feat: import samples additional attributes - flash point and refractive index

app/api/helpers/report_helpers.rb

@@ -556,7 +556,10 @@ def build_sql_reaction_sample(columns, c_id, ids, checkedAll = false)
         # deleted_at: ['wp.deleted_at', nil, 10],
         molecule_name: ['mn."name"', '"molecule name"', 1],
         molarity_value: ['s."molarity_value"', '"molarity_value"', 0],
+        molarity_unit: ['s."molarity_unit"', '"molarity_unit"', 0],
         dry_solvent: ['s."dry_solvent"', '"dry_solvent"', 0],
+        flash_point: ['s."flash_point"', '"flash point"', 0],
+        refractive_index: ['s."refractive_index"', '"refractive index"', 0],
       },
       sample_id: {
         external_label: ['s.external_label', '"sample external label"', 0],
@@ -634,14 +637,18 @@ def build_sql_reaction_sample(columns, c_id, ids, checkedAll = false)
     }.freeze
 
   def custom_column_query(table, col, selection, user_id, attrs)
-    if col == 'user_labels'
-      selection << "labels_by_user_sample(#{user_id}, s_id) as user_labels"
-    elsif col == 'literature'
-      selection << "literatures_by_element('Sample', s_id) as literatures"
-    elsif col == 'cas'
-      selection << "s.xref->>'cas' as cas"
+    column_map = {
+      'user_labels' => "labels_by_user_sample(#{user_id}, s_id) as user_labels",
+      'literature' => "literatures_by_element('Sample', s_id) as literatures",
+      'cas' => "s.xref->>'cas' as cas",
+      'refractive_index' => "s.xref->>'refractive_index' as refractive_index",
+      'flash_point' => "s.xref->>'flash_point' as flash_point",
+    }
+
+    if column_map[col]
+      selection << column_map[col]
     elsif (s = attrs[table][col.to_sym])
-      selection << ("#{s[1] && s[0]} as #{s[1] || s[0]}")
+      selection << "#{s[1] && s[0]} as #{s[1] || s[0]}"
     end
   end
 

app/packs/src/components/contextActions/ModalExport.js

@@ -53,16 +53,18 @@ export default class ModalExport extends React.Component {
           { value: ['molarity_value', 'molarity_unit'], text: 'molarity', checked: false },
           { value: 'density', text: 'density', checked: false },
           { value: 'molfile', text: 'molfile', checked: false },
-          //  {value: "purity", text: "purity", checked: false},
-          { value: "solvent", text: "solvent", checked: false },
-          { value: "location", text: "location", checked: false },
-          { value: "is_top_secret", text: "is top secret?", checked: false },
-          { value: "dry_solvent", text: "dry solvent", checked: false },
+          { value: 'purity', text: 'purity', checked: false },
+          { value: 'solvent', text: 'solvent', checked: false },
+          { value: 'location', text: 'location', checked: false },
+          { value: 'is_top_secret', text: 'is top secret?', checked: false },
+          { value: 'anhydrous', text: 'dry solvent', checked: false },
           //  {value: "ancestry", text: "ancestry", checked: false},
           { value: 'imported_readout', text: 'imported readout', checked: false },
           //  {value: "identifier", text: "identifier", checked: false},
           { value: 'melting_point', text: 'melting point', checked: false },
           { value: 'boiling_point', text: 'boiling point', checked: false },
+          { value: 'refractive_index', text: 'refractive index', checked: false },
+          { value: 'flash_point', text: 'flash point', checked: false },
           { value: 'created_at', text: 'created at', checked: true },
           { value: 'updated_at', text: 'updated at', checked: false },
           { value: 'user_labels', text: 'user labels', checked: false },
@@ -104,6 +106,7 @@ export default class ModalExport extends React.Component {
           { value: 'vendor', text: 'vendor', checked: false },
           { value: 'order_number', text: 'order number', checked: false },
           { value: 'amount', text: 'amount', checked: false },
+          { value: 'volume', text: 'volume', checked: false },
           { value: 'price', text: 'price', checked: false },
           { value: 'person', text: 'person', checked: false },
           { value: 'required_date', text: 'required date', checked: false },
@@ -112,7 +115,7 @@ export default class ModalExport extends React.Component {
           {
             value: ['safety_sheet_link_merck', 'safety_sheet_link_thermofischer'],
             text: 'safety sheet link',
-            checked: false
+            checked: false,
           },
           { value: ['product_link_merck', 'product_link_thermofischer'], text: 'product link', checked: false },
           { value: 'pictograms', text: 'pictograms', checked: false },

