labimotion 2.4.0.rc1 → 2.4.0.rc2

checksums.yaml

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data/CHANGELOG.md

@@ -1,5 +1,26 @@
 # LabIMotion Changelog
 
+## [Unreleased]
+* Features and enhancements:
+  * Added per-user, per-klass toolbar configuration (Overview/Arrange visibility) via `POST /user_klass_settings/save` (upsert) and `GET /user_klass_settings/fetch` ([chem-generic-ui#905](https://github.com/LabIMotion/chem-generic-ui/issues/905)). Each user stores their own `settings` (`{ toolbar: { overview, arrange } }`) per element/segment/dataset klass, keyed by the stable klass identifier so it applies to every instance of that klass across template versions. Requires host ELN twin migration `create_user_klass_settings`.
+  * Designer can enable/disable common layer functionalities (record time, add reaction, add/remove layer) per template; template-scoped and independent of template versions ([chem-generic-ui#904](https://github.com/LabIMotion/chem-generic-ui/issues/904)). Saved segments expose the effective klass `settings` so records honor the toggles after a reload. Requires host ELN twin migration `add_settings_to_klasses`.
+  * Support linking CellLine elements in the generic Link Element via the `Labimotion::CellLine` wrapper ([chem-generic-ui#906](https://github.com/LabIMotion/chem-generic-ui/issues/906)). Requires a host ELN `element_klasses` row for `cell_line` (migration) — see PR notes.
+  * `LinkedElement` resolves `cell_line` links to curated `CelllineSample` columns (previously an unknown el_klass misresolved to a generic `Labimotion::Element` sharing the same id).
+  * `LinkedElement` exposes two distinct names for `cell_line` links — the shared **Cell line name** (`material_name`, from the linked `CelllineMaterial`) and the per-sample **Name of specific sample** (`name`) — as separately selectable inline attributes.
+  * Element variations can be exported to and imported from Excel (`.xlsx`). The exported workbook is itself the import template: `GET /api/v1/element_variations/:element_id/export` and `POST /api/v1/element_variations/:element_id/import`.
+  * The exported sheet carries the grid's grouped header -- group, sub-group and field rows, merged as the grid draws them -- above the hidden key and unit rows. Workbooks from the earlier single-row header still import.
+  * Import merges rows by uuid, so a sheet only updates the columns it carries; a row with a blank `Row ID` is added as a new variation.
+  * `number`, `integer` and `system-defined` columns accept numbers only. A cell holding anything else is cleared with a warning rather than stored as text, which also cleans up text those columns already hold.
+  * Import warnings name the cell they came from (`Cell I6: ...`), so the user can go straight to it in the spreadsheet.
+* Bug fixes:
+  * `ElementFetchable#fetch_for_user`: the shared-records branch joined `collection_shares` directly on the element model (an association that only exists on `Collection`), raising `ActiveRecord::ConfigurationError` — rescued into empty search results for every element type. Now joins through `collections`.
+  * `Labimotion::Element.fetch_for_user` carried the same broken `collection_shares` join, so the generic-element `search_by_like` endpoint silently returned no shared records. Now joins through `collections` as well.
+  * `Labimotion::CellLine` delegation forwards keyword arguments on Ruby >= 3.0 (`ruby2_keywords`); without it `fetch_for_user(id, name:, short_label:, limit:)` raised `ArgumentError`.
+  * `SampleAssociation#update_sample_association` no longer creates `Labimotion::ElementsElement` join rows for drag_element values that link standard elements (e.g. `cell_line`, `reaction`), whose `el_id` is not a `Labimotion::Element` id.
+  * `Segmentable#save_segments` → `touch_analyses_properties` assumed every segmentable model defines `#analyses`; `CelllineSample` did not, so `POST /api/v1/cell_lines` raised `NameError` on create/update. Guard the analysis-vocabulary touch when `#analyses` is undefined so the save no longer fails.
+* Dependencies:
+  * Added `roo` (~> 2.10) for reading the uploaded workbook.
+
 ## [2.0.0]
 > 2025-03-25
 * Features and enhancements:

data/lib/labimotion/apis/element_variation_api.rb

@@ -1,15 +1,39 @@
 # frozen_string_literal: true
 
+require 'uri'
+
 module Labimotion
   class ElementVariationAPI < Grape::API
+    XLSX_CONTENT_TYPE = 'application/vnd.openxmlformats-officedocument.spreadsheetml.sheet'
+
     rescue_from ActiveRecord::RecordNotFound do
       error!('404 Element not found', 404)
     end
 
