fix: entity creation in sync collections

CHANGELOG.md

@@ -177,6 +177,25 @@
 ## [v1.9.3]
 > (2024-05-13)
 
+* Features and enhancements
+  * structure editor compatibility  ([#1894](https://github.com/ComPlat/chemotion_ELN/pull/1894))
+  * enable spectra report for samples  ([#1902](https://github.com/ComPlat/chemotion_ELN/pull/1902))
+  * activate segment visibility field in generic elements  ([#1702](https://github.com/ComPlat/chemotion_ELN/pull/1702))
+
+* Bug fixes
+  * advanced search  ([#1888](https://github.com/ComPlat/chemotion_ELN/pull/1888))
+  * converter inbox issue for NMR  ([#1903](https://github.com/ComPlat/chemotion_ELN/pull/1903))
+  * add updating of annotations also in reaction container  ([#1913](https://github.com/ComPlat/chemotion_ELN/pull/1913))
+  * Yield calculation with purity  ([#1904](https://github.com/ComPlat/chemotion_ELN/pull/1904))
+  * ensure wait_until is set when initializing cron delayed jobs ([#1892](https://github.com/ComPlat/chemotion_ELN/pull/1892))
+
+* Chores
+  * Bump react-pdf from 5.7.0 to 7.7.3  ([#1909](https://github.com/ComPlat/chemotion_ELN/pull/1909))
+
+
+## [v1.9.3]
+> (2024-05-13)
+
 * Features and enhancements
   * structure editor compatibility  ([#1894](https://github.com/ComPlat/chemotion_ELN/pull/1894))
   * enable spectra report for samples  ([#1902](https://github.com/ComPlat/chemotion_ELN/pull/1902))

app/api/chemotion/reaction_api.rb

@@ -246,6 +246,7 @@ class ReactionAPI < Grape::API
         optional :variations, type: [Hash]
         optional :vessel_size, type: Hash
         optional :gaseous, type: Boolean
+        optional :is_sync_to_me, type: Boolean, default: false
       end
 
       post do
@@ -257,9 +258,8 @@ class ReactionAPI < Grape::API
         container_info = params[:container]
         attributes.delete(:container)
         attributes.delete(:segments)
-        attributes.delete(:user_labels)
-
-        collection = current_user.collections.where(id: collection_id).take
+        is_sync_to_me = attributes.delete(:is_sync_to_me)
+
         attributes[:created_by] = current_user.id
         reaction = Reaction.create!(attributes)
         recent_ols_term_update('rxno', [params[:rxno]]) if params[:rxno].present?
@@ -294,26 +294,39 @@ class ReactionAPI < Grape::API
         reaction.save!
         update_element_labels(reaction, params[:user_labels], current_user.id)
         reaction.save_segments(segments: params[:segments], current_user_id: current_user.id)
-        CollectionsReaction.create(reaction: reaction, collection: collection) if collection.present?
 
-        is_shared_collection = false
-        if collection.blank?
+        if is_sync_to_me
           sync_collection = current_user.all_sync_in_collections_users.where(id: collection_id).take
-          if sync_collection.present?
-            is_shared_collection = true
-            sync_in_collection_receiver = Collection.find(sync_collection['collection_id'])
-            CollectionsReaction.create(reaction: reaction,
-                                       collection: sync_in_collection_receiver)
-            sync_out_collection_sharer = Collection.get_all_collection_for_user(sync_collection['shared_by_id'])
+
+          collection = Collection.find(sync_collection['collection_id'])
+          CollectionsReaction.create(reaction: reaction, collection: collection) if collection.present?
+
+          sync_out_collection_sharer = Collection.get_all_collection_for_user(sync_collection['shared_by_id'])
+          CollectionsReaction.create(reaction: reaction, collection: sync_out_collection_sharer)
+        else
+          collection = current_user.collections.where(id: collection_id).take
+          CollectionsReaction.create(reaction: reaction, collection: collection) if collection.present?
+
+          is_shared_collection = false
+          if collection.blank?
+            sync_collection = current_user.all_sync_in_collections_users.where(id: collection_id).take
+            if sync_collection.present?
+              is_shared_collection = true
+              sync_in_collection_receiver = Collection.find(sync_collection['collection_id'])
+              CollectionsReaction.create(reaction: reaction,
+                                         collection: sync_in_collection_receiver)
+              sync_out_collection_sharer = Collection.get_all_collection_for_user(sync_collection['shared_by_id'])
+              CollectionsReaction.create(reaction: reaction,
+                                         collection: sync_out_collection_sharer)
+            end
+          end
+
+          unless is_shared_collection
             CollectionsReaction.create(reaction: reaction,
-                                       collection: sync_out_collection_sharer)
+                                       collection: Collection.get_all_collection_for_user(current_user.id))
           end
         end
 