lib/export/export_chemicals.rb

@@ -3,7 +3,7 @@
 module Export
   class ExportChemicals
     CHEMICAL_FIELDS = %w[
-      chemical_sample_id cas status vendor order_number amount price person required_date
+      chemical_sample_id cas status vendor order_number amount volume price person required_date
       ordered_date required_by pictograms h_statements p_statements safety_sheet_link_merck
       safety_sheet_link_thermofischer product_link_merck product_link_thermofischer
       host_building host_room host_cabinet host_group owner borrowed_by current_building
@@ -20,6 +20,7 @@ class ExportChemicals
       person: ['c."chemical_data"->0->\'person\'', '"person"', nil],
       price: ['c."chemical_data"->0->\'price\'', '"price"', nil],
       amount: ['c."chemical_data"->0->\'amount\'', '"amount"', nil],
+      volume: ['c."chemical_data"->0->\'volume\'', '"volume"', nil],
       order_number: ['c."chemical_data"->0->\'order_number\'', '"order_number"', nil],
       required_date: ['c."chemical_data"->0->\'required_date\'', '"required_date"', nil],
       required_by: ['c."chemical_data"->0->\'required_by\'', '"required_by"', nil],
@@ -67,7 +68,7 @@ def self.format_chemical_results(result)
     end
 
     def self.construct_column_name(column_name, index, columns_index)
-      format_chemical_column = ['p statements', 'h statements', 'amount', 'safety sheet link thermofischer',
+      format_chemical_column = ['p statements', 'h statements', 'amount', 'volume', 'safety sheet link thermofischer',
                                 'safety sheet link merck', 'product link thermofischer', 'product link merck'].freeze
       if column_name.is_a?(String) && CHEMICAL_FIELDS.include?(column_name)
         column_name = column_name.tr('_', ' ')
@@ -84,12 +85,12 @@ def self.construct_column_name_hash(columns_index, column_name, index)
         columns_index['p_statements'] = index
       when 'h statements'
         columns_index['h_statements'] = index
-      when 'amount'
-        columns_index['amount'] = index
       when 'safety sheet link merck', 'safety sheet link thermofischer'
         columns_index['safety_sheet_link'].push(index)
       when 'product link merck', 'product link thermofischer'
         columns_index['product_link'].push(index)
+      else
+        columns_index[column_name] = index
       end
     end
 
@@ -110,8 +111,8 @@ def self.format_row(row, columns_index, indexes_to_delete)
         case index
         when columns_index['p_statements'], columns_index['h_statements']
           value = format_p_and_h_statements(value)
-        when columns_index['amount']
-          value = format_chemical_amount(value)
+        when columns_index['amount'], columns_index['volume']
+          value = format_chemical_amount_or_volume(value)
         when columns_index['safety_sheet_link'][0]
           value = format_link(value, row, columns_index['safety_sheet_link'][1], indexes_to_delete)
         when columns_index['product_link'][0]
@@ -126,10 +127,10 @@ def self.format_p_and_h_statements(value)
       keys.join('-')
     end
 
-    def self.format_chemical_amount(value)
-      amount_value_unit = JSON.parse(value).values
-      sorted = amount_value_unit.sort_by { |element| [element.is_a?(Integer) || element.is_a?(Float) ? 0 : 1, element] }
-      sorted.join
+    def self.format_chemical_amount_or_volume(value)
+      value_unit = JSON.parse(value).values
+      sorted = value_unit.sort_by { |element| [element.is_a?(Integer) || element.is_a?(Float) ? 0 : 1, element] }
+      sorted.join(' ')
     end
 
     def self.format_link(value, row, next_index, indexes_to_delete)

lib/export/export_excel.rb

@@ -127,6 +127,14 @@ def filter_with_permission_and_detail_level(sample)
             string.split(',').join(' - ')
           elsif column == 'solvent'
             extract_label_from_solvent_column(sample[column]) || ''
+          elsif column == 'refractive index'
+            sample['refractive_index']
+          elsif column == 'flash point'
+            flash_point_format(sample['flash_point'])
+          elsif column == 'molarity'
+            "#{sample['molarity_value']} #{sample['molarity_unit']}"
+          elsif column == 'density'
+            "#{sample['density']} g/ml"
           else
             sample[column]
           end

