feat: include chemicals with import and export of collections (#1604)

lib/export/export_collections.rb

@@ -125,6 +125,7 @@ def prepare_data
           'user_id' => 'User'
         })
         fetch_samples collection
+        fetch_chemicals collection
         fetch_reactions collection
         # fetch_elements collection if @gt == false
         fetch_wellplates collection if @gt == false
@@ -135,6 +136,14 @@ def prepare_data
 
     private
 
+    def fetch_chemicals(collection)
+      chemicals = collection.samples.filter_map(&:chemical)
+      fetch_many(chemicals, {
+                   'id' => 'Chemical',
+                   'sample_id' => 'Sample',
+                 })
+    end
+
     def fetch_samples(collection)
       # get samples in order of ancestry, but with empty ancestry first
       samples = collection.samples.order(Arel.sql("NULLIF(ancestry, '') ASC NULLS FIRST"))

lib/import/import_collections.rb

@@ -88,6 +88,7 @@ def import
         gate_collection if @gt == true
         import_collections if @gt == false
         import_samples
+        import_chemicals if @gt == false
         import_residues
         import_reactions
         import_reactions_samples
@@ -186,6 +187,21 @@ def fetch_bound(value)
       end
     end
 
+    def import_chemicals
+      @data.fetch('Chemical', {}).each do |_uuid, fields|
+        sample = @instances.fetch('Sample').fetch(fields.fetch('sample_id'))
+        next unless sample
+
+        chemical = Chemical.create!(fields.slice(
+          'cas',
+          'chemical_data',
+        ).merge(
+          sample_id: sample&.id,
+        ))
+        chemical.save!
+      end
+    end
+
     def import_samples
       @data.fetch('Sample', {}).each do |uuid, fields|
         # look for the molecule_name
@@ -241,6 +257,7 @@ def import_samples
           'decoupled',
           'molecular_mass',
           'sum_formula',
+          'inventory_sample',
         ).merge(
           created_by: @current_user_id,
           collections: fetch_many(

spec/factories/attachments.rb

@@ -99,5 +99,9 @@
     trait :with_researchplan_collection_zip do
       file_path { Rails.root.join('spec/fixtures/import/20230113_research_plan_one_attachment.zip') }
     end
+
+    trait :with_chemicals_collection_zip do
+      file_path { Rails.root.join('spec/fixtures/import/collection_chemicals.zip') }
+    end
   end
 end

spec/lib/export/export_collections_spec.rb

@@ -78,6 +78,32 @@
     end
   end
 
+  context 'with a chemical' do
+    let(:chemical) { create(:chemical, sample_id: sample.id) }
+
+    before do
+      sample.save!
+      chemical.save!
+      export = Export::ExportCollections.new(job_id, [collection.id], 'zip', true)
+      export.prepare_data
+      export.to_file
+    end
+
+    it 'exported file exists' do
+      file_path = File.join('public', 'zip', "#{job_id}.zip")
+      expect(File.exist?(file_path)).to be true
+    end
+
+    it 'Chemical key is present in export.json' do
+      file_path = File.join('public', 'zip', "#{job_id}.zip")
+      export_json_content = Zip::File.open(file_path) do |files|
+        json_file = files.detect { |file| file.name == 'export.json' }
+        JSON.parse(json_file.get_input_stream.read)
+      end
+      expect(export_json_content).to have_key('Chemical')
+    end
+  end
+
   def update_body_of_researchplan(research_plan, identifier_of_attachment) # rubocop:disable Metrics/MethodLength
     research_plan.body = [
       {

spec/lib/import/import_collections_spec.rb

@@ -171,6 +171,19 @@
         expect(attachment.attachment_data).not_to be_nil
       end
     end
+
+    describe 'import a collection with a chemical' do
+      let(:import_id) { 'collection_chemicals' }
+      let(:attachment) { create(:attachment, :with_chemicals_collection_zip) }
+
+      it 'successfully imported 1 chemical' do
+        importer.execute
+
+        collection = Collection.find_by(label: 'collection_with_chemical')
+        expect(collection).to be_present
+        expect(collection.samples.map(&:chemical).length).to eq(1)
+      end
+    end
   end
 
   def stub_rest_request(identifier)