-        unless is_shared_collection
-          CollectionsReaction.create(reaction: reaction,
-                                     collection: Collection.get_all_collection_for_user(current_user.id))
-        end
         CollectionsReaction.update_tag_by_element_ids(reaction.id)
         if reaction
           if attributes['origin'] && attributes['origin']['short_label'] && materials['products'].present?

app/api/chemotion/research_plan_api.rb

@@ -69,6 +69,7 @@ class ResearchPlanAPI < Grape::API
         requires :container, type: Hash, desc: 'Containers'
         optional :segments, type: Array, desc: 'Segments'
         optional :attachments, type: Array, desc: 'Attachments'
+        optional :is_sync_to_me, type: Boolean, default: false
       end
       post do
         attributes = {
@@ -85,24 +86,35 @@ class ResearchPlanAPI < Grape::API
         clone_attachs = params[:attachments]&.reject { |a| a[:is_new] }
         Usecases::Attachments::Copy.execute!(clone_attachs, research_plan, current_user.id) if clone_attachs
 
-        if params[:collection_id]
-          collection = current_user.collections.where(id: params[:collection_id]).take
-          research_plan.collections << collection if collection.present?
-        end
-
-        is_shared_collection = false
-        unless collection.present?
+        if params[:is_sync_to_me]
+          Rails.logger.debug('Creating rplan in sync collection due to user request (param :is_sync_to_me is set).')
           sync_collection = current_user.all_sync_in_collections_users.where(id: params[:collection_id]).take
           if sync_collection.present?
-            is_shared_collection = true
             research_plan.collections << Collection.find(sync_collection['collection_id'])
             research_plan.collections << Collection.get_all_collection_for_user(sync_collection['shared_by_id'])
+          else
+            error!('400 Bad Request (Cant find sync collection)', 400)
+          end
+        else
+          if params[:collection_id]
+            collection = current_user.collections.where(id: params[:collection_id]).take
+            research_plan.collections << collection if collection.present?
           end
-        end
 
-        unless is_shared_collection
-          all_coll = Collection.get_all_collection_for_user(current_user.id)
-          research_plan.collections << all_coll
+          is_shared_collection = false
+          if collection.blank?
+            sync_collection = current_user.all_sync_in_collections_users.where(id: params[:collection_id]).take
+            if sync_collection.present?
+              is_shared_collection = true
+              research_plan.collections << Collection.find(sync_collection['collection_id'])
+              research_plan.collections << Collection.get_all_collection_for_user(sync_collection['shared_by_id'])
+            end
+          end
+
+          unless is_shared_collection
+            all_coll = Collection.get_all_collection_for_user(current_user.id)
+            research_plan.collections << all_coll
+          end
         end
 
         present research_plan, with: Entities::ResearchPlanEntity, root: :research_plan

app/api/chemotion/sample_api.rb

@@ -480,6 +480,7 @@ class SampleAPI < Grape::API
         optional :inventory_sample, type: Boolean, default: false
         optional :molecular_mass, type: Float
         optional :sum_formula, type: String
+        optional :is_sync_to_me, type: Boolean, default: false
       end
       post do
         molecule_id = if params[:decoupled] && params[:molfile].blank?
@@ -551,24 +552,35 @@ class SampleAPI < Grape::API
 
         sample = Sample.new(attributes)
 
