labimotion 2.2.0.rc7 → 2.2.0.rc8

checksums.yaml

@@ -1,7 +1,7 @@
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data/lib/labimotion/apis/generic_element_api.rb

@@ -429,7 +429,6 @@ module Labimotion
       desc 'Return serialized elements of current user'
       params do
         optional :collection_id, type: Integer, desc: 'Collection id'
-        optional :sync_collection_id, type: Integer, desc: 'SyncCollectionsUser id'
         optional :el_type, type: String, desc: 'element klass name'
         optional :from_date, type: Integer, desc: 'created_date from in ms'
         optional :to_date, type: Integer, desc: 'created_date to in ms'

data/lib/labimotion/apis/labimotion_api.rb

@@ -12,8 +12,5 @@ module Labimotion
     mount Labimotion::LabimotionHubAPI
     mount Labimotion::StandardLayerAPI
     mount Labimotion::VocabularyAPI
-    mount Labimotion::MttAPI
-    mount Labimotion::DoseRespRequestAPI
-    mount Labimotion::ElementVariationAPI
   end
 end

data/lib/labimotion/entities/element_entity.rb

@@ -23,7 +23,6 @@ module Labimotion
       expose! :uuid
       expose! :user_labels
       expose! :preview_attachment # align with eln change
-      expose! :variations_count
     end
 
     with_options(anonymize_below: 10) do

data/lib/labimotion/helpers/element_helpers.rb

@@ -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(
@@ -247,27 +247,21 @@ module Labimotion
     end
 
     def list_serialized_elements(params, current_user)
-      collection_id =
-      if params[:collection_id]
-        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 = Labimotion::Element.none
 
-      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)
+      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
       else
-        Labimotion::Element.none
+        # All collection of current_user
+        scope = Labimotion::Element.for_user(current_user.id)
       end
 
       ## TO DO: refactor labimotion
@@ -278,7 +272,7 @@ 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/param_helpers.rb

@@ -146,11 +146,5 @@ 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

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

data/lib/labimotion/libs/nmr_mapper.rb

@@ -34,7 +34,7 @@ module Labimotion
         return Labimotion::ConState::NONE if att.nil?
 
         result = process(att)
-        return Labimotion::ConState::NONE if result.nil?
+        return Labimotion::ConState::WAIT if result.nil?
 
         handle_process_result(result, att, id, current_user)
       end
@@ -136,7 +136,7 @@ module Labimotion
         if result[:is_bagit]
           handle_bagit_result(att, id, current_user)
         elsif invalid_metadata?(result)
-          Labimotion::ConState::NONE
+          Labimotion::ConState::WAIT
         else
           handle_nmr_result(result, att, current_user)
         end

data/lib/labimotion/models/concerns/attachment_converter.rb

@@ -31,6 +31,7 @@ module Labimotion
         case con_state
         when Labimotion::ConState::NMR
           self.con_state = Labimotion::NmrMapper.process_ds(id, current_user)
+          return exec_converter if con_state == Labimotion::ConState::WAIT
           update_column(:con_state, con_state)
         when Labimotion::ConState::WAIT
           self.con_state = Labimotion::Converter.jcamp_converter(id, current_user)

data/lib/labimotion/models/concerns/element_fetchable.rb

@@ -26,9 +26,9 @@ module Labimotion
           joins(collections: :user).where(collections: { user_id: user_id })
         )
 
-        # Shared (synced) records
+        # Shared records
         shared = apply_filters.call(
-          joins(collections: :sync_collections_users).where(sync_collections_users: { user_id: user_id })
+          left_joins(:collection_shares).where(collection_shares: { shared_with_id: user_id })
         )
 
         # Combine (remove duplicates), order, and limit

data/lib/labimotion/models/element.rb

@@ -41,12 +41,6 @@ module Labimotion
     has_many :samples, through: :elements_samples, source: :sample
     has_one :container, :as => :containable
     has_many :elements_revisions, dependent: :destroy, class_name: 'Labimotion::ElementsRevision'
-    has_one :element_variation, dependent: :destroy, class_name: 'Labimotion::ElementVariation', foreign_key: :element_id
-
-    def variations_count
-      rows = element_variation&.variations
-      rows.is_a?(Hash) ? rows.size : 0
-    end
 
     accepts_nested_attributes_for :collections_elements
 
@@ -141,9 +135,9 @@ module Labimotion
         joins(collections: :user).where(collections: { user_id: user_id })
       )
 