+    helpers do
+      def configure_xlsx_response(filename)
+        env['api.format'] = :binary
+        content_type XLSX_CONTENT_TYPE
+        encoded = URI.encode_www_form_component(filename)
+        header('Content-Disposition', "attachment; filename=\"#{filename}\"; filename*=UTF-8''#{encoded}")
+      end
+
+      def uploaded_xlsx_path!(file)
+        filename = file[:filename].to_s
+        error!('400 Bad Request - expected an .xlsx file', 400) unless filename.downcase.end_with?('.xlsx')
+
+        tempfile = file[:tempfile]
+        error!('400 Bad Request - upload is empty', 400) if tempfile.nil?
+
+        tempfile.path
+      end
+    end
+
     resource :element_variations do
       params do
         requires :element_id, type: Integer, desc: 'Generic element id'
       end
+      # rubocop:disable Metrics/BlockLength
       route_param :element_id do
         before do
           @element = Labimotion::Element.find(params[:element_id])
@@ -32,14 +56,45 @@ module Labimotion
 
           record = Labimotion::ElementVariation.find_or_initialize_by(element_id: @element.id)
           record.variations = params[:variations] || {}
-          if params.key?(:layout) && record.class.column_names.include?('layout')
-            record.layout = params[:layout] || {}
-          end
+          record.layout = params[:layout] || {} if params.key?(:layout) && record.class.column_names.include?('layout')
           record.save!
 
           present record, with: Labimotion::ElementVariationEntity, root: 'element_variation'
         end
+
+        desc 'Export element variations as an xlsx workbook'
+        get :export do
+          exporter = Labimotion::ExportElementVariations.new(@element, user: current_user)
+          configure_xlsx_response(exporter.filename)
+          exporter.read
+        rescue StandardError => e
+          Labimotion.log_exception(e, current_user)
+          error!("500 Internal Server Error: #{e.message}", 500)
+        end
+
+        desc 'Import element variations from an xlsx workbook produced by the export'
+        params do
+          requires :file, type: File, desc: 'xlsx file'
+        end
+        post :import do
+          error!('401 Unauthorized', 401) unless ElementPolicy.new(current_user, @element).update?
+
+          path = uploaded_xlsx_path!(params[:file])
+          importer = Labimotion::ImportElementVariations.new(@element, path)
+          record = importer.execute!
+
+          {
+            element_variation: Labimotion::ElementVariationEntity.represent(record),
+            warnings: importer.warnings
+          }
+        rescue Labimotion::ImportElementVariations::InvalidWorkbook => e
+          error!(e.message, 422)
+        rescue StandardError => e
+          Labimotion.log_exception(e, current_user)
+          error!("500 Internal Server Error: #{e.message}", 500)
+        end
       end
+      # rubocop:enable Metrics/BlockLength
     end
   end
 end

data/lib/labimotion/apis/generic_klass_api.rb

@@ -14,7 +14,7 @@ module Labimotion
         desc 'export klass'
         params do
           requires :id, type: Integer, desc: 'element id'
-          requires :klass, type: String, desc: 'Klass', values: %w[ElementKlass SegmentKlass DatasetKlass]
+          requires :klass, type: String, desc: 'Klass', values: Labimotion::Constants::Klass::ALL
         end
         get do
           entity = "Labimotion::#{params[:klass]}".constantize.find_by(id: params[:id])
@@ -35,7 +35,7 @@ module Labimotion
       namespace :de_activate do
         desc 'activate or deactivate Generic Klass'
         params do
-          requires :klass, type: String, desc: 'Klass', values: %w[ElementKlass SegmentKlass DatasetKlass]
+          requires :klass, type: String, desc: 'Klass', values: Labimotion::Constants::Klass::ALL
           requires :id, type: Integer, desc: 'Klass ID'
           requires :is_active, type: Boolean, desc: 'Active or Inactive Klass'
         end
@@ -54,11 +54,33 @@ module Labimotion
         end
       end
 
