feat: 1878 copy 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 +101,36 @@ 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
+
       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

@@ -35,6 +35,8 @@ class CelllineSample < ApplicationRecord
   belongs_to :cellline_material
   belongs_to :creator, class_name: 'User', foreign_key: 'user_id'
 
+  has_many :sync_collections_users, through: :collections
+
   scope :by_sample_name, lambda { |query, collection_id|
                            joins(:collections).where(collections: { id: collection_id })
                                               .where('name ILIKE ?', "%#{sanitize_sql_like(query)}%")

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/fetchers/CellLinesFetcher.js

@@ -1,4 +1,5 @@
 import CellLine from 'src/models/cellLine/CellLine';
+import Container from 'src/models/Container';
 import BaseFetcher from 'src/fetchers/BaseFetcher';
 import AttachmentFetcher from 'src/fetchers/AttachmentFetcher';
 import GenericElsFetcher from 'src/fetchers/GenericElsFetcher';
@@ -125,6 +126,26 @@ export default class CellLinesFetcher {
     }).then((response) => response.json());
   }
 
+  static copyCellLine(cellLineId, collectionId){
+    const params = {
+      id: cellLineId,
+      collection_id: collectionId,
+      container: Container.init()
+    }
+
+    return fetch('/api/v1/cell_lines/copy/', {
+      credentials: 'same-origin',
+      headers: {
+        Accept: 'application/json',
+        'Content-Type': 'application/json'
+      },
+      method: 'POST',
+      body: JSON.stringify(params)
+    }).then((response) => response.json())
+    .then((json) => CellLine.createFromRestResponse(collectionId, json))
+
+  }
+
   static update(cellLineItem) {
     const params = extractApiParameter(cellLineItem);
     const promise = CellLinesFetcher.uploadAttachments(cellLineItem)

app/packs/src/stores/alt/actions/ElementActions.js

@@ -485,6 +485,17 @@ class ElementActions {
     return cellLineSample;
   }
 
+  copyCellLineFromId(id,collectionId ) {
+    return (dispatch) => {
+      CellLinesFetcher.copyCellLine(id,collectionId)
+        .then((result) => {
+          dispatch(result);
+        }).catch((errorMessage) => {
+          console.log(errorMessage);
+        });
+    };
+  }
+
   splitAsSubsamples(ui_state) {
     return (dispatch) => {
       SamplesFetcher.splitAsSubsamples(ui_state)

app/packs/src/stores/alt/stores/ElementStore.js

@@ -189,6 +189,7 @@ class ElementStore {
       handleCopyReaction: ElementActions.copyReaction,
       handleCopyResearchPlan: ElementActions.copyResearchPlan,
       handleCopyElement: ElementActions.copyElement,
+      handleCopyCellLine: ElementActions.copyCellLineFromId,
       handleOpenReactionDetails: ElementActions.openReactionDetails,
 
       handleBulkCreateWellplatesFromSamples:
@@ -1008,6 +1009,10 @@ class ElementStore {
     Aviator.navigate(`/collection/${result.colId}/${result.element.type}/copy`);
   }
 
+  handleCopyCellLine(result){
+    Aviator.navigate(`/collection/${result.collectionId}/cell_line/${result.id}`);
+  }
+
   handleOpenReactionDetails(reaction) {
     this.changeCurrentElement(reaction);
     this.handleRefreshElements('sample')

app/usecases/cell_lines/copy.rb

@@ -0,0 +1,55 @@
+# frozen_string_literal: true
+
+module Usecases
+  module CellLines
+    class Copy
+      def initialize(cell_line_sample_to_copy, current_user, collection_id)
+        @current_user = current_user
+        @cell_line_sample_to_copy = cell_line_sample_to_copy
+        @collection_id = collection_id
+      end
+
+      def execute!
+        @current_user.increment_counter('celllines') # rubocop: disable Rails/SkipsModelValidations
+        copied_cell_line_sample = copy_cellline_sample
+        create_collection_links(copied_cell_line_sample.id)
+        copied_cell_line_sample
+      end
+
+      private
+
+      def copy_cellline_sample
+        CelllineSample.create(
+          cellline_material: @cell_line_sample_to_copy.cellline_material,
+          creator: @current_user,
+          amount: @cell_line_sample_to_copy[:amount],
+          unit: @cell_line_sample_to_copy[:unit],
+          passage: @cell_line_sample_to_copy[:passage],
+          contamination: @cell_line_sample_to_copy[:contamination],
+          name: @cell_line_sample_to_copy[:name],
+          description: @cell_line_sample_to_copy[:description],
+          short_label: create_short_label,
+        )
+      end
+
+      def create_short_label
+        "#{@current_user.name_abbreviation}-C#{@current_user.counters['celllines']}"
+      end
+
+      def create_collection_links(id)
+        CollectionsCellline.create(
+          collection: Collection.find(@collection_id),
+          cellline_sample_id: id,
+        )
+        CollectionsCellline.create(
+          collection: all_collection_of_current_user,
+          cellline_sample_id: id,
+        )
+      end
+
+      def all_collection_of_current_user
+        Collection.get_all_collection_for_user(@current_user.id)
+      end
+    end
+  end
+end