labimotion 2.2.0.rc8 → 2.2.0.rc9

data/lib/labimotion/helpers/element_helpers.rb

@@ -200,7 +200,7 @@ module Labimotion
     def element_revisions(params)
       klass = Labimotion::Element.find(params[:id])
       list = klass.elements_revisions unless klass.nil?
-      list&.order(created_at: :desc)&.limit(10)
+      list&.order(created_at: :desc)&.limit(params[:limit])
     rescue StandardError => e
       Labimotion.log_exception(e, current_user)
       raise e
@@ -215,7 +215,7 @@ module Labimotion
         layer, field = params[:sort_column].split('.')
 
         element_klass = Labimotion::ElementKlass.find_by(name: params[:el_type])
-        allowed_fields = element_klass&.properties_release&.dig(Labimotion::Prop::LAYERS, layer, Labimotion::Prop::FIELDS)&.pluck('field') || []
+        allowed_fields = element_klass.properties_release.dig(Labimotion::Prop::LAYERS, layer, Labimotion::Prop::FIELDS)&.pluck('field') || []
 
         if field.in?(allowed_fields)
           query = ActiveRecord::Base.sanitize_sql(
@@ -247,21 +247,27 @@ module Labimotion
     end
 
     def list_serialized_elements(params, current_user)
-      scope = Labimotion::Element.none
-
+      collection_id =
       if params[:collection_id]
-        begin
-          collection = Collection.accessible_for(current_user).find(params[:collection_id])
-          scope = collection.elements
-                            .joins(:element_klass)
-                            .where(element_klasses: { name: params[:el_type] })
-                            .includes(:tag)
-        rescue ActiveRecord::RecordNotFound
-          Labimotion::Element.none
-        end
+        Collection
+          .belongs_to_or_shared_by(current_user.id, current_user.group_ids)
+          .find_by(id: params[:collection_id])&.id
+      elsif params[:sync_collection_id]
+        current_user
+          .all_sync_in_collections_users
+          .find_by(id: params[:sync_collection_id])&.collection&.id
+      end
+
+      scope =
+      if collection_id
+        Labimotion::Element
+          .joins(:element_klass, :collections_elements)
+          .where(
+            element_klasses: { name: params[:el_type] },
+            collections_elements: { collection_id: collection_id },
+          ).includes(:tag, collections: :sync_collections_users)
       else
-        # All collection of current_user
-        scope = Labimotion::Element.for_user(current_user.id)
+        Labimotion::Element.none
       end
 
       ## TO DO: refactor labimotion
@@ -272,7 +278,7 @@ module Labimotion
         layer, field = params[:sort_column].split('.')
 
         element_klass = Labimotion::ElementKlass.find_by(name: params[:el_type])
-        allowed_fields = element_klass&.properties_release&.dig(Labimotion::Prop::LAYERS, layer, Labimotion::Prop::FIELDS)&.pluck('field') || []
+        allowed_fields = element_klass.properties_release.dig(Labimotion::Prop::LAYERS, layer, Labimotion::Prop::FIELDS)&.pluck('field') || []
 
         if field.in?(allowed_fields)
           query = ActiveRecord::Base.sanitize_sql(

data/lib/labimotion/helpers/generic_helpers.rb

@@ -95,7 +95,7 @@ module Labimotion
     def list_klass_revisions(params)
       klass = "Labimotion::#{params[:klass]}".constantize.find_by(id: params[:id])
       list = klass.send("#{params[:klass].underscore}es_revisions") unless klass.nil?
-      list&.order(released_at: :desc)&.limit(10)
+      list&.order(released_at: :desc)&.limit(params[:limit])
     rescue StandardError => e
       Labimotion.log_exception(e, current_user)
       raise e

