Add BioEddie integration [SCI-5654][SCI-5657][SCI-5658][SCI-5670] (#3391)

* Add backend for bioeddie [SCI-5654]

* Add modal for bioeddie [SCI-5654]

* Add bio eddie editor to steps and results [SCI-5654]

* Fix markup and code styling

app/assets/javascripts/sitewide/bio_eddie.js

@@ -0,0 +1,152 @@
+/* global HelperModule I18n */
+var bioEddieEditor = (function() {
+  var BIO_EDDIE;
+  var CHEMAXON;
+  var bioEddieIframe;
+  var bioEddieModal;
+
+  function importMolecule() {
+    var monomerModel = BIO_EDDIE.getMonomerModel();
+    var monomerImporter = new CHEMAXON.HelmImportModule();
+    var molecule = bioEddieModal.data('molecule') || '';
+    monomerImporter.import(molecule, monomerModel)
+      .then(builder => BIO_EDDIE.setModel(builder.graphStoreData));
+  }
+
+  function loadBioEddie() {
+    BIO_EDDIE = bioEddieIframe.contentWindow.bioEddieEditor;
+    CHEMAXON = bioEddieIframe.contentWindow.chemaxon;
+
+    if (typeof BIO_EDDIE === 'undefined' || typeof CHEMAXON === 'undefined') {
+      setTimeout(function() {
+        loadBioEddie();
+      }, 2000);
+    } else {
+      importMolecule();
+    }
+  }
+
+  function initIframe() {
+    if (typeof BIO_EDDIE === 'undefined' || typeof CHEMAXON === 'undefined') {
+      bioEddieIframe.src = bioEddieIframe.dataset.src;
+      loadBioEddie();
+    } else {
+      importMolecule();
+    }
+  }
+
+  function saveMolecule(svg, structure) {
+    var moleculeName = bioEddieModal.find('.file-name input').val();
+    $.post(bioEddieModal.data('create-url'), {
+      description: structure,
+      object_id: bioEddieModal.data('object_id'),
+      object_type: bioEddieModal.data('object_type'),
+      name: moleculeName,
+      image: svg
+    }, function(result) {
+      var newAsset = $(result.html);
+      if (bioEddieModal.data('object_type') === 'Step') {
+        newAsset.find('.file-preview-link').css('top', '-300px');
+        newAsset.addClass('new').prependTo($(bioEddieModal.data('assets_container')));
+        setTimeout(function() {
+          newAsset.find('.file-preview-link').css('top', '0px');
+        }, 200);
+        bioEddieModal.modal('hide');
+      } else if (bioEddieModal.data('object_type') === 'Result') {
+        window.location.reload();
+      }
+    });
+  }
+
+  function updateMolecule(svg, structure) {
+    var moleculeName = bioEddieModal.find('.file-name input').val();
+    $.ajax({
+      url: bioEddieModal.data('update-url'),
+      data: {
+        description: structure,
+        name: moleculeName,
+        image: svg
+      },
+      dataType: 'json',
+      type: 'PUT',
+      success: function(json) {
+        $('#modal_link' + json.id + ' img').attr('src', json.url);
+        $('#modal_link' + json.id + ' .attachment-label').html(json.file_name);
+        bioEddieModal.modal('hide');
+      },
+      error: function(response) {
+        if (response.status === 403) {
+          HelperModule.flashAlertMsg(I18n.t('general.no_permissions'), 'danger');
+        }
+      }
+    });
+  }
+
+  function generateImage(structure) {
+    var imageGenerator = new CHEMAXON.ImageGenerator();
+    var emptySVG = document.createElementNS('http://www.w3.org/2000/svg', 'svg');
+    imageGenerator.generateSVGFromHelm(emptySVG, structure)
+      .then(svg => {
+        if (bioEddieModal.data('edit-mode')) {
+          updateMolecule(svg, structure);
+        } else {
+          saveMolecule(svg, structure);
+        }
+      });
+  }
+
+  $(document).on('turbolinks:load', function() {
+    bioEddieIframe = document.getElementById('bioEddieIframe');
+    bioEddieModal = $('#bioEddieModal');
+
+    bioEddieModal.on('shown.bs.modal', function() {
+      initIframe();
+    });
+
+    bioEddieModal.on('click', '.file-save-link', function() {
+      var model = BIO_EDDIE.getModel();
+      var monomerModel = BIO_EDDIE.getMonomerModel();
+      var monomerExporter = new CHEMAXON.Helm2ExportModule();
+
+      monomerExporter.export(model, monomerModel)
+        .then(structure => generateImage(structure));
+    });
+  });
+
+  return {
+    open_new: (objectId, objectType, container) => {
+      bioEddieModal.data('object_id', objectId);
+      bioEddieModal.data('object_type', objectType);
+      bioEddieModal.data('assets_container', container);
+      bioEddieModal.find('.file-name input').val('');
+      bioEddieModal.modal('show');
+    },
+
+    open_edit: (name, molecule, updateUrl) => {
+      bioEddieModal.data('edit-mode', true);
+      bioEddieModal.data('molecule', molecule);
+      bioEddieModal.data('update-url', updateUrl);
+      bioEddieModal.find('.file-name input').val(name);
+      bioEddieModal.modal('show');
+    }
+  };
+}());
+
+(function() {
+  $(document).on('click', '.new-bio-eddie-upload-button', function() {
+    bioEddieEditor.open_new(
+      this.dataset.objectId,
+      this.dataset.objectType,
+      this.dataset.assetsContainer
+    );
+  });
+
+  $(document).on('click', '.bio-eddie-edit-button', function() {
+    $('#filePreviewModal').modal('hide');
+    bioEddieEditor.open_edit(
+      this.dataset.moleculeName,
+      this.dataset.moleculeDescription,
+      this.dataset.updateUrl
+    );
+  });
+}());