-      # Shared (synced) elements
+      # Shared elements
       shared = apply_filters.call(
-        joins(collections: :sync_collections_users).where(sync_collections_users: { user_id: user_id })
+        left_joins(:collection_shares).where(collection_shares: { shared_with_id: user_id })
       )
 
       # Combine (remove duplicates), order, and limit

data/lib/labimotion/utils/search.rb

@@ -12,7 +12,7 @@ module Labimotion
     end
 
     def self.elements_search(params, current_user, c_id, dl)
-      collection = Collection.belongs_to_or_shared_by(current_user.id, current_user.group_ids).find(c_id)
+      collection = Collection.accessible_for(current_user).find(c_id)
       element_scope = Labimotion::Element.joins(:collections_elements).where('collections_elements.collection_id = ?', collection.id).joins(:element_klass).where('element_klasses.id = elements.element_klass_id AND element_klasses.name = ?', params[:selection][:genericElName])
       element_scope = element_scope.where('elements.name like (?)', "%#{params[:selection][:searchName]}%") if params[:selection][:searchName].present?
       element_scope = element_scope.where('elements.short_label like (?)', "%#{params[:selection][:searchShowLabel]}%") if params[:selection][:searchShowLabel].present?
@@ -97,7 +97,7 @@ module Labimotion
     def self.samples_search(c_id = @c_id)
       sqls = []
       sps = params[:selection][:searchProperties]
-      collection = Collection.belongs_to_or_shared_by(current_user.id, current_user.group_ids).find(c_id)
+      collection = Collection.accessible_for(current_user).find(c_id)
       element_scope = Sample.joins(:collections_samples).where('collections_samples.collection_id = ?', collection.id)
       return element_scope if sps.empty?
 

data/lib/labimotion/version.rb

@@ -2,5 +2,5 @@
 
 ## Labimotion Version
 module Labimotion
-  VERSION = '2.2.0.rc7'
+  VERSION = '2.2.0.rc8'
 end

data/lib/labimotion.rb

@@ -27,9 +27,6 @@ module Labimotion
   autoload :ExporterAPI, 'labimotion/apis/exporter_api'
   autoload :StandardLayerAPI, 'labimotion/apis/standard_layer_api'
   autoload :VocabularyAPI, 'labimotion/apis/vocabulary_api'
-  autoload :MttAPI, 'labimotion/apis/mtt_api'
-  autoload :DoseRespRequestAPI, 'labimotion/apis/dose_resp_request_api'
-  autoload :ElementVariationAPI, 'labimotion/apis/element_variation_api'
 
   ######## Entities
   autoload :PropertiesEntity, 'labimotion/entities/properties_entity'
@@ -52,7 +49,6 @@ module Labimotion
   autoload :SegmentRevisionEntity, 'labimotion/entities/segment_revision_entity'
   ## autoload :DatasetRevisionEntity, 'labimotion/entities/dataset_revision_entity'
   autoload :VocabularyEntity, 'labimotion/entities/vocabulary_entity'
-  autoload :ElementVariationEntity, 'labimotion/entities/element_variation_entity'
 
   ######## Helpers
   autoload :GenericHelpers, 'labimotion/helpers/generic_helpers'
@@ -118,14 +114,11 @@ module Labimotion
   autoload :StdLayersRevision, 'labimotion/models/std_layers_revision'
 
   autoload :DeviceDescription, 'labimotion/models/device_description'
-  autoload :DoseRespRequest, 'labimotion/models/dose_resp_request'
-  autoload :DoseRespOutput, 'labimotion/models/dose_resp_output'
   autoload :Reaction, 'labimotion/models/reaction'
   autoload :ResearchPlan, 'labimotion/models/research_plan'
   autoload :Sample, 'labimotion/models/sample'
   autoload :Screen, 'labimotion/models/screen'
   autoload :Wellplate, 'labimotion/models/wellplate'
-  autoload :ElementVariation, 'labimotion/models/element_variation'
 