data/lib/labimotion/helpers/mtt_helpers.rb

@@ -0,0 +1,428 @@
+# frozen_string_literal: true
+
+require 'grape'
+require 'net/http'
+require 'uri'
+require 'zip'
+
+module Labimotion
+  ## MTT Helpers
+  module MttHelpers
+    extend Grape::API::Helpers
+
+    TPA_EXPIRATION = 72.hours
+
+    def token_url(dose_resp_request)
+      # Build the callback URL with token in path
+      api_base_url = ENV['PUBLIC_URL'] || 'http://172.28.156.100:3000'
+      callback_path = "/api/v1/public/mtt_apps/#{dose_resp_request.access_token}"
+      callback_url = "#{api_base_url}#{callback_path}"
+
+      callback_url
+    end
+
+    def get_external_app_url
+      ENV['MTT_EXTERNAL_APP_URL'] || 'http://localhost:4050'
+    end
+
+    def validate_token(token)
+      # Find the request by access token
+      request = Labimotion::DoseRespRequest.find_by(access_token: token)
+      error!('Token not found', 404) unless request
+
+      # Check expiration
+      error!('Token expired', 403) if request.expired?
+
+      # Check revocation
+      error!('Token revoked', 403) if request.revoked?
+
+      request
+    end
+
+    def validate_user_access(dose_resp_request)
+      # Get element and user
+      element = dose_resp_request.element
+      error!('Element not found', 404) unless element
+
+      user = dose_resp_request.creator
+      error!('User not found', 404) unless user
+
+      # Check user has update permission on element using ElementPolicy
+      policy = ElementPolicy.new(user, element)
+      error!('Unauthorized', 403) unless policy.update?
+
+      { element: element, user: user }
+    end
+
+    def download_json_to_external_app
+      # Get token from route params
+      token = params[:token]
+      dose_resp_request = validate_token(token)
+
+      # Validate user access
+      validate_user_access(dose_resp_request)
+
+      # Track access and update state
+      # dose_resp_request.track_access!
+      dose_resp_request.mark_processing! if dose_resp_request.state == Labimotion::DoseRespRequest::STATE_INITIAL
+      # Return wellplates metadata as JSON
+      # Access the wellplates array from the metadata structure
+      wellplates_data = dose_resp_request.wellplates_metadata&.dig('wellplates') ||
+                        dose_resp_request.wellplates_metadata&.dig(:wellplates) ||
+                        []
+
+      response_data = {
+        id: dose_resp_request.id.to_s,
+        request_id: dose_resp_request.request_id,
+        element_info: extract_element_properties(dose_resp_request.element),
+        wellplates: wellplates_data
+      }
+
+      status 200
+      response_data
+    rescue => e
+      error!("Error: #{e.message}", 500)
+    end
+
+    def upload_json_from_external_app
+      # Get token from route params
+      token = params[:token]
+      dose_resp_request = validate_token(token)
+
+      # Validate user access
+      access_info = validate_user_access(dose_resp_request)
+      user = access_info[:user]
+      element = access_info[:element]
+      # Handle file upload
+      file_param = params['file'] || params[:file]
+      error!('No file uploaded', 400) unless file_param && file_param.is_a?(Hash) && file_param['tempfile']
+
+      tempfile = file_param['tempfile']
+      filename = file_param['filename'] || 'upload'
+      # Check if it's a zip file
+      if filename.end_with?('.zip')
+        # Process zip file
+        wellplates_data, csv_data = process_zip_file(tempfile)
+
+        error!('Missing JSON data in zip file', 400) unless wellplates_data
+
+        # Create analysis container and dataset with CSV if present
+        # if csv_data
+        #   create_analysis_with_csv(element, user, csv_data, dose_resp_request, wellplates_data)
+        # end
+      # else
+      #   # Handle single JSON file
+      #   file_content = tempfile.read
+      #   tempfile.rewind
+      #   json_data = JSON.parse(file_content).with_indifferent_access
+      #   wellplates_data = json_data[:Output]
+
+      #   error!('Missing wellplates data', 400) unless wellplates_data
+      end
+
+      dose_resp_request.track_access!
+
+      # Save output data to dose_resp_outputs table
+      output = dose_resp_request.dose_resp_outputs.create!(
+        output_data: { Output: wellplates_data }
+      )
+      if csv_data
+        create_analysis_with_csv(element, user, csv_data, dose_resp_request, output)
+      end
+
+      dose_resp_request.update!(
+        wellplates_metadata: { wellplates: wellplates_data },
+        resp_message: 'Data updated successfully'
+      )
+
+      # Mark as completed
+      dose_resp_request.mark_completed!
+
+      status 200
+      {
+        success: true,
+        message: 'Data updated successfully',
+        request_id: dose_resp_request.id
+      }
+    rescue JSON::ParserError => e
+      error!("Invalid JSON: #{e.message}", 400)
+    rescue ActiveRecord::RecordInvalid => e
+      dose_resp_request.mark_error!(e.message) if dose_resp_request