app/assets/stylesheets/bio_eddie.scss

@@ -0,0 +1,75 @@
+// scss-lint:disable SelectorDepth
+// scss-lint:disable NestingDepth
+// scss-lint:disable SelectorFormat
+// scss-lint:disable ImportantRule
+// scss-lint:disable IdSelector
+
+@import "constants";
+@import "mixins";
+
+// MarvinJs modal
+.modal-bio-eddie {
+  background: transparent;
+  font-size: $font-size-base;
+  padding: 0 !important;
+
+  .modal-dialog {
+    height: 100%;
+    margin: 0;
+    padding: 0;
+    width: auto;
+  }
+
+  .modal-content {
+    background: transparent;
+    border: 0;
+    box-shadow: none;
+    height: 100%;
+    width: auto;
+  }
+
+  .modal-header {
+    background: $color-white;
+    display: flex;
+    height: 60px;
+    line-height: 40px;
+    padding: 10px 15px;
+    text-align: center;
+
+    .file-save-link {
+      flex-shrink: 0;
+      margin: 0 20px 0 0;
+    }
+
+    .file-name {
+      align-items: center;
+      display: flex;
+      flex-shrink: 0;
+      float: left;
+      margin-right: auto;
+
+      input {
+        border-radius: 5px;
+        box-shadow: none;
+        color: $color-black;
+        height: 40px;
+        margin-left: 5px;
+        outline: 0;
+        padding: 5px 10px;
+        position: relative;
+        width: 350px;
+      }
+    }
+  }
+
+  .modal-body {
+    height: calc(100% - 60px);
+    padding: 0;
+
+    iframe {
+      height: 100%;
+      position: relative;
+      width: 100%;
+    }
+  }
+}

app/assets/stylesheets/shared/assets.scss

@@ -61,6 +61,34 @@
       }
     }
 
+    &.bio_eddie {
+
+      &::before,
+      &::after {
+        border-radius: 1em 0 0 1em;
+        bottom: 1em;
+        content: "";
+        display: block;
+        height: 2em;
+        line-height: 2em;
+        position: absolute;
+        right: -1em;
+        width: 2.25em;
+      }
+
+      &::before {
+        background: $bio-eddie-color;
+      }
+
+      &::after {
+        background-image: url("/images/icon_small/bio_eddie_white.png");
+        background-repeat: no-repeat;
+        height: 1.85em;
+        right: -1.15em;
+        width: 2em;
+      }
+    }
+
     .fas {
       font-size: 100px;
       line-height: 160px;

app/assets/stylesheets/shared_styles/constants/colors.scss

@@ -41,6 +41,9 @@ $office-ms-powerpoint: #d24726;
 // MarvinJS color:
 $marvinjs-color: #29999c;
 