lib/export/export_sdf.rb

@@ -34,6 +34,28 @@ def read
 
     private
 
+    def concatenate_data(sample, data, headers = @headers)
+      headers.each do |column|
+        next unless column
+
+        raw_value = case column
+                    when 'molarity'
+                      "#{sample['molarity_value']} #{sample['molarity_unit']}"
+                    when 'flash point'
+                      sample['flash_point']
+                    when 'refractive index'
+                      sample['refractive_index']
+                    when 'density'
+                      "#{sample['density']} g/mL"
+                    else
+                      sample[column]
+                    end
+        column_data = format_field(column, raw_value)
+        data.concat(column_data)
+      end
+      data
+    end
+
     def filter_with_permission_and_detail_level(sample)
       if sample['shared_sync'] == 'f' || sample['shared_sync'] == false
         data = validate_molfile(sample['molfile'])
@@ -44,10 +66,7 @@ def filter_with_permission_and_detail_level(sample)
         end
         data = data.rstrip
         data += "\n"
-        @headers.each do |column|
-          column_data = format_field(column, sample[column])
-          data.concat(column_data)
-        end
+        data = concatenate_data(sample, data)
       else
         # return no data if molfile not allowed
         return nil if sample['dl_s'].zero?
@@ -62,12 +81,8 @@ def filter_with_permission_and_detail_level(sample)
         # NB: as of now , only dl 0 and 10 are implemented
         dl = 10 if dl.positive?
         headers = instance_variable_get("headers#{sample['dl_s']}#{dl}")
-        headers.each do |column|
-          next unless column
+        data = concatenate_data(sample, data, headers)
 
-          column_data = format_field(column, sample[column])
-          data.concat(column_data)
-        end
       end
       data.concat("\$\$\$\$\n")
     end
@@ -81,11 +96,14 @@ def extract_reference_values(raw_value)
     def format_field(column, raw_value)
       field = column.gsub(/\s+/, '_').upcase
       reference_values = ['melting pt', 'boiling pt']
+      flash_point = ['flash point', 'flash_point']
       sample_column =
         if reference_values.include?(column)
           extract_reference_values(raw_value)
         elsif column == 'solvent'
           extract_label_from_solvent_column(raw_value) || ''
+        elsif flash_point.include?(column)
+          flash_point_format(raw_value)
         else
           raw_value
         end

lib/export/export_table.rb

@@ -110,11 +110,32 @@ def generate_headers_reaction
       }
     end
 
+    def flash_point_format(value)
+      return if value.blank?
+
+      # Add quotes around unquoted keys & values
+      value = value.gsub(/(\w+):/, '"\1":')
+      value = value.gsub(/:\s*([^",{}\s]+)/, ':"\1"')
+
+      flash_point = JSON.parse(value)
+      "#{flash_point['value']} #{flash_point['unit']}"
+    rescue JSON::ParserError => e
+      Rails.logger.warn("Failed to parse flash_point JSON: #{e.message}")
+      nil
+    end
+
     def format_headers(headers)
       headers.map! do |header|
-        header.tr('_', ' ')
+        header = header.tr('_', ' ')
+        if header.scan('molarity value').first == 'molarity value'
+          'molarity'
+        elsif header == 'molarity unit'
+          nil
+        else
+          header
+        end
       end
-      headers
+      headers.compact
     end
 
     def generate_headers_sample

lib/import/import_chemicals.rb

@@ -4,6 +4,7 @@ module Import
   class ImportChemicals
     SAFETY_PHRASES = %w[pictograms h_statements p_statements].freeze
     AMOUNT = %w[amount].freeze
+    VOLUME = %w[volume].freeze
     SAFETY_SHEET = %w[safety_sheet_link_merck product_link_merck].freeze
     KEYS_TO_EXCLUDE = SAFETY_SHEET + %w[cas].freeze
     SIGMA_ALDRICH_PATTERN = /(sigmaaldrich|merck)/.freeze
@@ -14,13 +15,14 @@ class ImportChemicals
       THERMOFISCHER_PATTERN => 'Alfa',
     }.freeze
     CHEMICAL_FIELDS = [
-      'cas', 'status', 'vendor', 'order number', 'amount', 'price', 'person', 'required date', 'ordered date',
+      'cas', 'status', 'vendor', 'order number', 'amount', 'volume', 'price', 'person', 'required date', 'ordered date',
       'required by', 'pictograms', 'h statements', 'p statements', 'safety sheet link', 'product link', 'host building',
       'host room', 'host cabinet', 'host group', 'owner', 'borrowed by', 'current building', 'current room',
       'current cabinet', 'current group', 'disposal info', 'important notes'
     ].freeze
     GHS_VALUES = %w[GHS01 GHS02 GHS03 GHS04 GHS05 GHS06 GHS07 GHS08 GHS09].freeze
     AMOUNT_UNITS = %w[g mg μg].freeze
+    VOLUME_UNITS = %w[ml l μl].freeze
 
