feat: Copy research plan (#1667)

* add copy research plan feature

* create new derivatives for copy research plan

* update copied annonated file

* update identifier in copied research plan body

* update copy attachment method


---------

Co-authored-by: Mehreen <mehreen.mansur>

app/api/chemotion/research_plan_api.rb

@@ -68,19 +68,22 @@ class ResearchPlanAPI < Grape::API
         optional :collection_id, type: Integer, desc: 'Collection ID'
         requires :container, type: Hash, desc: 'Containers'
         optional :segments, type: Array, desc: 'Segments'
+        optional :attachments, type: Array, desc: 'Attachments'
       end
       post do
         attributes = {
           name: params[:name],
           body: params[:body]
         }
 
+        attributes.delete(:can_copy)
         research_plan = ResearchPlan.new attributes
         research_plan.creator = current_user
         research_plan.container = update_datamodel(params[:container])
         research_plan.save!
         research_plan.save_segments(segments: params[:segments], current_user_id: current_user.id)
-
+        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
@@ -157,7 +160,8 @@ class ResearchPlanAPI < Grape::API
       end
       route_param :id do
         before do
-          error!('401 Unauthorized', 401) unless ElementPolicy.new(current_user, ResearchPlan.find(params[:id])).read?
+          @element_policy = ElementPolicy.new(current_user, ResearchPlan.find(params[:id]))
+          error!('401 Unauthorized', 401) unless @element_policy.read?
         end
         get do
           research_plan = ResearchPlan.find(params[:id])
@@ -170,7 +174,8 @@ class ResearchPlanAPI < Grape::API
           {
             research_plan: Entities::ResearchPlanEntity.represent(
               research_plan,
-              detail_levels: ElementDetailLevelCalculator.new(user: current_user, element: research_plan).detail_levels
+              detail_levels: ElementDetailLevelCalculator.new(user: current_user, element: research_plan).detail_levels,
+              policy: @element_policy,
             ),
             attachments: Entities::AttachmentEntity.represent(research_plan.attachments),
           }

app/api/entities/application_entity.rb

@@ -82,6 +82,10 @@ def detail_levels
       minimal_default_levels.merge(options[:detail_levels])
     end
 
+    def can_copy
+      options[:policy].try(:copy?) || false
+    end
+
     class MissingCurrentUserError < StandardError
     end
   end

app/api/entities/reaction_entity.rb

@@ -56,10 +56,6 @@ def can_update
       options[:policy].try(:update?) || false
     end
 
-    def can_copy
-      options[:policy].try(:copy?) || false
-    end
-
     def code_log
       displayed_in_list? ? nil : object.code_log
     end

app/api/entities/research_plan_entity.rb

@@ -4,6 +4,7 @@ module Entities
   class ResearchPlanEntity < ApplicationEntity
     # rubocop:disable Layout/ExtraSpacing
     with_options(anonymize_below: 0) do
+      expose! :can_copy,                                     unless: :displayed_in_list
       expose! :body
       expose! :container,                                    using: 'Entities::ContainerEntity'
       expose! :id

app/api/entities/sample_entity.rb

@@ -86,10 +86,6 @@ def can_update
       options[:policy].try(:update?) || false
     end
 
-    def can_copy
-      options[:policy].try(:copy?) || false
-    end
-
     def can_publish
       options[:policy].try(:destroy?) || false
     end

app/models/attachment.rb

@@ -75,14 +75,6 @@ class Attachment < ApplicationRecord
     where(attachable_type: 'Template')
   }
 
-  def copy(**args)
-    d = dup
-    d.identifier = nil
-    d.duplicated = true
-    d.update(args)
-    d
-  end
-
   def extname
     File.extname(filename.to_s)
   end

app/models/research_plan.rb

@@ -66,6 +66,7 @@ class ResearchPlan < ApplicationRecord
   before_destroy :delete_attachment
   accepts_nested_attributes_for :collections_research_plans
 