   ######## Models/Concerns
   autoload :GenericKlassRevisions, 'labimotion/models/concerns/generic_klass_revisions'
@@ -133,6 +126,6 @@ module Labimotion
   autoload :ElementFetchable, 'labimotion/models/concerns/element_fetchable'
   autoload :Segmentable, 'labimotion/models/concerns/segmentable'
   autoload :Datasetable, 'labimotion/models/concerns/datasetable'
-  autoload :AttachmentConverter, 'labimotion/models/concerns/attachment_converter'
+  autoload :AttachmentConverter, 'labimotion/models/concerns/attachment_converter.rb'
   autoload :LinkedProperties, 'labimotion/models/concerns/linked_properties'
 end

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: labimotion
 version: !ruby/object:Gem::Version
-  version: 2.2.0.rc7
+  version: 2.2.0.rc8
 platform: ruby
 authors:
 - Chia-Lin Lin
@@ -9,7 +9,7 @@ authors:
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2026-05-04 00:00:00.000000000 Z
+date: 2026-05-05 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: caxlsx
@@ -55,15 +55,12 @@ extra_rdoc_files: []
 files:
 - lib/labimotion.rb
 - lib/labimotion/apis/converter_api.rb
-- lib/labimotion/apis/dose_resp_request_api.rb
-- lib/labimotion/apis/element_variation_api.rb
 - lib/labimotion/apis/exporter_api.rb
 - lib/labimotion/apis/generic_dataset_api.rb
 - lib/labimotion/apis/generic_element_api.rb
 - lib/labimotion/apis/generic_klass_api.rb
 - lib/labimotion/apis/labimotion_api.rb
 - lib/labimotion/apis/labimotion_hub_api.rb
-- lib/labimotion/apis/mtt_api.rb
 - lib/labimotion/apis/segment_api.rb
 - lib/labimotion/apis/standard_api.rb
 - lib/labimotion/apis/standard_layer_api.rb
@@ -78,7 +75,6 @@ files:
 - lib/labimotion/entities/element_entity.rb
 - lib/labimotion/entities/element_klass_entity.rb
 - lib/labimotion/entities/element_revision_entity.rb
-- lib/labimotion/entities/element_variation_entity.rb
 - lib/labimotion/entities/eln_element_entity.rb
 - lib/labimotion/entities/generic_entity.rb
 - lib/labimotion/entities/generic_klass_entity.rb
@@ -94,7 +90,6 @@ files:
 - lib/labimotion/helpers/element_helpers.rb
 - lib/labimotion/helpers/exporter_helpers.rb
 - lib/labimotion/helpers/generic_helpers.rb
-- lib/labimotion/helpers/mtt_helpers.rb
 - lib/labimotion/helpers/param_helpers.rb
 - lib/labimotion/helpers/repository_helpers.rb
 - lib/labimotion/helpers/sample_association_helpers.rb
@@ -134,12 +129,9 @@ files:
 - lib/labimotion/models/dataset_klasses_revision.rb
 - lib/labimotion/models/datasets_revision.rb
 - lib/labimotion/models/device_description.rb
-- lib/labimotion/models/dose_resp_output.rb
-- lib/labimotion/models/dose_resp_request.rb
 - lib/labimotion/models/element.rb
 - lib/labimotion/models/element_klass.rb
 - lib/labimotion/models/element_klasses_revision.rb
-- lib/labimotion/models/element_variation.rb
 - lib/labimotion/models/elements_element.rb
 - lib/labimotion/models/elements_revision.rb
 - lib/labimotion/models/elements_sample.rb

