save metadata into csv for CV layout and add CDS layout (#1273)

Co-authored-by: Lan Le <[email protected]>

.service-dependencies

@@ -1,4 +1,4 @@
 #syntax=v1
 CONVERTER=ComPlat/[email protected]
 KETCHER=ptrxyz/chemotion-ketchersvc@main
-SPECTRA=ComPlat/[email protected].2-patch.1
+SPECTRA=ComPlat/[email protected].3

app/models/concerns/attachment_jcamp_aasm.rb

@@ -165,8 +165,31 @@ def generate_json_att(json_tmp, addon, to_edit = false)
     generate_att(json_tmp, addon, to_edit, 'json')
   end
 
-  def generate_csv_att(csv_tmp, addon, to_edit = false)
-    generate_att(csv_tmp, addon, to_edit, 'csv')
+  def generate_csv_att(csv_tmp, addon, to_edit = false, params={})
+    csv_reader = CSV.new(csv_tmp)
+    csv_data = csv_reader.read
+    sample_id_field = csv_data[2]
+    sample_id_field[1] = params[:sample_id]
+    analysis_id_field = csv_data[3]
+    analysis_id_field[1] = params[:analysis_id]
+    dataset_id_field = csv_data[4]
+    dataset_id_field[1] = params[:dataset_id]
+    dataset_name_field = csv_data[5]
+    dataset_name_field[1] = params[:dataset_name]
+
+    csv_data[2] = sample_id_field
+    csv_data[3] = analysis_id_field
+    csv_data[4] = dataset_id_field
+    csv_data[5] = dataset_name_field
+    Tempfile.create(['jcamp', '.csv']) do |new_csv_tmp|
+      CSV.open(new_csv_tmp, 'wb') do |csv|
+        csv_data.each do |row|
+          csv << row
+        end
+      end
+      new_csv_tmp.rewind
+      generate_att(new_csv_tmp, addon, to_edit, 'csv')
+    end
   end
 
   def generate_nmrium_att(nmrium_tmp, addon, to_edit = false)
@@ -176,8 +199,17 @@ def generate_nmrium_att(nmrium_tmp, addon, to_edit = false)
   def build_params(params = {})
     _, extname = extension_parts
     params[:mass] = 0.0
+    params[:dataset_id] = attachable.id
+    params[:dataset_name] = attachable.name
     if attachable&.root_element.is_a?(Sample)
       params[:mass] = attachable&.root_element&.molecule&.exact_molecular_weight || 0.0
+      params[:sample_id] = attachable&.root_element.id
+
+      attachable.ancestors.each do |ancestor|
+        if ancestor.container_type == 'analysis'
+          params[:analysis_id] = ancestor.id
+        end
+      end
     end
     params[:ext] = extname.downcase
     params[:fname] = filename.to_s
@@ -217,7 +249,7 @@ def create_process(is_regen)
     check_invalid_molfile(invalid_molfile)
 
     if spc_type == 'bagit'
-      read_bagit_data(arr_jcamp, arr_img, arr_csv, spc_type, is_regen)
+      read_bagit_data(arr_jcamp, arr_img, arr_csv, spc_type, is_regen, params)
     elsif arr_jcamp.length > 1
       read_processed_data(arr_jcamp, arr_img, spc_type, is_regen)
     else
@@ -251,7 +283,7 @@ def edit_process(is_regen, orig_params)
 
     unless arr_csv.nil? || arr_csv.length == 0
       curr_tmp_csv = arr_csv[0]
-      csv_att = generate_csv_att(curr_tmp_csv, 'edit', false)
+      csv_att = generate_csv_att(curr_tmp_csv, 'edit', false, params)
       tmp_files_to_be_deleted.push(*arr_csv)
       delete_related_csv(csv_att)
     end
@@ -331,7 +363,7 @@ def read_processed_data(arr_jcamp, arr_img, spc_type, is_regen)
     jcamp_att
   end
 
-  def read_bagit_data(arr_jcamp, arr_img, arr_csv, spc_type, is_regen)
+  def read_bagit_data(arr_jcamp, arr_img, arr_csv, spc_type, is_regen, params)
     jcamp_att = nil
     tmp_to_be_deleted = []
     tmp_img_to_deleted = []
@@ -344,7 +376,7 @@ def read_bagit_data(arr_jcamp, arr_img, arr_csv, spc_type, is_regen)
       tmp_img_to_deleted.push(img_att)
 
       curr_tmp_csv = arr_csv[idx]
-      _ = generate_csv_att(curr_tmp_csv, "#{idx + 1}_bagit")
+      _ = generate_csv_att(curr_tmp_csv, "#{idx + 1}_bagit", false, params)
       tmp_to_be_deleted.push(curr_tmp_csv)
 
       jcamp_att = curr_jcamp_att if idx == 0

package.json

@@ -10,8 +10,8 @@
     "@babel/preset-env": "^7.11.0",
     "@babel/preset-react": "7.10.4",
     "@citation-js/plugin-isbn": "0.3.0",
-    "@complat/chem-spectra-client": "0.11.4",
-    "@complat/react-spectra-editor": "0.11.4",
+    "@complat/chem-spectra-client": "0.11.5",
+    "@complat/react-spectra-editor": "0.11.5",
     "@novnc/novnc": "^1.2.0",
     "@rails/ujs": "^6.1.3-1",
     "@rails/webpacker": "https://github.com/rails/webpacker.git",