+  attr_accessor :can_copy
 
   unless Dir.exists?(path = Rails.root.to_s + '/public/images/research_plans')
     Dir.mkdir path
@@ -98,15 +99,25 @@ def svg_files
     svg_files
   end
 
+  def update_body_attachments(original_identifier, copy_identifier)
+    attach = body&.detect { |x| x['value']['public_name'] == original_identifier }
+    if attach.present?
+      attach['id'] = SecureRandom.uuid
+      attach['value']['public_name'] = copy_identifier
+    end
+
+    save!
+  end
+
   private
+
   def delete_attachment
     if Rails.env.production?
-      attachments.each { |attachment|
+      attachments.each do |attachment|
         attachment.delay(run_at: 96.hours.from_now, queue: 'attachment_deletion').destroy!
-      }
+      end
     else
       attachments.each(&:destroy!)
     end
   end
-
 end

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

@@ -9,6 +9,7 @@ import {
 import { unionBy, findIndex } from 'lodash';
 import Immutable from 'immutable';
 import ElementCollectionLabels from 'src/apps/mydb/elements/labels/ElementCollectionLabels';
+import UIStore from 'src/stores/alt/stores/UIStore';
 import UIActions from 'src/stores/alt/actions/UIActions';
 import ElementActions from 'src/stores/alt/actions/ElementActions';
 import DetailActions from 'src/stores/alt/actions/DetailActions';
@@ -36,6 +37,7 @@ import HeaderCommentSection from 'src/components/comments/HeaderCommentSection';
 import CommentSection from 'src/components/comments/CommentSection';
 import CommentActions from 'src/stores/alt/actions/CommentActions';
 import CommentModal from 'src/components/common/CommentModal';
+import CopyElementModal from 'src/components/common/CopyElementModal';
 import { formatTimeStampsOfElement } from 'src/utilities/timezoneHelper';
 import UserStore from 'src/stores/alt/stores/UserStore';
 import MatrixCheck from 'src/components/common/MatrixCheck';
@@ -487,7 +489,16 @@ export default class ResearchPlanDetails extends Component {
   } /* eslint-enable */
 
   renderPanelHeading(researchPlan) {
+    const { currentCollection } = UIStore.getState();
+    const rootCol = currentCollection && currentCollection.is_shared === false &&
+      currentCollection.is_locked === false && currentCollection.label !== 'All' ? currentCollection.id : null;
     const titleTooltip = formatTimeStampsOfElement(researchPlan || {});
+    const copyBtn = (
+      <CopyElementModal
+        element={researchPlan}
+        defCol={rootCol}
+      />
+    );
 
     return (
       <Panel.Heading>
@@ -513,14 +524,15 @@ export default class ResearchPlanDetails extends Component {
             <i className="fa fa-floppy-o" aria-hidden="true" />
           </Button>
         </OverlayTrigger>
-        <OverlayTrigger placement="bottom" overlay={<Tooltip id="fullSample">Fullresearch_plan</Tooltip>}>
+        <OverlayTrigger placement="bottom" overlay={<Tooltip id="fullSample">Full Research Plan</Tooltip>}>
           <Button bsStyle="info" bsSize="xsmall" className="button-right" onClick={this.toggleFullScreen}>
             <i className="fa fa-expand" aria-hidden="true" />
           </Button>
         </OverlayTrigger>
         {researchPlan.isNew
           ? null
           : <OpenCalendarButton isPanelHeader eventableId={researchPlan.id} eventableType="ResearchPlan" />}
+        {copyBtn}
       </Panel.Heading>
     );
   }
@@ -623,7 +635,7 @@ export default class ResearchPlanDetails extends Component {
           <ButtonToolbar>
             <Button bsStyle="primary" onClick={() => DetailActions.close(researchPlan)}>Close</Button>
             {
-              researchPlan.changed ? (
+              (researchPlan.changed || researchPlan.is_copy) ? (
                 <Button bsStyle="warning" onClick={() => this.handleSubmit()}>
                   {researchPlan.isNew ? 'Create' : 'Save'}
                 </Button>

app/packs/src/apps/mydb/elements/details/researchPlans/researchPlanTab/ResearchPlanDetailsName.js