+      error!("Validation error: #{e.message}", 422)
+    rescue => e
+      dose_resp_request.mark_error!(e.message) if dose_resp_request
+      error!("Error: #{e.message}", 500)
+    end
+
+    def process_zip_file(tempfile)
+      wellplates_data = nil
+      csv_data = nil
+
+      Zip::File.open(tempfile.path) do |zip_file|
+        zip_file.each do |entry|
+          if entry.name.end_with?('.json')
+            # Read JSON file
+            json_content = entry.get_input_stream.read
+            json_data = JSON.parse(json_content).with_indifferent_access
+            wellplates_data = json_data[:Output]
+          elsif entry.name.end_with?('.xls', '.xlsx', '.csv')
+            # Read CSV/Excel file - extract just the basename without path
+            csv_content = entry.get_input_stream.read
+            csv_data = {
+              filename: File.basename(entry.name),
+              content: csv_content
+            }
+          end
+        end
+      end
+
+      [wellplates_data, csv_data]
+    end
+
+    def create_analysis_with_csv(element, user, csv_data, dose_resp_request, output)
+      analysis, dataset = create_analysis_with_dataset(
+        element: element,
+        analysis_name: "MTT Analysis #{dose_resp_request.request_id}-#{output&.id}",
+        dataset_name: 'new',
+        analysis_attributes: {}
+      )
+
+      # Determine content type based on file extension
+      content_type = case File.extname(csv_data[:filename]).downcase
+                     when '.xlsx'
+                       'application/vnd.openxmlformats-officedocument.spreadsheetml.sheet'
+                     when '.xls'
+                       'application/vnd.ms-excel'
+                     when '.csv'
+                       'text/csv'
+                     else
+                       'application/octet-stream'
+                     end
+
+      # Create a temporary file for the attachment
+      temp_file = Tempfile.new([File.basename(csv_data[:filename], '.*'), File.extname(csv_data[:filename])])
+      begin
+        temp_file.binmode
+        temp_file.write(csv_data[:content])
+        temp_file.rewind
+
+        # Create attachment for CSV/Excel file
+        attachment = Attachment.new(
+          filename: csv_data[:filename],
+          file_path: temp_file.path,
+          created_by: user.id,
+          created_for: user.id,
+          attachable_type: 'Container',
+          attachable_id: dataset.id,
+          content_type: content_type
+        )
+        attachment.save! if attachment.valid?
+
+        { analysis: analysis, dataset: dataset, attachment: attachment }
+      ensure
+        temp_file.close
+        temp_file.unlink
+      end
+    end
+
+    def create_analysis_with_dataset(
+      element:,
+      analysis_name: 'New Analysis',
+      dataset_name: 'New Dataset',
+      analysis_attributes: {}
+    )
+      # Ensure the element has a root container
+      ensure_root_container(element)
+
+      # Get or create the analyses container
+      analyses_container = element.container.children.find_or_create_by(container_type: 'analyses')
+
+      # Prepare default extended_metadata for analysis
+      default_metadata = {
+        'content' => '{"ops":[{"insert":""}]}',
+        'report' => true
+      }
+      extended_metadata = default_metadata.merge(analysis_attributes[:extended_metadata] || {})
+
+      # Create the analysis container
+      analysis_container = analyses_container.children.create(
+        container_type: 'analysis',
+        name: analysis_name,
+        description: analysis_attributes[:description] || '',
+        extended_metadata: extended_metadata
+      )
+
+      # Create the dataset container nested under the analysis
+      dataset_container = analysis_container.children.create(
+        container_type: 'dataset',
+        name: dataset_name,
+        description: '',
+        extended_metadata: {}
+      )
+
+      [analysis_container, dataset_container]
+    end
+
+    def ensure_root_container(element)
+      return if element.container.present?
+
+      element.container = Container.create_root_container
+    end
+    # def send_mtt_request(current_user, params)
+
+    #   token_uri = token_url(current_user, params)
+
+
+    #   uri = URI.parse(api_url)
+    #   http = Net::HTTP.new(uri.host, uri.port)
+    #   http.use_ssl = (uri.scheme == 'https')
+    #   http.read_timeout = 30
+
+    #   # Ensure path is not empty, default to '/' if needed
+    #   path = uri.path.empty? ? '/' : uri.path
+    #   request = Net::HTTP::Post.new(path, { 'Content-Type' => 'application/json' })
+    #   request.body = json_data.to_json
+
+    #   response = http.request(request)
+
+    #   {
+    #     success: response.is_a?(Net::HTTPSuccess),
+    #     status: response.code,
+    #     body: (JSON.parse(response.body) rescue response.body),
+    #     message: response.message
+    #   }
+    # rescue StandardError => e
+    #   {
+    #     success: false,
+    #     error: e.message,
+    #     backtrace: e.backtrace.first(5)