+// BioEddie color:
+$bio-eddie-color: #ffa000;
+
 $pdf-color: #f40f02;
 
 // Don't use them

app/controllers/bio_eddie_assets_controller.rb

@@ -0,0 +1,99 @@
+# frozen_string_literal: true
+
+class BioEddieAssetsController < ApplicationController
+  include ActiveStorage::SetCurrent
+
+  before_action :load_vars, except: :create
+  before_action :load_create_vars, only: :create
+
+  before_action :check_read_permission
+  before_action :check_edit_permission, only: %i(update create start_editing)
+
+  def create
+    asset = BioEddieService.create_molecule(bio_eddie_params, current_user, current_team)
+
+    if asset && bio_eddie_params[:object_type] == 'Step'
+      render json: {
+        html: render_to_string(partial: 'assets/asset.html.erb', locals: {
+                                 asset: asset,
+                                 gallery_view_id: bio_eddie_params[:object_id]
+                               })
+      }
+    elsif asset && bio_eddie_params[:object_type] == 'Result'
+      render json: { status: 'created' }, status: :ok
+    else
+      render json: asset.errors, status: :unprocessable_entity
+    end
+  end
+
+  def update
+    asset = BioEddieService.update_molecule(bio_eddie_params, current_user, current_team)
+
+    if asset
+      render json: { url: rails_representation_url(asset.medium_preview),
+                     id: asset.id,
+                     file_name: asset.blob.metadata['name'] }
+    else
+      render json: { error: t('bio_eddie.no_molecules_found') }, status: :unprocessable_entity
+    end
+  end
+
+  def start_editing
+    # Activity here
+  end
+
+  private
+
+  def load_vars
+    @asset = current_team.assets.find_by(id: params[:id])
+    return render_404 unless @asset
+
+    @assoc = @asset.step || @asset.result
+
+    case @assoc
+    when Step
+      @protocol = @assoc.protocol
+    when Result
+      @my_module = @assoc.my_module
+    end
+  end
+
+  def load_create_vars
+    case bio_eddie_params[:object_type]
+    when 'Step'
+      @assoc = Step.find_by(id: bio_eddie_params[:object_id])
+      @protocol = @assoc.protocol
+    when 'Result'
+      @assoc = MyModule.find_by(id: bio_eddie_params[:object_id])
+      @my_module = @assoc
+    end
+  end
+
+  def check_read_permission
+    case @assoc
+    when Step
+      return render_403 unless can_read_protocol_in_module?(@protocol) ||
+                               can_read_protocol_in_repository?(@protocol)
+    when Result, MyModule
+      return render_403 unless can_read_experiment?(@my_module.experiment)
+    else
+      render_403
+    end
+  end
+
+  def check_edit_permission
+    case @assoc
+    when Step
+      return render_403 unless can_manage_protocol_in_module?(@protocol) ||
+                               can_manage_protocol_in_repository?(@protocol)
+    when Result, MyModule
+      return render_403 unless can_manage_module?(@my_module)
+    else
+      render_403
+    end
+  end
+
+  def bio_eddie_params
+    params.permit(:id, :description, :object_id, :object_type, :name, :image)
+  end
+end