@@ -53,6 +53,7 @@ export default class ResearchPlanDetailsName extends Component {
                   value={value || ''}
                   onChange={(event) => onChange(event.target.value)}
                   disabled={disabled}
+                  name="research_plan_name"
                 />
               </FormGroup>
             </Col>

app/packs/src/components/common/CopyElementModal.js

@@ -61,6 +61,8 @@ export default class CopyElementModal extends React.Component {
       ClipboardActions.fetchElementAndBuildCopy(element, selectedCol, 'copy_sample');
     } else if (element.type === 'reaction') {
       ElementActions.copyReaction(element, selectedCol);
+    } else if (element.type === 'research_plan') {
+      ElementActions.copyResearchPlan(element, selectedCol);
     } else {
       ElementActions.copyElement(element, selectedCol);
     }

app/packs/src/models/Attachment.js

@@ -1,5 +1,6 @@
 /* eslint-disable no-underscore-dangle */
 import Element from 'src/models/Element';
+import { cloneDeep } from 'lodash';
 
 export default class Attachment extends Element {
   static NO_PREVIEW_AVAILABLE_PATH = '/images/wild_card/not_available.svg';
@@ -36,6 +37,11 @@ export default class Attachment extends Element {
     this._preview = preview;
   }
 
+  static buildCopy(_attachments) {
+    const newAttachments = cloneDeep(_attachments);
+    return newAttachments;
+  }
+
   serialize() {
     return super.serialize({
       filename: this.filename,

app/packs/src/models/ResearchPlan.js

@@ -3,6 +3,7 @@ import Element from 'src/models/Element';
 import Container from 'src/models/Container';
 import Segment from 'src/models/Segment';
 import Wellplate from 'src/models/Wellplate';
+import Attachment from './Attachment';
 
 const uuidv4 = require('uuid/v4');
 
@@ -267,4 +268,37 @@ export default class ResearchPlan extends Element {
     return this.attachments
       .filter((attachment) => attachment.is_deleted === true && !attachment.is_new);
   }
+
+  buildCopy(params = {}) {
+    const copy = super.buildCopy();
+    Object.assign(copy, params);
+    copy.attachments = this.attachments;
+    copy.container = Container.init();
+    copy.is_new = true;
+    copy.is_copy = true;
+    copy.can_update = true;
+    copy.can_copy = true;
+
+    return copy;
+  }
+
+  static copyFromResearchPlanAndCollectionId(research_plan, collection_id) {
+    const attachments = research_plan.attachments.map(
+      attach => Attachment.buildCopy(attach)
+    );
+    const params = {
+      collection_id,
+      name: research_plan.name,
+      body: research_plan.body,
+    }
+    const copy = research_plan.buildCopy(params);
+    copy.can_copy = false;
+    copy.changed = true;
+    copy.collection_id = collection_id;
+    copy.mode = 'edit';
+    copy.attachments = attachments;
+    copy.origin = { id: research_plan.id };
+
+    return copy;
+  }
 }

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

@@ -627,6 +627,17 @@ class ElementActions {
     };
   }
 
+  copyResearchPlan(research_plan, colId) {
+    return (dispatch) => {
+      ResearchPlansFetcher.fetchById(research_plan.id)
+        .then((result) => {
+          dispatch({ research_plan: result, colId: colId });
+        }).catch((errorMessage) => {
+        console.log(errorMessage);
+      });
+    };
+  }
+
   copyElement(element, colId) {
     return (
       { element: element, colId: colId }

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

@@ -15,6 +15,7 @@ import UIStore from 'src/stores/alt/stores/UIStore';
 import ClipboardStore from 'src/stores/alt/stores/ClipboardStore';
 import Sample from 'src/models/Sample';
 import Reaction from 'src/models/Reaction';
+import ResearchPlan from 'src/models/ResearchPlan';
 import Wellplate from 'src/models/Wellplate';
 import Screen from 'src/models/Screen';
 
