   def setup_test_case_investigation