Split cell lines

app/api/chemotion/cell_line_api.rb

@@ -5,23 +5,21 @@ class CellLineAPI < Grape::API
     include Grape::Kaminari
     helpers ParamsHelpers
     helpers ContainerHelpers
+    helpers CellLineApiParamsHelpers
 
     rescue_from ActiveRecord::RecordNotFound do
       error!('Ressource not found', 401)
     end
     resource :cell_lines do
       desc 'return cell lines of a collection'
       params do
-        optional :collection_id, type: Integer, desc: 'Collection id'
-        optional :sync_collection_id, type: Integer, desc: 'SyncCollectionsUser id'
-        optional :filter_created_at, type: Boolean, desc: 'filter by created at or updated at'
-        optional :from_date, type: Integer, desc: 'created_date from in ms'
-        optional :to_date, type: Integer, desc: 'created_date to in ms'
+        use :cell_line_get_params
       end
       paginate per_page: 5, offset: 0
       before do
         params[:per_page].to_i > 50 && (params[:per_page] = 50)
       end
+
       get do
         scope = if params[:collection_id]
                   begin
@@ -82,29 +80,7 @@ class CellLineAPI < Grape::API
 
       desc 'Create a new Cell line sample'
       params do
-        optional :organism, type: String, desc: 'name of the donor organism of the cell'
-        optional :tissue, type: String, desc: 'tissue from which the cell originates'
-        requires :amount, type: Integer, desc: 'amount of cells'
-        requires :unit, type: String, desc: 'unit of cell amount'
-        requires :passage, type: Integer, desc: 'passage of cells'
-        optional :disease, type: String, desc: 'deasease of cells'
-        requires :material_names, type: String, desc: 'names of cell line e.g. name1;name2'
-        requires :collection_id, type: Integer, desc: 'Collection of the cell line sample'
-        optional :cell_type, type: String, desc: 'type of cells'
-        optional :biosafety_level, type: String, desc: 'biosafety_level of cells'
-        optional :growth_medium, type: String, desc: 'growth medium of cells'
-        optional :variant, type: String, desc: 'variant of cells'
-        optional :optimal_growth_temp, type: Float, desc: 'optimal_growth_temp of cells'
-        optional :cryo_pres_medium, type: String, desc: 'cryo preservation medium of cells'
-        optional :gender, type: String, desc: 'gender of donor organism'
-        optional :material_description, type: String, desc: 'description of cell line concept'
-        optional :contamination, type: String, desc: 'contamination of a cell line sample'
-        requires :source, type: String, desc: 'source of a cell line sample'
-        optional :name, type: String, desc: 'name of a cell line sample'
-        optional :mutation, type: String, desc: 'mutation of a cell line'
-        optional :description, type: String, desc: 'description of a cell line sample'
-        optional :short_label, type: String, desc: 'short label of a cell line sample'
-        requires :container, type: Hash, desc: 'root Container of element'
+        use :cell_line_creation_params
       end
       post do
         error!('401 Unauthorized', 401) unless current_user.collections.find(params[:collection_id])
@@ -116,28 +92,7 @@ class CellLineAPI < Grape::API
       end
       desc 'Update a Cell line sample'
       params do
-        requires :cell_line_sample_id, type: String, desc: 'id of the cell line to update'
-        optional :organism, type: String, desc: 'name of the donor organism of the cell'
-        optional :mutation, type: String, desc: 'mutation of a cell line'
-        optional :tissue, type: String, desc: 'tissue from which the cell originates'
-        requires :amount, type: Integer, desc: 'amount of cells'
-        requires :unit, type: String, desc: 'unit of amount of cells'
-        optional :passage, type: Integer, desc: 'passage of cells'
-        optional :disease, type: String, desc: 'deasease of cells'
-        optional :material_names, type: String, desc: 'names of cell line e.g. name1;name2'
-        optional :collection_id, type: Integer, desc: 'Collection of the cell line sample'
-        optional :cell_type, type: String, desc: 'type of cells'
-        optional :biosafety_level, type: String, desc: 'biosafety_level of cells'
-        optional :variant, type: String, desc: 'variant of cells'
-        optional :optimal_growth_temp, type: Float, desc: 'optimal_growth_temp of cells'
-        optional :cryo_pres_medium, type: String, desc: 'cryo preservation medium of cells'
-        optional :gender, type: String, desc: 'gender of donor organism'
-        optional :material_description, type: String, desc: 'description of cell line concept'
-        optional :contamination, type: String, desc: 'contamination of a cell line sample'
-        optional :source, type: String, desc: 'source of a cell line sample'
-        optional :name, type: String, desc: 'name of a cell line sample'
-        optional :description, type: String, desc: 'description of a cell line sample'
-        requires :container, type: Hash, desc: 'root Container of element'
+        use :cell_line_update_params
       end
       put do
         use_case = Usecases::CellLines::Update.new(params, current_user)
@@ -146,12 +101,59 @@ class CellLineAPI < Grape::API
         return present cell_line_sample, with: Entities::CellLineSampleEntity
       end
 