app/services/bio_eddie_service.rb

@@ -0,0 +1,78 @@
+# frozen_string_literal: true
+
+class BioEddieService
+  class << self
+    def url
+      ApplicationSettings.instance.values['bio_eddie_url']
+    end
+
+    def enabled?
+      url.present?
+    end
+
+    def create_molecule(params, current_user, current_team)
+      file = image_io(params)
+
+      asset = Asset.new(created_by: current_user,
+                          last_modified_by: current_user,
+                          team_id: current_team.id)
+      attach_file(asset.file, file, params)
+      asset.save!
+      asset.post_process_file(current_team)
+      connect_asset(asset, params, current_user)
+    end
+
+    def update_molecule(params, _current_user, current_team)
+      asset = current_team.assets.find(params[:id])
+      attachment = asset&.file
+
+      return unless attachment
+
+      file = image_io(params)
+      attach_file(attachment, file, params)
+      asset
+    end
+
+    private
+
+    def connect_asset(asset, params, current_user)
+      case params[:object_type]
+      when 'Step'
+        object = params[:object_type].constantize.find(params[:object_id])
+        asset.update!(view_mode: object.assets_view_mode)
+        object.assets << asset
+      when 'Result'
+        my_module = MyModule.find_by(id: params[:object_id])
+        return unless my_module
+
+        Result.create(user: current_user,
+                      my_module: my_module,
+                      name: prepare_name(params[:name]),
+                      asset: asset,
+                      last_modified_by: current_user)
+      end
+      asset
+    end
+
+    def image_io(params)
+      StringIO.new(params[:image])
+    end
+
+    def attach_file(attachment, file, params)
+      attachment.attach(
+        io: file,
+        filename: "#{prepare_name(params[:name])}.svg",
+        content_type: 'image/svg+xml',
+        metadata: {
+          name: prepare_name(params[:name]),
+          description: params[:description],
+          asset_type: 'bio_eddie'
+        }
+      )
+    end
+
+    def prepare_name(sketch_name)
+      sketch_name.presence || I18n.t('bio_eddie.new_molecule')
+    end
+  end
+end

app/views/assets/bio_eddie/_create_bio_eddie_li.html.erb

@@ -0,0 +1,11 @@
+<li>
+  <a
+    class="new-bio-eddie-upload-button"
+    data-object-id="<%= element_id %>"
+    data-object-type="<%= element_type %>"
+    data-assets-container="<%= assets_container %>"
+  >
+    <%= image_tag 'icon_small/bio_eddie.png' %>
+    <%= t('bio_eddie.new_button') %>
+  </a>
+</li>

app/views/my_modules/results.html.erb

@@ -29,6 +29,8 @@
           </li>
           <%= render partial: '/assets/marvinjs/create_marvin_sketch_li',
                        locals: {  element_id: @my_module.id, element_type: 'Result',  sketch_container: "#results[data-module-id=#{@my_module.id}]" } %>
+          <%= render partial: '/assets/bio_eddie/create_bio_eddie_li.html.erb',
+                     locals: {  element_id: @my_module.id, element_type: 'Result',  assets_container:"#results[data-module-id=#{@my_module.id}]" } %>
           <%= render partial: "assets/wopi/create_wopi_file_li",
                      locals: {  element_id: @my_module.id, element_type: 'Result' } %>
         </ul>
@@ -69,6 +71,9 @@
   </div>
 </div>
 
+<%= render partial: "shared/bio_eddie_modal.html.erb" %>
+
+
 <%= javascript_include_tag "handsontable.full" %>
 
 <!-- Libraries for formulas -->

app/views/protocols/_steps.html.erb

@@ -34,3 +34,5 @@
 
 <%= javascript_include_tag "assets/wopi/create_wopi_file" %>
 <%= javascript_include_tag "protocols/steps" %>
+
+<%= render partial: "shared/bio_eddie_modal.html.erb" %>

app/views/shared/_bio_eddie_modal.html.erb

@@ -0,0 +1,33 @@
+<% if BioEddieService.enabled? %>
+  <div id="bioEddieModal"
+       class="modal modal-bio-eddie"
+       role="dialog"
+       aria-labelledby="bioEddieModal"
+       aria-hidden="true"
+       data-create-url="<%= bio_eddie_assets_path %>"
+       data-backdrop="static"
+       data-keyboard="false">
+    <div class="modal-dialog">
+      <div class="modal-content">
+        <div class="modal-header">
+          <span class="file-name">
+            <div class="sci-input-container ">
+              <%= text_field_tag :molecule_name, '', placeholder: t('bio_eddie.molecule_name_placeholder'), class: 'sci-input-field' %>
+            </div>
+          </span>
+          <button class="file-save-link btn btn-light">
+            <i class="fas fa-save"></i>
+            <%= t('SaveClose')%>
+          </button>
+          <button class="preview-close btn btn-light icon-btn" data-dismiss="modal">
+            <i class="fas fa-times"></i>
+          </button>
+        </div>
+        <div class="modal-body">
+          <iframe id="bioEddieIframe" data-src="<%= BioEddieService.url %>/index.html" frameBorder="0" ></iframe>
+        </div>
+      </div>
+    </div>
+  </div>
+<% end %>
+