data/lib/labimotion/apis/dose_resp_request_api.rb

@@ -1,241 +0,0 @@
-# frozen_string_literal: true
-
-require 'labimotion/version'
-
-module Labimotion
-  # Dose Response Request API
-  class DoseRespRequestAPI < Grape::API
-    helpers Labimotion::ParamHelpers
-
-    resource :dose_resp_requests do
-      desc 'Get all dose response requests for current user'
-      params do
-        optional :element_id, type: Integer, desc: 'Filter by element ID'
-        optional :state, type: Integer, desc: 'Filter by state (-1, 0, 1, 2)'
-        optional :page, type: Integer, desc: 'Page number', default: 1
-        optional :per_page, type: Integer, desc: 'Items per page', default: 20
-      end
-      get do
-        requests = Labimotion::DoseRespRequest.where(created_by: current_user.id)
-
-        # Apply filters
-        requests = requests.where(element_id: params[:element_id]) if params[:element_id]
-        requests = requests.where(state: params[:state]) if params[:state]
-
-        # Pagination
-        page = params[:page] || 1
-        per_page = [params[:per_page] || 20, 100].min # Max 100 per page
-
-        total = requests.count
-        requests = requests.order(created_at: :desc)
-                          .offset((page - 1) * per_page)
-                          .limit(per_page)
-
-        {
-          requests: requests.map do |req|
-            {
-              id: req.id,
-              request_id: req.request_id,
-              element_id: req.element_id,
-              state: req.state,
-              state_label: state_label(req.state),
-              expires_at: req.expires_at,
-              created_at: req.created_at,
-              updated_at: req.updated_at,
-              first_accessed_at: req.first_accessed_at,
-              last_accessed_at: req.last_accessed_at,
-              access_count: req.access_count,
-              resp_message: req.resp_message,
-              active: req.active?
-            }
-          end,
-          pagination: {
-            page: page,
-            per_page: per_page,
-            total: total,
-            total_pages: (total.to_f / per_page).ceil
-          }
-        }
-      rescue StandardError => e
-        error!("Error: #{e.message}", 500)
-      end
-
-      desc 'Get a dose response request by ID'
-      params do
-        requires :id, type: Integer, desc: 'Request ID'
-      end
-      get ':id' do
-        request = Labimotion::DoseRespRequest.find_by(id: params[:id])
-        error!('Request not found', 404) unless request
-
-        # Check authorization
-        error!('Unauthorized', 403) unless request.created_by == current_user.id
-
-        {
-          id: request.id,
-          request_id: request.request_id,
-          element_id: request.element_id,
-          state: request.state,
-          state_label: state_label(request.state),
-          wellplates_metadata: request.wellplates_metadata,
-          input_metadata: request.input_metadata,
-          expires_at: request.expires_at,
-          revoked_at: request.revoked_at,
-          created_at: request.created_at,
-          updated_at: request.updated_at,
-          first_accessed_at: request.first_accessed_at,
-          last_accessed_at: request.last_accessed_at,
-          access_count: request.access_count,
-          resp_message: request.resp_message,
-          active: request.active?,
-          expired: request.expired?,
-          revoked: request.revoked?
-        }
-      rescue StandardError => e
-        error!("Error: #{e.message}", 500)
-      end
-
-      desc 'Update a dose response request'
-      params do
-        requires :id, type: Integer, desc: 'Request ID'
-        optional :state, type: Integer, desc: 'State', values: [-1, 0, 1, 2]
-        optional :resp_message, type: String, desc: 'Response message'
-        optional :wellplates_metadata, type: Hash, desc: 'Wellplates metadata'
-      end
-      put ':id' do
-        request = Labimotion::DoseRespRequest.find_by(id: params[:id])
-        error!('Request not found', 404) unless request
-
-        # Check authorization
-        error!('Unauthorized', 403) unless request.created_by == current_user.id
-
-        update_params = {}
-        update_params[:state] = params[:state] if params[:state]
-        update_params[:resp_message] = params[:resp_message] if params[:resp_message]
-        update_params[:wellplates_metadata] = params[:wellplates_metadata] if params[:wellplates_metadata]
-
-        request.update!(update_params)
-
-        {
-          success: true,
-          message: 'Request updated successfully',
-          request: {
-            id: request.id,
-            request_id: request.request_id,
-            state: request.state,
-            state_label: state_label(request.state),
-            resp_message: request.resp_message,
-            updated_at: request.updated_at
-          }
-        }
-      rescue ActiveRecord::RecordInvalid => e
-        error!("Validation error: #{e.message}", 422)
-      rescue StandardError => e
-        error!("Error: #{e.message}", 500)
-      end
-
-      desc 'Revoke a dose response request'
-      params do
-        requires :id, type: Integer, desc: 'Request ID'
-      end
-      post ':id/revoke' do
-        request = Labimotion::DoseRespRequest.find_by(id: params[:id])
-        error!('Request not found', 404) unless request
-
-        # Check authorization
-        error!('Unauthorized', 403) unless request.created_by == current_user.id
-
-        request.revoke!
-
-        {
-          success: true,
-          message: 'Request revoked successfully',
-          request: {
-            id: request.id,
-            request_id: request.request_id,
-            state: request.state,
-            revoked_at: request.revoked_at,
-            active: request.active?
-          }
-        }
-      rescue StandardError => e
-        error!("Error: #{e.message}", 500)
-      end
-
-      desc 'Delete a dose response request'
-      params do
-        requires :id, type: Integer, desc: 'Request ID'
-      end
-      delete ':id' do
-        request = Labimotion::DoseRespRequest.find_by(id: params[:id])
-        error!('Request not found', 404) unless request
-
-        # Check authorization
-        error!('Unauthorized', 403) unless request.created_by == current_user.id
-
-        # Soft delete if acts_as_paranoid is enabled
-        request.destroy
-
-        {
-          success: true,
-          message: 'Request deleted successfully'
-        }
-      rescue StandardError => e
-        error!("Error: #{e.message}", 500)
-      end
-
-      desc 'Get dose response requests by element ID'
-      params do
-        requires :element_id, type: Integer, desc: 'Element ID'
-      end
-      get 'by_element/:element_id' do
-        element = Labimotion::Element.find_by(id: params[:element_id])
-        error!('Element not found', 404) unless element
-
-        # Check if user has access to element
-        policy = ElementPolicy.new(current_user, element)
-        error!('Unauthorized', 403) unless policy.read?
-
-        requests = Labimotion::DoseRespRequest.where(element_id: params[:element_id])
-                                               .where(created_by: current_user.id)
-                                               .order(created_at: :desc)
-
-        {
-          element_id: element.id,
-          element_name: element.name,
-          requests: requests.map do |req|
-            {
-              id: req.id,
-              request_id: req.request_id,
-              state: req.state,
-              state_label: state_label(req.state),
-              expires_at: req.expires_at,
-              created_at: req.created_at,
-              access_count: req.access_count,
-              active: req.active?
-            }
-          end
-        }
-      rescue StandardError => e
-        error!("Error: #{e.message}", 500)
-      end
-    end
-
-    helpers do
-      def state_label(state)
-        case state
-        when Labimotion::DoseRespRequest::STATE_ERROR
-          'error'
-        when Labimotion::DoseRespRequest::STATE_INITIAL
-          'initial'
-        when Labimotion::DoseRespRequest::STATE_PROCESSING
-          'processing'
-        when Labimotion::DoseRespRequest::STATE_COMPLETED
-          'completed'
-        else
-          'unknown'
-        end
-      end
-    end
-  end
-end