+      desc 'Copy a cell line'
+      params do
+        requires :id, type: Integer, desc: 'id of cell line sample to copy'
+        requires :collection_id, type: Integer, desc: 'id of collection of copied cell line sample'
+        requires :container, type: Hash, desc: 'root container of element'
+      end
+      namespace :copy do
+        post do
+          cell_line_to_copy = @current_user.cellline_samples.where(id: [params[:id]]).reorder('id')
+
+          error!('401 Unauthorized', 401) unless ElementsPolicy.new(@current_user, cell_line_to_copy).update?
+
+          begin
+            use_case = Usecases::CellLines::Copy.new(cell_line_to_copy.first, @current_user, params[:collection_id])
+            copied_cell_line_sample = use_case.execute!
+            copied_cell_line_sample.container = update_datamodel(params[:container])
+          rescue StandardError => e
+            error!(e, 400)
+          end
+          return present copied_cell_line_sample, with: Entities::CellLineSampleEntity
+        end
+      end
+
+      desc 'Splits a cell line'
+      params do
+        requires :id, type: Integer, desc: 'id of cell line sample to copy'
+        requires :collection_id, type: Integer, desc: 'id of collection of copied cell line sample'
+        optional :container, type: Hash, desc: 'root container of element'
+      end
+      namespace :split do
+        post do
+          cell_line_to_copy = @current_user.cellline_samples.where(id: [params[:id]]).reorder('id')
+
+          error!('401 Unauthorized', 401) unless ElementsPolicy.new(@current_user, cell_line_to_copy).update?
+
+          begin
+            use_case = Usecases::CellLines::Split.new(cell_line_to_copy.first, @current_user, params[:collection_id])
+            splitted_cell_line_sample = use_case.execute!
+            splitted_cell_line_sample.container = update_datamodel(params[:container]) if @params.key?('container')
+          rescue StandardError => e
+            error!(e, 400)
+          end
+          return present splitted_cell_line_sample, with: Entities::CellLineSampleEntity
+        end
+      end
+
       resource :names do
         desc 'Returns all accessable cell line material names and their id'
         get 'all' do
           return present CelllineMaterial.all, with: Entities::CellLineMaterialNameEntity
         end
       end
+
       resource :material do
         params do
           requires :id, type: Integer, desc: 'id of cell line material to load'

app/api/helpers/cell_line_api_params_helpers.rb

@@ -0,0 +1,64 @@
+# frozen_string_literal: true
+
+module CellLineApiParamsHelpers
+  extend Grape::API::Helpers
+
+  params :cell_line_get_params do
+    optional :collection_id, type: Integer, desc: 'Collection id'
+    optional :sync_collection_id, type: Integer, desc: 'SyncCollectionsUser id'
+    optional :filter_created_at, type: Boolean, desc: 'filter by created at or updated at'
+    optional :from_date, type: Integer, desc: 'created_date from in ms'
+    optional :to_date, type: Integer, desc: 'created_date to in ms'
+  end
+
+  params :cell_line_creation_params do
+    optional :organism, type: String, desc: 'name of the donor organism of the cell'
+    optional :tissue, type: String, desc: 'tissue from which the cell originates'
+    requires :amount, type: Integer, desc: 'amount of cells'
+    requires :unit, type: String, desc: 'unit of cell amount'
+    requires :passage, type: Integer, desc: 'passage of cells'
+    optional :disease, type: String, desc: 'deasease of cells'
+    requires :material_names, type: String, desc: 'names of cell line e.g. name1;name2'
+    requires :collection_id, type: Integer, desc: 'Collection of the cell line sample'
+    optional :cell_type, type: String, desc: 'type of cells'
+    optional :biosafety_level, type: String, desc: 'biosafety_level of cells'
+    optional :growth_medium, type: String, desc: 'growth medium of cells'
+    optional :variant, type: String, desc: 'variant of cells'
+    optional :optimal_growth_temp, type: Float, desc: 'optimal_growth_temp of cells'
+    optional :cryo_pres_medium, type: String, desc: 'cryo preservation medium of cells'
+    optional :gender, type: String, desc: 'gender of donor organism'
+    optional :material_description, type: String, desc: 'description of cell line concept'
+    optional :contamination, type: String, desc: 'contamination of a cell line sample'
+    requires :source, type: String, desc: 'source of a cell line sample'
+    optional :name, type: String, desc: 'name of a cell line sample'
+    optional :mutation, type: String, desc: 'mutation of a cell line'
+    optional :description, type: String, desc: 'description of a cell line sample'
+    optional :short_label, type: String, desc: 'short label of a cell line sample'
+    requires :container, type: Hash, desc: 'root Container of element'
+  end
+
+  params :cell_line_update_params do
+    requires :cell_line_sample_id, type: String, desc: 'id of the cell line to update'
+    optional :organism, type: String, desc: 'name of the donor organism of the cell'
+    optional :mutation, type: String, desc: 'mutation of a cell line'
+    optional :tissue, type: String, desc: 'tissue from which the cell originates'
+    requires :amount, type: Integer, desc: 'amount of cells'
+    requires :unit, type: String, desc: 'unit of amount of cells'
+    optional :passage, type: Integer, desc: 'passage of cells'
+    optional :disease, type: String, desc: 'deasease of cells'
+    optional :material_names, type: String, desc: 'names of cell line e.g. name1;name2'
+    optional :collection_id, type: Integer, desc: 'Collection of the cell line sample'
+    optional :cell_type, type: String, desc: 'type of cells'
+    optional :biosafety_level, type: String, desc: 'biosafety_level of cells'
+    optional :variant, type: String, desc: 'variant of cells'
+    optional :optimal_growth_temp, type: Float, desc: 'optimal_growth_temp of cells'
+    optional :cryo_pres_medium, type: String, desc: 'cryo preservation medium of cells'
+    optional :gender, type: String, desc: 'gender of donor organism'
+    optional :material_description, type: String, desc: 'description of cell line concept'
+    optional :contamination, type: String, desc: 'contamination of a cell line sample'
+    optional :source, type: String, desc: 'source of a cell line sample'
+    optional :name, type: String, desc: 'name of a cell line sample'
+    optional :description, type: String, desc: 'description of a cell line sample'
+    requires :container, type: Hash, desc: 'root Container of element'
+  end
+end