app/views/shared/file_preview/_content.html.erb

@@ -21,6 +21,16 @@
           <span class="fas fa-pencil-alt"></span>
           <%= t('assets.file_preview.edit_in_marvinjs') %>
         </button>
+      <% elsif asset.file.metadata[:asset_type] == 'bio_eddie' %>
+        <button class="btn btn-light bio-eddie-edit-button"
+          data-molecule-id="<%= asset.id %>"
+          data-update-url="<%= bio_eddie_asset_path(asset) %>"
+          data-molecule-name="<%= asset.file.metadata[:name] %>"
+          data-molecule-description="<%= asset.file.metadata[:description] %>"
+        >
+          <span class="fas fa-pencil-alt"></span>
+          <%= t('assets.file_preview.edit_in_bio_eddie') %>
+        </button>
       <% elsif asset.editable_image? %>
         <button class="btn btn-light image-edit-button"
           data-image-id="<%= asset.id %>"

app/views/steps/attachments/_list.html.erb

@@ -24,10 +24,11 @@
             data-step-id="<%= step.id %>"
             data-state-save-url="<%= update_view_state_step_path(step.id) %>">
           <li class="divider-label"><%= t("protocols.steps.attachments.add") %></li>
-          <li>
-            <%= render partial: '/assets/marvinjs/create_marvin_sketch_li.html.erb',
-                       locals: {  element_id: step.id, element_type: 'Step',  sketch_container: ".attachments[data-step-id=#{step.id}]" } %>
-          </li>
+          <%= render partial: '/assets/marvinjs/create_marvin_sketch_li.html.erb',
+                     locals: {  element_id: step.id, element_type: 'Step',  sketch_container: ".attachments[data-step-id=#{step.id}]" } %>
+          <%= render partial: '/assets/bio_eddie/create_bio_eddie_li.html.erb',
+                     locals: {  element_id: step.id, element_type: 'Step',  assets_container: ".attachments[data-step-id=#{step.id}]" } %>
+
           <li>
             <%= render partial: '/assets/wopi/create_wopi_file_li.html.erb',
                        locals: {  element_id: step.id, element_type: 'Step' } %>

config/locales/en.yml

@@ -2396,6 +2396,7 @@ en:
     file_preview:
       edit_in_scinote: "Edit in SciNote"
       edit_in_marvinjs: "Edit in Marvin JS"
+      edit_in_bio_eddie: "Edit in BioEddie"
     context_menu:
       set_view_size: "SET VIEW SIZE"
       delete: "Delete file"
@@ -2635,6 +2636,12 @@ en:
     invite_users:
       permission_error: "You don't have permission to invite additional users to this team. Contact its administrator/s."
 
+  bio_eddie:
+    new_molecule: "New Molecule"
+    new_button: "Create Biomolecule"
+    molecule_name_placeholder: "Click here to enter Molecule name"
+    no_molecules_found: "No Molecules Found"
+
   marvinjs:
     new_sketch: "New Chemical Drawing"
     new_button: "Create Chemical Drawing"
@@ -2642,6 +2649,7 @@ en:
     structure_placeholder: "Click here to enter Chemical Drawing name"
     modal_name_title: "Chemical Drawing name:"
     checmical_drawing: "Chemical drawings"
+    no_sketches_found: "No Sketches Found"
 
   pdf_preview:
     fit_to_screen: 'Fit to screen'

config/routes.rb

@@ -773,6 +773,12 @@ Rails.application.routes.draw do
     end
   end
 
+  resources :bio_eddie_assets, only: %i(create update) do
+    member do
+      post :start_editing
+    end
+  end
+
   post 'global_activities', to: 'global_activities#index'
 
   constraints WopiSubdomain do