+      namespace :update_settings do
+        desc 'update Generic Klass settings'
+        params do
+          requires :klass, type: String, desc: 'Klass', values: Labimotion::Constants::Klass::ALL
+          requires :id, type: Integer, desc: 'Klass ID'
+          requires :settings, type: Hash, desc: 'Klass settings'
+        end
+        after_validation do
+          authenticate_admin!(params[:klass].gsub(/(Klass)/, 's').downcase)
+          fetch_klass(params[:klass], params[:id])
+        end
+        post do
+          updated_klass = update_klass_settings(params)
+          entity_class = "Labimotion::#{params[:klass]}Entity".constantize
+          serialized_data = entity_class.represent(updated_klass)
+          { mc: 'ss00', data: serialized_data }
+        rescue StandardError => e
+          Labimotion.log_exception(e, current_user)
+          { mc: 'se00', msg: e.message, data: {} }
+        end
+      end
+
       namespace :fetch do
         desc 'fetch Generic Klass by id'
         params do
           requires :id, type: Integer, desc: 'Klass ID'
-          requires :klass, type: String, desc: 'Klass', values: %w[ElementKlass SegmentKlass DatasetKlass]
+          requires :klass, type: String, desc: 'Klass', values: Labimotion::Constants::Klass::ALL
         end
         get do
           klass_obj = fetch_klass(params[:klass], params[:id])

data/lib/labimotion/apis/labimotion_api.rb

@@ -13,6 +13,7 @@ module Labimotion
     mount Labimotion::StandardLayerAPI
     mount Labimotion::VocabularyAPI
     mount Labimotion::UserAPI
+    mount Labimotion::UserKlassSettingsAPI
     mount Labimotion::MttAPI
     mount Labimotion::ElementVariationAPI
     mount Labimotion::LabimotionDoiAPI

data/lib/labimotion/apis/user_klass_settings_api.rb

@@ -0,0 +1,70 @@
+# frozen_string_literal: true
+
+require 'labimotion/version'
+
+module Labimotion
+  # Per-user, per-klass UI settings API (toolbar Overview/Arrange visibility).
+  # Every route is scoped to the authenticated user via created_by, so a user
+  # only ever reads/writes their own setting; no klass-edit permission needed.
+  class UserKlassSettingsAPI < Grape::API
+    helpers Labimotion::ParamHelpers
+
+    helpers do
+      def settings_scope
+        Labimotion::UserKlassSetting.where(created_by: current_user.id)
+      end
+
+      def klass_toolbar(settings)
+        (settings || {})['toolbar'] || (settings || {})[:toolbar] || {}
+      end
+    end
+
+    resource :user_klass_settings do
+      desc 'Fetch the current user UI setting for a klass'
+      params do
+        requires :klass, type: String, values: %w[ElementKlass SegmentKlass DatasetKlass], desc: 'Klass type'
+        requires :identifier, type: String, desc: 'Klass identifier'
+      end
+      get 'fetch' do
+        error!('401 Unauthorized', 401) unless current_user
+
+        record = settings_scope.find_by(klass: params[:klass], klass_identifier: params[:identifier])
+        data = record ? Labimotion::UserKlassSettingEntity.represent(record) : nil
+        { mc: 'ss00', data: data }
+      rescue StandardError => e
+        Labimotion.log_exception(e, current_user)
+        { mc: 'se00', msg: e.message, data: nil }
+      end
+
+      desc 'Upsert the current user UI setting for a klass'
+      params do
+        use :user_klass_settings_save
+      end
+      post 'save' do
+        error!('401 Unauthorized', 401) unless current_user
+
+        record = settings_scope.find_or_initialize_by(
+          klass: params[:klass], klass_identifier: params[:klass_identifier]
+        )
+        record.klass_label = params[:klass_label] if params[:klass_label]
+        record.created_by ||= current_user.id
+        record.settings = (record.settings || {}).merge('toolbar' => klass_toolbar(params[:settings]))
+        record.save!
+        { mc: 'ss00', data: Labimotion::UserKlassSettingEntity.represent(record) }
+      rescue StandardError => e
+        Labimotion.log_exception(e, current_user)
+        { mc: 'se00', msg: e.message, data: {} }
+      end
+
+      desc 'List all UI settings of the current user'
+      get 'list' do
+        error!('401 Unauthorized', 401) unless current_user
+
+        { mc: 'ss00', data: Labimotion::UserKlassSettingEntity.represent(settings_scope.to_a) }
+      rescue StandardError => e
+        Labimotion.log_exception(e, current_user)
+        { mc: 'se00', msg: e.message, data: [] }
+      end
+    end
+  end
+end