spec/models/attachment_spec.rb

@@ -723,9 +723,44 @@
 
   describe '#generate_csv_att' do
     it 'calls #generate_att with ext = csv and all other parameters verbatim' do
-      expect(attachment).to receive(:generate_att).with('somethingThatGetsPassed', 'foo', false, 'csv')
+      csv_temp = Tempfile.new(['jcamp', '.csv'])
+      csv_data = Array.new(10) {
+        Array.new(5) {|i| i.to_s }
+      }
+      CSV.open(csv_temp, 'wb') do |csv|
+        csv_data.each do |row|
+          csv << row
+        end
+      end
+
+      params = {
+        sample_id: 10,
+        dataset_id: 1,
+        dataset_name: 'root',
+        analysis_id: 2,
+      }
+
+      expected_csv_data = Array.new(10) { |line|
+        Array.new(5) { |i|
+          if line == 2 && i == 1
+            params[:sample_id].to_s
+          elsif line == 3 && i == 1
+            params[:analysis_id].to_s
+          elsif line == 4 && i == 1
+            params[:dataset_id].to_s
+          elsif line == 5 && i == 1
+            params[:dataset_name].to_s
+          else
+            i.to_s
+          end
+        }
+      }
 
-      attachment.generate_csv_att('somethingThatGetsPassed', 'foo')
+      att = attachment.generate_csv_att(csv_temp, 'foo', false, params)
+      generated_csv = att.read_file
+      csv_reader = CSV.new(generated_csv)
+      generated_csv_data = csv_reader.read
+      expect(generated_csv_data).to eq expected_csv_data
     end
   end
 
@@ -777,6 +812,8 @@
           mass: 0.0,
           ext: 'txt',
           fname: 'upload.txt',
+          dataset_id: attachment.attachable.id,
+          dataset_name: attachment.attachable.name,
         }
 
         expect(attachment.build_params({ foo: :bar })).to eq(expected_result)

yarn.lock

@@ -1355,12 +1355,12 @@
   resolved "https://registry.yarnpkg.com/@colors/colors/-/colors-1.5.0.tgz#bb504579c1cae923e6576a4f5da43d25f97bdbd9"
   integrity sha512-ooWCrlZP11i8GImSjTHYHLkvFDP48nS4+204nGb1RiX/WXYHmJA2III9/e2DWVabCESdW7hBAEzHRqUn9OUVvQ==
 
-"@complat/[email protected].4":
-  version "0.11.4"
-  resolved "https://registry.yarnpkg.com/@complat/chem-spectra-client/-/chem-spectra-client-0.11.4.tgz#651d3255bfb8a7a693bee9b15fd74b0a31b1e273"
-  integrity sha512-97V6Q1ztaJkUshl162kInedzusDXNDPZ3TRw40DJIMmFuCzma/bAXPEQhoIQVZzJ9ufEPzke+dl6o8RvVG7D2Q==
+"@complat/[email protected].5":
+  version "0.11.5"
+  resolved "https://registry.yarnpkg.com/@complat/chem-spectra-client/-/chem-spectra-client-0.11.5.tgz#fdfa6510a34673207f91a2efe19a94735bdef178"
+  integrity sha512-Rrky504uYdRfxN/mdY0SQbhTCkR46bsiQhskYdzrh2jg+fIbot+aC6DyiRFM9bIwoCG4BLRwlLwFYhrwkfgdJw==
   dependencies:
-    "@complat/react-spectra-editor" "0.11.4"
+    "@complat/react-spectra-editor" "0.11.5"
     "@material-ui/core" "^3.9.4"
     "@material-ui/icons" "^3.0.2"
     axios "^0.21.1"
@@ -1377,10 +1377,10 @@
     redux-form "^8.3.7"
     redux-saga "^1.1.3"
 
-"@complat/[email protected].4":
-  version "0.11.4"
-  resolved "https://registry.yarnpkg.com/@complat/react-spectra-editor/-/react-spectra-editor-0.11.4.tgz#5abfc4268fd2bc9a2bd954f91a0b3708843bac63"
-  integrity sha512-CFcDog6IriKF63FhyuG4A8kUvfncbHrQx5BphUfdUe0Ke3SOUuSZgzO5HmvB7LOMBnyTFiIu8cZAvRLNWkd2sg==
+"@complat/[email protected].5":
+  version "0.11.5"
+  resolved "https://registry.yarnpkg.com/@complat/react-spectra-editor/-/react-spectra-editor-0.11.5.tgz#b2322eeda7233fddc4d1de0f34d14849f56dc80b"
+  integrity sha512-BNxh8XOB3wxPRNzRZx7zRXj5EFrsc0XMDjM0foTNYHPAcL8GjxCU1LSsXwfO3yBd75lhlZLYc8Qc0fUm5zXdww==
   dependencies:
     "@complat/react-svg-file-zoom-pan" "1.0.15"
     "@material-ui/core" "^4.10.0"