-        if params[:collection_id]
-          collection = current_user.collections.where(id: params[:collection_id]).take
-          sample.collections << collection if collection.present?
-        end
-
-        is_shared_collection = false
-        if collection.blank?
+        if params[:is_sync_to_me]
+          Rails.logger.debug('Creating sample in sync collection due to user request (param :is_sync_to_me is set).')
           sync_collection = current_user.all_sync_in_collections_users.where(id: params[:collection_id]).take
           if sync_collection.present?
-            is_shared_collection = true
             sample.collections << Collection.find(sync_collection['collection_id'])
             sample.collections << Collection.get_all_collection_for_user(sync_collection['shared_by_id'])
+          else
+            error!('400 Bad Request (Cant find sync collection)', 400)
+          end
+        else
+          if params[:collection_id]
+            collection = current_user.collections.where(id: params[:collection_id]).take
+            sample.collections << collection if collection.present?
           end
-        end
 
-        unless is_shared_collection
-          all_coll = Collection.get_all_collection_for_user(current_user.id)
-          sample.collections << all_coll
+          is_shared_collection = false
+          if collection.blank?
+            sync_collection = current_user.all_sync_in_collections_users.where(id: params[:collection_id]).take
+            if sync_collection.present?
+              is_shared_collection = true
+              sample.collections << Collection.find(sync_collection['collection_id'])
+              sample.collections << Collection.get_all_collection_for_user(sync_collection['shared_by_id'])
+            end
+          end
+
+          unless is_shared_collection
+            all_coll = Collection.get_all_collection_for_user(current_user.id)
+            sample.collections << all_coll
+          end
         end
 
         sample.container = update_datamodel(params[:container])

app/api/chemotion/screen_api.rb

@@ -172,6 +172,7 @@ class ScreenAPI < Grape::API
         requires :container, type: Hash
         optional :segments, type: Array, desc: 'Segments'
         optional :component_graph_data, type: JSON
+        optional :is_sync_to_me, type: Boolean, default: false
       end
       post do
         attributes = {
@@ -191,24 +192,35 @@ class ScreenAPI < Grape::API
         screen.save!
         screen.save_segments(segments: params[:segments], current_user_id: current_user.id)
 
-        #save to profile
+        # save to profile
         kinds = screen.container&.analyses&.pluck(Arel.sql("extended_metadata->'kind'"))
         recent_ols_term_update('chmo', kinds) if kinds&.length&.positive?
 
-        collection = current_user.collections.where(id: params[:collection_id]).take
-        screen.collections << collection if collection.present?
-
-        is_shared_collection = false
-        unless collection.present?
+        if params[:is_sync_to_me]
+          Rails.logger.debug('Creating screen in sync collection due to user request (param :is_sync_to_me is set).')
           sync_collection = current_user.all_sync_in_collections_users.where(id: params[:collection_id]).take
           if sync_collection.present?
-            is_shared_collection = true
             screen.collections << Collection.find(sync_collection['collection_id'])
             screen.collections << Collection.get_all_collection_for_user(sync_collection['shared_by_id'])
+          else
+            error!('400 Bad Request (Cant find sync collection)', 400)
+          end
+        else
+          collection = current_user.collections.where(id: params[:collection_id]).take
+          screen.collections << collection if collection.present?
+
+          is_shared_collection = false
+          if collection.blank?
+            sync_collection = current_user.all_sync_in_collections_users.where(id: params[:collection_id]).take
+            if sync_collection.present?
+              is_shared_collection = true
+              screen.collections << Collection.find(sync_collection['collection_id'])
+              screen.collections << Collection.get_all_collection_for_user(sync_collection['shared_by_id'])
+            end
           end
-        end
 