data/lib/labimotion/apis/element_variation_api.rb

@@ -1,45 +0,0 @@
-# frozen_string_literal: true
-
-module Labimotion
-  class ElementVariationAPI < Grape::API
-    rescue_from ActiveRecord::RecordNotFound do
-      error!('404 Element not found', 404)
-    end
-
-    resource :element_variations do
-      params do
-        requires :element_id, type: Integer, desc: 'Generic element id'
-      end
-      route_param :element_id do
-        before do
-          @element = Labimotion::Element.find(params[:element_id])
-          error!('401 Unauthorized', 401) unless ElementPolicy.new(current_user, @element).read?
-        end
-
-        desc 'Return element variations for a generic element'
-        get do
-          record = Labimotion::ElementVariation.find_or_initialize_by(element_id: @element.id)
-          present record, with: Labimotion::ElementVariationEntity, root: 'element_variation'
-        end
-
-        desc 'Upsert element variations for a generic element'
-        params do
-          requires :variations, type: Hash, desc: 'Variations keyed by row uuid'
-          optional :layout, type: Hash, desc: 'Column layout (selected/order/units/rowOrder)'
-        end
-        put do
-          error!('401 Unauthorized', 401) unless ElementPolicy.new(current_user, @element).update?
-
-          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.save!
-
-          present record, with: Labimotion::ElementVariationEntity, root: 'element_variation'
-        end
-      end
-    end
-  end
-end