@@ -186,6 +187,7 @@ class ElementStore {
       handleCreateReaction: ElementActions.createReaction,
       handleCopyReactionFromId: ElementActions.copyReactionFromId,
       handleCopyReaction: ElementActions.copyReaction,
+      handleCopyResearchPlan: ElementActions.copyResearchPlan,
       handleCopyElement: ElementActions.copyElement,
       handleOpenReactionDetails: ElementActions.openReactionDetails,
 
@@ -986,6 +988,11 @@ class ElementStore {
     Aviator.navigate(`/collection/${result.colId}/reaction/copy`);
   }
 
+  handleCopyResearchPlan(result) {
+    this.changeCurrentElement(ResearchPlan.copyFromResearchPlanAndCollectionId(result.research_plan, result.colId));
+    Aviator.navigate(`/collection/${result.colId}/research_plan/copy`);
+  }
+
   handleCopyElement(result) {
     this.changeCurrentElement(GenericEl.copyFromCollectionId(result.element, result.colId));
     Aviator.navigate(`/collection/${result.colId}/${result.element.type}/copy`);

app/packs/src/utilities/routesUtils.js

@@ -218,6 +218,8 @@ const researchPlanShowOrNew = (e) => {
 
   if (research_planID === 'new') {
     ElementActions.generateEmptyResearchPlan(collectionID);
+  } else if (research_planID === 'copy') {
+    //
   } else if (index < 0) {
     ElementActions.fetchResearchPlanById(research_planID);
   } else if (index !== activeKey) {

app/usecases/attachments/annotation/annotation_loader.rb

@@ -15,7 +15,7 @@ def get_annotation_of_attachment(attachment_id)
           annotation = File.open(location_of_annotation, 'rb') if File.exist?(location_of_annotation)
           raise 'could not find annotation of attachment (file not found)' unless annotation
 
-          annotation.read
+          annotation.read.force_encoding('UTF-8')
         end
 
         def annotation_json_present(data)

app/usecases/attachments/annotation/annotation_updater.rb

@@ -81,6 +81,14 @@ def replace_link_with_base64(location_of_file, svg_string, mime_type)
           xml
         end
 
+        def updated_annotated_string(annotation_data, attachment_id)
+          annotation_data = annotation_data.gsub(
+            %r{/api/v1/attachments/image/([0-9])*},
+            "/api/v1/attachments/image/#{attachment_id}",
+          )
+          update_annotation(annotation_data, attachment_id)
+        end
+
         class ThumbnailerWrapper
           def create_thumbnail(tmp_path)
             Thumbnailer.create(tmp_path)

app/usecases/attachments/copy.rb

@@ -0,0 +1,41 @@
+# frozen_string_literal: true
+
+module Usecases
+  module Attachments
+    class Copy
+      def self.execute!(attachments, element, current_user_id)
+        attachments.each do |attach|
+          original_attach = Attachment.find attach[:id]
+          copy_attach = Attachment.new(
+            attachable_id: element.id,
+            attachable_type: element.class.name,
+            created_by: current_user_id,
+            created_for: current_user_id,
+            filename: original_attach.filename,
+          )
+          copy_attach.save
+
+          copy_io = original_attach.attachment_attacher.get.to_io
+          attacher = copy_attach.attachment_attacher
+          attacher.attach copy_io
+          copy_attach.file_path = copy_io.path
+          copy_attach.save
+
+          update_annotation(original_attach.id, copy_attach.id)
+
+          if element.instance_of?(::ResearchPlan)
+            element.update_body_attachments(original_attach.identifier, copy_attach.identifier)
+          end
+        end
+      end
+
+      def self.update_annotation(original_attach_id, copy_attach_id)
+        loader = Usecases::Attachments::Annotation::AnnotationLoader.new
+        svg = loader.get_annotation_of_attachment(original_attach_id)
+
+        updater = Usecases::Attachments::Annotation::AnnotationUpdater.new
+        updater.updated_annotated_string(svg, copy_attach_id)
+      end
+    end
+  end
+end