feat: chemical associations to support sequence-based macromolecules (SBMM)

    - Add SBMM foreign key to chemicals table and update models for polymorphic-like association
    - Enforce mutual exclusivity and presence validation for sample_id and sequence_based_macromolecule_id
    - Update API, fetchers, and UI components to handle both sample- and SBMM-linked chemicals
    - Extend state management and tests for new association logic
    - Enable inventory tab functionality for sequence-based macromolecule samples

Author: adambasha0

app/api/chemotion/chemical_api.rb

@@ -8,28 +8,47 @@ class ChemicalAPI < Grape::API
       params do
         requires :chemical_data, type: Array[Hash], desc: 'chemical data'
         optional :cas, type: String, desc: 'cas number'
+        optional :sample_id, type: Integer
+        optional :sequence_based_macromolecule_sample_id, type: Integer
+        exactly_one_of :sample_id, :sequence_based_macromolecule_sample_id
       end
-      route_param :sample_id do
-        put do
-          Chemotion::ChemicalsService.handle_exceptions do
-            attributes = declared(params, include_missing: false)
-            if params[:chemical_data].present? || params[:cas].present?
-              Chemical.find_by(sample_id: params[:sample_id]).update!(attributes)
-            else
-              status 204
-            end
+      put do
+        Chemotion::ChemicalsService.handle_exceptions do
+          attributes = declared(params, include_missing: false)
+          if params[:chemical_data].present? || params[:cas].present?
+            chemical = if params[:sequence_based_macromolecule_sample_id]
+                         attributes[:sample_id] = nil
+                         Chemical.find_by(
+                           sequence_based_macromolecule_sample_id: params[:sequence_based_macromolecule_sample_id],
+                         )
+                       else
+                         attributes[:sequence_based_macromolecule_sample_id] = nil
+                         Chemical.find_by(sample_id: params[:sample_id])
+                       end
+            error!('chemical not found', 404) unless chemical
+            chemical.update!(attributes)
+          else
+            status 204
           end
         end
       end
 
-      desc 'Return chemical by sample_id'
+      desc 'Return chemical by sample_id or sequence_based_macromolecule_sample_id'
       params do
-        requires :sample_id, type: Integer, desc: 'sample id'
+        optional :sample_id, type: Integer, desc: 'sample id'
+        optional :sequence_based_macromolecule_sample_id, type: Integer, desc: 'sequence based macromolecule id'
+        exactly_one_of :sample_id, :sequence_based_macromolecule_sample_id
       end
 
       get do
         Chemotion::ChemicalsService.handle_exceptions do
-          Chemical.find_by(sample_id: params[:sample_id]) || Chemical.new
+          if params[:sequence_based_macromolecule_sample_id]
+            Chemical.find_by(
+              sequence_based_macromolecule_sample_id: params[:sequence_based_macromolecule_sample_id],
+            ) || Chemical.new
+          else
+            Chemical.find_by(sample_id: params[:sample_id]) || Chemical.new
+          end
         end
       end
 
@@ -38,12 +57,21 @@ class ChemicalAPI < Grape::API
         params do
           requires :chemical_data, type: Array[Hash], desc: 'chemical data'
           requires :cas, type: String
-          requires :sample_id, type: Integer
+          optional :sample_id, type: Integer
+          optional :sequence_based_macromolecule_sample_id, type: Integer
+          exactly_one_of :sample_id, :sequence_based_macromolecule_sample_id
         end
 
         post do
           Chemotion::ChemicalsService.handle_exceptions do
-            attributes = declared(params, include_missing: false)
+            attributes = declared(params, include_missing: false) || {}
+            if params[:sequence_based_macromolecule_sample_id]
+              attributes[:sample_id] = nil
+              attributes[:sequence_based_macromolecule_sample_id] = params[:sequence_based_macromolecule_sample_id]
+            else
+              attributes[:sequence_based_macromolecule_sample_id] = nil
+              attributes[:sample_id] = params[:sample_id]
+            end
             Chemical.create!(attributes)
           end
         end

app/api/entities/sequence_based_macromolecule_sample_entity.rb

@@ -33,6 +33,7 @@ class SequenceBasedMacromoleculeSampleEntity < ApplicationEntity
     expose! :type
     expose! :changed
     expose! :errors
+    expose! :inventory_sample
 
     expose! :heterologous_expression, if: ->(_object, _options) { !uniprot_protein? }
     expose! :organism, if: ->(_object, _options) { !uniprot_protein? }

app/api/helpers/params_helpers.rb

@@ -176,6 +176,7 @@ module ParamsHelpers
   params :sbmm_sample_params do
     optional :name, type: String
     optional :collection_id, type: Integer
+    optional :inventory_sample, type: Boolean, default: false
     optional :external_label, type: String
     optional :function_or_application, type: String
     optional :concentration_value, type: Float

app/javascript/src/apps/mydb/elements/details/ElementDetailSortTab.js

@@ -37,6 +37,13 @@ export default class ElementDetailSortTab extends Component {
     CollectionStore.listen(this.onChangeUI);
   }
 
+  componentDidUpdate(prevProps) {
+    if (prevProps.addInventoryTab !== this.props.addInventoryTab
+      || !_.isEqual(prevProps.availableTabs, this.props.availableTabs)) {
+      this.onChangeUI();
+    }
+  }
+
   componentWillUnmount() {
     UserStore.unlisten(this.onChangeUser);
     CollectionStore.unlisten(this.onChangeUI);

app/javascript/src/apps/mydb/elements/details/samples/SampleDetails.js

@@ -608,6 +608,7 @@ export default class SampleDetails extends React.Component {
         <ListGroupItem>
           <ChemicalTab
             sample={sample}
+            type="sample"
             handleUpdateSample={(s) => this.setState({ sample: s })}
             setSaveInventory={(v) => this.setState({ saveInventoryAction: v })}
             saveInventory={saveInventoryAction}