-        screen.collections << Collection.get_all_collection_for_user(current_user.id) unless is_shared_collection
+          screen.collections << Collection.get_all_collection_for_user(current_user.id) unless is_shared_collection
+        end
 
         params[:wellplate_ids].each do |id|
           ScreensWellplate.find_or_create_by(wellplate_id: id, screen_id: screen.id)

app/api/chemotion/wellplate_api.rb

@@ -183,6 +183,7 @@ class WellplateAPI < Grape::API # rubocop:disable Metrics/ClassLength
         optional :height, type: Integer, default: 8, values: 1..100
         optional :width, type: Integer, default: 12, values: 1..100
         optional :segments, type: Array, desc: 'Segments'
+        optional :is_sync_to_me, type: Boolean, default: false
       end
       post do
         container = params[:container]

app/packs/src/apps/mydb/elements/details/reactions/ReactionDetails.js

@@ -142,6 +142,8 @@ export default class ReactionDetails extends Component {
 
     const { reaction } = this.state;
     if (reaction && reaction.isNew) {
+      const { currentCollection } = UIStore.getState();
+      reaction["is_sync_to_me"] = currentCollection ? Boolean(currentCollection["is_sync_to_me"]) : false;
       ElementActions.createReaction(reaction);
     } else {
       ElementActions.updateReaction(reaction, closeView);

app/packs/src/apps/mydb/elements/details/researchPlans/ResearchPlanDetails.js

@@ -111,6 +111,8 @@ export default class ResearchPlanDetails extends Component {
     this.context.attachmentNotificationStore.clearMessages();
 
     if (researchPlan.isNew) {
+      const { currentCollection } = UIStore.getState();
+      researchPlan["is_sync_to_me"] = currentCollection ? Boolean(currentCollection["is_sync_to_me"]) : false;
       ElementActions.createResearchPlan(researchPlan);
     } else {
       ElementActions.updateResearchPlan(researchPlan);

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

@@ -355,6 +355,8 @@ export default class SampleDetails extends React.Component {
       const wellplate = sample.belongTo;
       ElementActions.updateSampleForWellplate(sample, wellplate);
     } else if (sample.isNew) {
+      const { currentCollection } = UIStore.getState();
+      sample["is_sync_to_me"] = currentCollection ? Boolean(currentCollection["is_sync_to_me"]) : false;
       ElementActions.createSample(sample, closeView);
     } else {
       sample.cleanBoilingMelting();

app/packs/src/apps/mydb/elements/details/screens/ScreenDetails.js

@@ -99,6 +99,8 @@ export default class ScreenDetails extends Component {
     LoadingActions.start();
 
     if (screen.isNew) {
+      const { currentCollection } = UIStore.getState();
+      screen["is_sync_to_me"] = currentCollection ? Boolean(currentCollection["is_sync_to_me"]) : false;
       ElementActions.createScreen(screen);
     } else {
       ElementActions.updateScreen(screen);

app/packs/src/apps/mydb/elements/details/wellplates/WellplateDetails.js

@@ -98,6 +98,8 @@ export default class WellplateDetails extends Component {
     this.context.attachmentNotificationStore.clearMessages();
     LoadingActions.start();
     if (wellplate.isNew) {
+      const { currentCollection } = UIStore.getState();
+      wellplate["is_sync_to_me"] = currentCollection ? Boolean(currentCollection["is_sync_to_me"]) : false;
       ElementActions.createWellplate(wellplate);
     } else {
       ElementActions.updateWellplate(wellplate);

app/packs/src/components/generic/GenericElDetails.js

@@ -61,6 +61,9 @@ const onNaviClick = (type, id) => {
 export default class GenericElDetails extends Component {
   constructor(props) {
     super(props);
+    // generic type
+    this.type = props.genericEl.type;
+
     this.state = {
       genericEl: props.genericEl,
       activeTab: 0,
@@ -82,6 +85,33 @@ export default class GenericElDetails extends Component {
     this.handleExport = this.handleExport.bind(this);
   }
 