+    #   }
+    # end
+
+    def extract_readout_titles(wellplate)
+      # Extract readout titles from wellplate
+      if wellplate.respond_to?(:readout_titles)
+        titles = wellplate.readout_titles
+        return titles if titles.is_a?(Array)
+        return JSON.parse(titles) if titles.is_a?(String)
+      end
+      []
+    end
+
+    def extract_wells(wellplate)
+      # Extract wells data from wellplate
+      wells = wellplate.wells || []
+      wells.map do |well|
+        # Position might be stored as a hash or separate fields
+        position = if well.respond_to?(:position) && well.position.is_a?(Hash)
+                     well.position
+                   elsif well.respond_to?(:position_x)
+                     { x: well.position_x, y: well.position_y }
+                   else
+                     { x: 0, y: 0 }
+                   end
+
+        well_data = {
+          id: well.id,
+          position: position
+        }
+
+        # Only include readouts if they have values
+        readouts = extract_readouts(well)
+        well_data[:readouts] = readouts if readouts.present?
+
+        # Only include sample if it exists
+        sample = extract_sample(well)
+        well_data[:sample] = sample if sample.present?
+
+        well_data
+      end
+    end
+
+    def extract_readouts(well)
+      # Extract readouts from well
+      # Readouts are typically stored as JSON data in the well
+      readouts = if well.respond_to?(:readouts) && well.readouts.is_a?(Array)
+                   well.readouts
+                 elsif well.respond_to?(:readouts) && well.readouts.is_a?(String)
+                   JSON.parse(well.readouts) rescue []
+                 elsif well.respond_to?(:readouts) && well.readouts.is_a?(Hash)
+                   well.readouts.values rescue []
+                 else
+                   []
+                 end
+
+      # Filter out empty readouts (both unit and value are blank)
+      readouts.select do |readout|
+        readout.is_a?(Hash) &&
+        (readout['unit'].to_s.present? || readout['value'].to_s.present? ||
+         readout[:unit].to_s.present? || readout[:value].to_s.present?)
+      end
+    end
+
+    def extract_sample(well)
+      # Extract sample information from well
+      if well.respond_to?(:sample) && well.sample.present?
+        sample = well.sample
+        return {
+          id: sample.id,
+          short_label: sample.short_label,
+          conc: sample.try(:molarity_value) || 0
+        }
+      end
+      nil
+    end
+
+    def generate_wellplates_metadata(wellplates)
+      wellplates.map do |wellplate|
+        {
+          id: wellplate.id.to_s,
+          readoutTitles: extract_readout_titles(wellplate),
+          wells: extract_wells(wellplate)
+        }
+      end
+    end
+
+    def extract_element_properties(element)
+      props = {
+        id: element.id.to_s,
+        name: element.name
+      }
+
+      layers = element.properties.dig('layers', 'general_information', 'fields') ||
+               element.properties.dig(:layers, :general_information, :fields) || []
+
+      endpoint_field = layers.find { |f| f['field'] == 'Endpoint' || f[:field] == 'Endpoint' }
+      props[:endpoint] = endpoint_field['value'] || endpoint_field[:value] if endpoint_field
+
+      props
+    end
+
+
+    def generate_element_metadata(element)
+      {
+        id: wellplate.id.to_s,
+        readoutTitles: extract_readout_titles(wellplate),
+        wells: extract_wells(wellplate)
+      }
+    end
+
+
+    def generate_json_data(wellplates)
+      # # Generate wellplates metadata
+      wellplates_metadata = generate_wellplates_metadata(wellplates)
+
+      # Generate JSON structure
+      json_data = {
+        id: element.id.to_s,
+        request_id: dose_resp_request.id.to_s,
+        wellplates: wellplates_metadata
+      }
+      # Save to JSON file
+      filename = "mtt_request_#{element.id}_#{dose_resp_request.id}.json"
+      filepath = Rails.root.join('tmp', filename)
+      File.write(filepath, JSON.pretty_generate(json_data))
+      json_data
+    end
+  end
+end

data/lib/labimotion/helpers/param_helpers.rb

@@ -146,5 +146,11 @@ module Labimotion
       requires :layer_id, type: String, desc: 'layer identifier'
       requires :field_id, type: String, desc: 'field identifier'
     end
+
+
+    params :create_mtt_request_params do
+      requires :id, type: Integer, desc: 'Element ID'
+      requires :wellplate_ids, type: Array, desc: 'Selected Wellplates'
+    end
   end
 end

data/lib/labimotion/libs/converter.rb

@@ -125,8 +125,7 @@ module Labimotion
         tmp_file.rewind
 
         filename = oat.filename
-        # name = "#{File.basename(filename, '.*')}.zip"
-        name = "#{File.basename(filename, '.*')}#{File.extname(filename) == '.zip' ? '.bagit.zip' : '.zip'}"
+        name = "#{File.basename(filename, '.*')}.zip"
         att = Attachment.new(
           filename: name,
           file_path: tmp_file.path,