labimotion 2.3.0.rc1 → 2.4.0.rc1

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA256:
-  metadata.gz: ed76c84363276af955102072d3491035f014dedb9fcdc835b4ec9c2e9ba199ee
-  data.tar.gz: 8a5e3a1d1c5ac1fb497d278c1f9a3237dfc0f93271729e05c602339879d6a204
+  metadata.gz: 20affa359afd5082ac4bc5e900b3e66c2c537a4b83fc9032883e33f25dc60362
+  data.tar.gz: e8bb4ae665e5de5166790ac27ecf42a95394057a2fd93d5deebc95dc858a5189
 SHA512:
-  metadata.gz: 1d9d033f42be38117263ab30d502a3eafa5f9fa3b983f834dd1b1e14ab55537c91fafafd5b1643a6d3e2ea5e2e2ec17a8a072220cef56a4b80a34deca8f6600c
-  data.tar.gz: 926082586397c99e47f634733d2e258b463a9340809e45d5a0d4a788ff508c0335279e80baabef1f89b851691777d764b8657b6825b40a420e962dab4c6e6f36
+  metadata.gz: 7e6d407b44837ccb8758aa2a86b6c4b109350dfa50dde7ebb3affae93b070c1efba512b4db2b08f0608b165a25c1a53c4caaa3450f55c1a15e5c1401a1ca87de
+  data.tar.gz: 60c1e3df69128dda039990086d98ad816e7fcedbf74e1a90b896b9b94eb7446b3e5feb613e42770be1f8807d72e5ee3a7c07ec8eb8e158b776d5904335d07671

data/lib/labimotion/apis/converter_api.rb

@@ -2,39 +2,103 @@
 
 module Labimotion
   class ConverterAPI < Grape::API
+    helpers Labimotion::DatasetHelpers
     helpers do
+      def load_converter_config!
+        @conf = Rails.configuration.converter&.url
+        @profile = Rails.configuration.converter&.profile
+        error!(406) unless @conf && @profile
+      end
+
+      def require_converter_admin!
+        error!(401) unless current_user.profile&.data&.fetch('converter_admin', false)
+      end
+
+      def uploaded_file
+        params[:file].is_a?(Array) ? params[:file][0] : params[:file]
+      end
     end
+
     resource :converter do
+      resource :datasets do
+        desc 'list Generic Dataset Klass'
+        get do
+          list = klass_list(true, false)
+          list.map do |kl|
+            pr = kl.properties_release
+            pr['name'] = kl.label
+            pr['ols'] = kl.ols_term_id
+            pr
+          end || []
+        end
+      end
+
+      resource :datasets_units do
+        desc 'list Generic Dataset Klass'
+        get do
+          Labimotion::Units::FIELDS
+        end
+      end
+
       resource :profiles do
+
         before do
-          @conf = Rails.configuration.try(:converter).try(:url)
-          @profile = Rails.configuration.try(:converter).try(:profile)
-          error!(406) unless @conf && @profile
+          load_converter_config!
         end
-        desc 'fetch profiles'
+
+        desc 'Fetch profiles (no admin required)'
         get do
           profiles = Labimotion::Converter.fetch_profiles
           { profiles: profiles, client: @profile }
         end
-        desc 'create profile'
+
+        desc 'Create profile'
         post do
+          require_converter_admin!
           Labimotion::Converter.create_profile(params)
         end
-        desc 'update profile'
+
         route_param :id do
+          desc 'Update profile'
           put do
+            require_converter_admin!
             Labimotion::Converter.update_profile(params)
           end
-        end
-        desc 'delete profile'
-        route_param :id do
+
+          desc 'Delete profile'
           delete do
-            id = params[:id]
-            Labimotion::Converter.delete_profile(id)
+            require_converter_admin!
+            Labimotion::Converter.delete_profile(params[:id])
           end
         end
-      end
 
+        resource :restore do
+          route_param :profile_id,
+                      requirements: {
+                        profile_id: /[0-9a-fA-F]{8}-[0-9a-fA-F]{4}-[0-9a-fA-F]{4}-[0-9a-fA-F]{4}-[0-9a-fA-F]{12}/
+                      } do
+
+            route_param :profile_version,
+                        requirements: {
+                          profile_version: /\d+\.\d+/
+                        } do
+              get do
+                {test_version: params[:profile_id], version: params[:profile_version]}
+              end
+              desc 'Restore profile'
+              post do
+                require_converter_admin!
+
+                Labimotion::Converter.restore(
+                  params[:profile_id],
+                  params[:profile_version],
+                  params[:hard]
+                )
+              end
+            end
+          end
+        end
+      end
       resource :structure do
         helpers do
           def convert_structure(molfile)
@@ -66,10 +130,8 @@ module Labimotion
 
       resource :options do
         before do
-          error!(401) unless current_user.profile&.data['converter_admin'] == true
-          @conf = Rails.configuration.try(:converter).try(:url)
-          @profile = Rails.configuration.try(:converter).try(:profile)
-          error!(406) unless @conf && @profile
+          load_converter_config!
+          require_converter_admin!
         end
         desc 'fetch options'
         get do
@@ -80,18 +142,31 @@ module Labimotion
 