+  /**
+   * This method retrieves values for the detailed
+   * layout. If the user profile lacks these values,
+   * they are automatically added.
+   */
+  setupDetailLayoutProfile() {
+
+    const userProfile = UserStore.getState().profile;
+    const layout = userProfile && userProfile.data && userProfile.data[`layout_detail_${this.type}`];
+    if(!layout) {
+      const layoutName = `data.layout_detail_${this.type}`;
+      const defaultLayout = {
+        properties: 1, analyses: 2, attachments: 3
+      };
+      const currentCollection = UIStore.getState().currentCollection;
+      let tabSegment = currentCollection?.tabs_segment;
+      lowdashset(tabSegment, `${this.type}`, defaultLayout);
+      tabSegment = { ...tabSegment, [`${this.type}`]: defaultLayout };
+      if (currentCollection && !currentCollection.is_sync_to_me) {
+        CollectionActions.updateTabsSegment({ segment: tabSegment, cId: currentCollection.id });
+      }
+      lowdashset(userProfile, layoutName, defaultLayout);
+
+      UserActions.updateUserProfile(userProfile);
+    }
+  }
+
   componentDidMount() {
     UIStore.listen(this.onChangeUI);
     ElementStore.listen(this.onChangeElement);

app/packs/src/fetchers/ReactionsFetcher.js

@@ -86,7 +86,7 @@ export default class ReactionsFetcher {
         Accept: 'application/json',
         'Content-Type': 'application/json'
       },
-      body: JSON.stringify(reaction.serialize())
+      body: JSON.stringify({...reaction.serialize(), is_sync_to_me: reaction["is_sync_to_me"]})
     }).then((response) => response.json())
       .then((json) => GenericElsFetcher.uploadGenericFiles(reaction, json.reaction.id, 'Reaction')
         .then(() => ReactionsFetcher.updateAnnotationsInReaction(reaction))

app/packs/src/fetchers/ResearchPlansFetcher.js

@@ -40,7 +40,7 @@ export default class ResearchPlansFetcher {
         Accept: 'application/json',
         'Content-Type': 'application/json'
       },
-      body: JSON.stringify(researchPlan.serialize())
+      body: JSON.stringify({...researchPlan.serialize(), is_sync_to_me: researchPlan["is_sync_to_me"]})
     })
       .then((response) => response.json())
       .then((json) => AttachmentFetcher.updateAttachables(

app/packs/src/fetchers/SamplesFetcher.js

@@ -99,7 +99,7 @@ export default class SamplesFetcher {
         Accept: 'application/json',
         'Content-Type': 'application/json'
       },
-      body: JSON.stringify(sample.serialize())
+      body: JSON.stringify({...sample.serialize(), is_sync_to_me: sample["is_sync_to_me"]})
     }).then((response) => response.json())
       .then((json) => GenericElsFetcher.uploadGenericFiles(sample, json.sample.id, 'Sample')
         .then(() => this.fetchById(json.sample.id))).catch((errorMessage) => {

app/packs/src/fetchers/ScreensFetcher.js

@@ -65,7 +65,7 @@ export default class ScreensFetcher {
         Accept: 'application/json',
         'Content-Type': 'application/json'
       },
-      body: JSON.stringify(screen.serialize())
+      body: JSON.stringify({...screen.serialize(), is_sync_to_me: screen["is_sync_to_me"]})
     }).then(response => response.json())
       .then(json => GenericElsFetcher.uploadGenericFiles(screen, json.screen.id, 'Screen')
         .then(() => this.fetchById(json.screen.id))).catch((errorMessage) => {