     def self.build_chemical(row, header)
       chemical = Chemical.new
@@ -46,28 +48,32 @@ def self.skip_import?(value, column_header)
       value.blank? || column_header.nil?
     end
 
-    def self.process_column(chemical, column_header, value)
-      map_column = CHEMICAL_FIELDS.find { |e| e == column_header.downcase.rstrip }
-      key = to_snake_case(column_header)
-      format_value = value.strip
+    def self.build_chemical_data(map_column, chemical, key, formated_value)
       if map_column.present? && should_process_key(key)
-        chemical['chemical_data'][0][key] = format_value
+        chemical['chemical_data'][0][key] = formated_value
       elsif SAFETY_SHEET.include?(key)
-        set_safety_sheet(chemical, key, format_value)
+        set_safety_sheet(chemical, key, formated_value)
       elsif SAFETY_PHRASES.include?(key)
-        set_safety_phrases(chemical, key, format_value)
-      elsif AMOUNT.include?(key)
-        set_amount(chemical, format_value)
+        set_safety_phrases(chemical, key, formated_value)
+      elsif AMOUNT.include?(key) || VOLUME.include?(key)
+        set_chemical_amount_or_volume(chemical, key, formated_value)
       end
     end
 
+    def self.process_column(chemical, column_header, value)
+      map_column = CHEMICAL_FIELDS.find { |e| e == column_header.downcase.rstrip }
+      key = to_snake_case(column_header)
+      formated_value = value.strip
+      build_chemical_data(map_column, chemical, key, formated_value)
+    end
+
     def self.to_snake_case(column_header)
       key = column_header.downcase.rstrip.gsub(/\s+/, '_')
       key == 'owner' ? 'host_owner' : key
     end
 
     def self.should_process_key(key)
-      KEYS_TO_EXCLUDE.exclude?(key) && (AMOUNT + SAFETY_PHRASES).exclude?(key)
+      KEYS_TO_EXCLUDE.exclude?(key) && (AMOUNT + VOLUME + SAFETY_PHRASES).exclude?(key)
     end
 
     def self.set_safety_sheet(chemical, key, value)
@@ -159,14 +165,30 @@ def self.set_safety_phrases(chemical, key, value)
       assign_phrases(key, values, phrases)
     end
 
-    def self.set_amount(chemical, value)
-      chemical['chemical_data'][0]['amount'] = {} if chemical['chemical_data'][0]['amount'].nil?
-      quantity = value.to_f
-      unit = value.gsub(/\d+(\.\d+)?/, '')
-      return chemical unless AMOUNT_UNITS.include?(unit)
+    def self.extract_quantity(value)
+      value.to_f
+    end
+
+    def self.extract_unit(value)
+      value.gsub(/[0-9.]+/, '').strip
+    end
+
+    def self.format_value_unit(chemical, key, value, unit)
+      chemical['chemical_data'][0][key] ||= {}
+      chemical['chemical_data'][0][key]['value'] = value
+      chemical['chemical_data'][0][key]['unit'] = unit
+      chemical
+    end
+
+    def self.set_chemical_amount_or_volume(chemical, key, value)
+      quantity = extract_quantity(value)
+      unit = extract_unit(value)
+
+      return chemical if key == 'amount' && AMOUNT_UNITS.exclude?(unit)
+
+      return chemical if key == 'volume' && VOLUME_UNITS.exclude?(unit)
 
-      chemical['chemical_data'][0]['amount']['value'] = quantity
-      chemical['chemical_data'][0]['amount']['unit'] = unit
+      format_value_unit(chemical, key, quantity, unit)
     end
   end
 end