data/lib/labimotion/entities/generic_klass_entity.rb

@@ -9,6 +9,7 @@ module Labimotion
     expose :properties_template, **DISPLAYED_IN_LIST_CONDITION, anonymize_with: {}
     expose :properties_release, **DISPLAYED_IN_LIST_CONDITION, anonymize_with: {}
     expose :metadata, **DISPLAYED_IN_LIST_CONDITION, anonymize_with: {}
+    expose :settings, **DISPLAYED_IN_LIST_CONDITION, anonymize_with: {}
     expose_timestamps(timestamp_fields: %i[released_at created_at updated_at sync_time])
   end
 end

data/lib/labimotion/entities/segment_entity.rb

@@ -9,9 +9,17 @@ module Labimotion
     expose :properties, **DISPLAYED_IN_LIST_CONDITION, anonymize_with: {}
     expose :properties_release, **DISPLAYED_IN_LIST_CONDITION, anonymize_with: {}
     expose :metadata, **DISPLAYED_IN_LIST_CONDITION, anonymize_with: {}
+    expose :settings, **DISPLAYED_IN_LIST_CONDITION, anonymize_with: {}
 
     def klass_label
       object.segment_klass.label
     end
+
+    # Saved segments are serialized without their klass, so surface the
+    # template-scoped settings here; guarded for hosts not yet migrated.
+    def settings
+      klass = object.segment_klass
+      klass.respond_to?(:settings) ? klass.settings || {} : {}
+    end
   end
 end

data/lib/labimotion/entities/user_klass_setting_entity.rb

@@ -0,0 +1,10 @@
+# frozen_string_literal: true
+
+require 'labimotion/entities/application_entity'
+module Labimotion
+  # Per-user, per-klass UI setting entity
+  class UserKlassSettingEntity < Labimotion::ApplicationEntity
+    expose :id, :klass, :klass_identifier, :klass_label, :settings
+    expose_timestamps(timestamp_fields: %i[created_at])
+  end
+end

data/lib/labimotion/helpers/generic_helpers.rb

@@ -36,6 +36,15 @@ module Labimotion
       raise e
     end
 
+    def update_klass_settings(params)
+      klz = fetch_klass(params[:klass], params[:id])
+      klz&.update!(settings: (klz.settings || {}).merge(params[:settings] || {}))
+      klz
+    rescue StandardError => e
+      Labimotion.log_exception(e, current_user)
+      raise e
+    end
+
     def delete_klass(params)
       authenticate_admin!(params[:klass].gsub(/(Klass)/, 's').downcase)
       klz = fetch_klass(params[:klass], params[:id])

data/lib/labimotion/helpers/param_helpers.rb

@@ -14,6 +14,7 @@ module Labimotion
       optional :klass_prefix, type: String, desc: 'Klass klass_prefix'
       optional :icon_name, type: String, desc: 'Klass icon_name'
       optional :metadata, type: Hash, desc: 'Klass metadata'
+      optional :settings, type: Hash, desc: 'Klass settings'
       requires :properties_template, type: Hash, desc: 'Klass template'
       optional :properties_release, type: Hash, desc: 'Klass release'
       optional :released_at, type: DateTime, desc: 'Klass released_at'
@@ -72,6 +73,7 @@ module Labimotion
       requires :label, type: String, desc: 'Klass label'
       optional :desc, type: String, desc: 'Klass desc'
       optional :metadata, type: Hash, desc: 'Klass metadata'
+      optional :settings, type: Hash, desc: 'Klass settings'
       requires :properties_template, type: Hash, desc: 'Klass template'
       optional :properties_release, type: Hash, desc: 'Klass release'
       optional :released_at, type: DateTime, desc: 'Klass released_at'
@@ -153,5 +155,17 @@ module Labimotion
       requires :id, type: Integer, desc: 'Element ID'
       requires :wellplate_ids, type: Array, desc: 'Selected Wellplates'
     end
+
+    params :user_klass_settings_save do
+      requires :klass, type: String, values: %w[ElementKlass SegmentKlass DatasetKlass], desc: 'Klass type'
+      requires :klass_identifier, type: String, desc: 'Stable klass identifier'
+      optional :klass_label, type: String, desc: 'Klass label (display only)'
+      requires :settings, type: Hash do
+        optional :toolbar, type: Hash do
+          optional :overview, type: Boolean, default: true
+          optional :arrange, type: Boolean, default: true
+        end
+      end
+    end
   end
 end