app/models/cellline_sample.rb

@@ -22,6 +22,7 @@
 # rubocop:disable Rails/InverseOf, Rails/HasManyOrHasOneDependent
 class CelllineSample < ApplicationRecord
   acts_as_paranoid
+  has_ancestry
 
   include ElementUIStateScopes
   include Taggable
@@ -35,6 +36,10 @@ class CelllineSample < ApplicationRecord
   belongs_to :cellline_material
   belongs_to :creator, class_name: 'User', foreign_key: 'user_id'
 
+  has_many :sync_collections_users, through: :collections
+
+  after_create :create_root_container
+
   scope :by_sample_name, lambda { |query, collection_id|
                            joins(:collections).where(collections: { id: collection_id })
                                               .where('name ILIKE ?', "%#{sanitize_sql_like(query)}%")
@@ -46,5 +51,9 @@ class CelllineSample < ApplicationRecord
       .where('collections.id=?', collection_id)
       .where('cellline_materials.name ILIKE ?', "%#{sanitize_sql_like(query)}%")
   }
+
+  def create_root_container
+    self.container = Container.create_root_container if container.nil?
+  end
 end
 # rubocop:enable Rails/InverseOf, Rails/HasManyOrHasOneDependent

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

@@ -78,6 +78,11 @@ export default class CreateButton extends React.Component {
     return uiState.reaction.checkedIds.first();
   }
 
+  getCellLineId(){
+    let uiState = UIStore.getState();
+    return uiState.cell_line.checkedIds.first();
+  }
+
   isCopySampleDisabled() {
     let sampleFilter = this.getSampleFilter();
     return !sampleFilter.all && sampleFilter.included_ids.size == 0;
@@ -105,6 +110,17 @@ export default class CreateButton extends React.Component {
     ElementActions.copyReactionFromId(reactionId);
   }
 
+  isCopyCellLineDisabled() {
+    let cellLineId = this.getCellLineId();
+    return !cellLineId;
+  }
+
+  copyCellLine() {
+    let uiState = UIStore.getState();
+    let cellLineId = this.getCellLineId();
+    ElementActions.copyCellLineFromId(parseInt(cellLineId),uiState.currentCollection.id);
+  }
+
   createWellplateFromSamples() {
     let uiState = UIStore.getState();
     let sampleFilter = this.filterParamsFromUIStateByElementType(uiState, "sample");
@@ -272,8 +288,8 @@ export default class CreateButton extends React.Component {
           <MenuItem divider />
           <MenuItem onSelect={() => this.copySample()} disabled={this.isCopySampleDisabled()}>Copy Sample</MenuItem>
           <MenuItem onSelect={() => this.copyReaction()} disabled={this.isCopyReactionDisabled()}>Copy Reaction</MenuItem>
+          <MenuItem onSelect={() => this.copyCellLine()} disabled={this.isCopyCellLineDisabled()}>Copy Cell line</MenuItem>
         </SplitButton>
-
     )
   }
 }

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

@@ -85,6 +85,12 @@ export default class SplitElementBtn extends React.Component {
         >
           Split Wellplate
         </MenuItem>
+        <MenuItem
+          onSelect={() => ElementActions.splitAsSubCellLines(UIStore.getState())}
+          disabled={this.noSelected('cell_line') || this.isAllCollection()}
+        >
+          Split Cell line
+        </MenuItem>
         {itemTables}
       </DropdownButton>
     );