       resource :tables do
         before do
-          error!(401) unless current_user.profile&.data['converter_admin'] == true
-          @conf = Rails.configuration.try(:converter).try(:url)
-          @profile = Rails.configuration.try(:converter).try(:profile)
-          error!(406) unless @conf && @profile
+          load_converter_config!
+          require_converter_admin!
         end
         desc 'create tables'
         post do
-          res = Labimotion::Converter.create_tables(params[:file][0]['tempfile']) unless params[:file].empty?
-          res['metadata']['file_name'] = params[:file][0]['filename']
+          file = uploaded_file
+          res = Labimotion::Converter.create_tables(file['tempfile']) unless file.nil?
+          res['metadata']['file_name'] = file['filename']
           res
         end
       end
+
+      resource :conversions do
+        before do
+          load_converter_config!
+          require_converter_admin!
+        end
+        desc 'convert file'
+        post do
+          file = uploaded_file
+          res = Labimotion::Converter.test_conversions(file['tempfile'], params[:format]) unless file.nil?
+          res
+        end
+      end
+
     end
   end
-end
+end

data/lib/labimotion/apis/generic_element_api.rb

@@ -88,6 +88,28 @@ module Labimotion
         end
       end
 
+      namespace :linked_attributes do
+        desc 'List the selectable inline attributes of an element linked from a drag_element field'
+        params do
+          optional :el_klass, type: String, desc: 'Generic element klass name or permit-target key (reaction, sample, ...)'
+          optional :el_type, type: String, desc: 'Linked element type (element, sample, molecule, ...)'
+          requires :el_id, type: Integer, desc: 'Linked element id'
+        end
+        get do
+          linked = Labimotion::LinkedElement.new(params[:el_klass], params[:el_id], params[:el_type])
+          record = linked.record
+          error!('404 Not Found', 404) if record.nil?
+          # Reference data (molecules) is public; everything else is collection-scoped.
+          readable = record.is_a?(::Molecule) || ElementPolicy.new(current_user, record).read?
+          error!('401 Unauthorized', 401) unless readable
+
+          { attributes: linked.available }
+        rescue StandardError => e
+          Labimotion.log_exception(e, current_user)
+          { attributes: [], error: e.message }
+        end
+      end
+
       namespace :search_basic_by_like do
         desc 'Search basic elements by name and short label (case-insensitive like search)'
         params do

data/lib/labimotion/entities/properties_entity.rb

@@ -20,6 +20,7 @@ module Labimotion
 
     def process_fields(key, layer)
       process_sample_and_molecule_fields(key, layer)
+      process_linked_attr_fields(key, layer)
       process_reaction_fields(key, layer)
       process_table_fields(key, layer)
       # process_voc_fields(key, layer)
@@ -32,6 +33,18 @@ module Labimotion
       end
     end
 
+    # Resolve the linked attributes a user chose to surface inline on a drag field
+    # (stored as value['el_attrs']). Only the selection is persisted; the current
+    # values are refreshed here from the linked element on every load. Works for
+    # drag_element (generic element or any permit-target type) as well as
+    # drag_sample / drag_molecule.
+    def process_linked_attr_fields(key, layer)
+      select_fields(layer, [Labimotion::FieldType::DRAG_ELEMENT, Labimotion::FieldType::DRAG_SAMPLE,
+                            Labimotion::FieldType::DRAG_MOLECULE]).each do |field, idx|
+        update_linked_attr_field(key, field, idx)
+      end
+    end
+
     def process_reaction_fields(key, layer)
       select_fields(layer, [Labimotion::FieldType::SYS_REACTION]).each do |field, idx|
         update_reaction_field(key, field, idx)
@@ -80,6 +93,21 @@ module Labimotion
                          })
     end
 
+    def update_linked_attr_field(key, field, idx)
+      return unless field['value'].is_a?(Hash)
+
+      attrs = field.dig('value', 'el_attrs')
+      return unless attrs.is_a?(Array) && attrs.present?
+      return unless object.properties.dig(Labimotion::Prop::LAYERS, key, Labimotion::Prop::FIELDS, idx,
+                                          'value').present?
+
+      el_klass = field.dig('value', 'el_klass')
+      el_id = field.dig('value', 'el_id')
+      el_type = field.dig('value', 'el_type')
+      object.properties[Labimotion::Prop::LAYERS][key][Labimotion::Prop::FIELDS][idx]['value']['el_attrs'] =
+        Labimotion::LinkedElement.new(el_klass, el_id, el_type).resolve(attrs)
+    end
+
     def update_reaction_field(key, field, idx)
       return unless field['value'].is_a?(Hash)
 

data/lib/labimotion/helpers/param_helpers.rb

@@ -91,6 +91,7 @@ module Labimotion
       optional :desc, type: String, desc: 'Segment Klass Desc'
       optional :place, type: String, desc: 'Segment Klass Place', default: '100'
       optional :identifier, type: String, desc: 'Segment Identifier'
+      optional :metadata, type: Hash, desc: 'Klass metadata'
     end
 
     params :create_segment_klass_params do

data/lib/labimotion/libs/linked_element.rb

@@ -0,0 +1,193 @@
+# frozen_string_literal: true
+
+module Labimotion
+  # Resolves the "inline attributes" of an element linked from a generic
+  # drag_element field.
+  #
+  # A drag_element link target is identified by the stored value's +el_klass+:
+  #   * a generic element klass name  -> the target is a Labimotion::Element and
+  #     its selectable attributes are its own property fields (layer + field);
+  #   * a permit-target key (reaction, sample, molecule, wellplate, screen,
+  #     research_plan, device_description) -> the target is a standard ELN model
+  #     and its selectable attributes are a curated set of database columns.
+  #
+  # Used both to list the attributes a user can pick (#available) and to refresh
+  # the current values of a previously stored selection (#resolve).
+  class LinkedElement
+    SOURCE_PROPERTY = 'property'
+    SOURCE_COLUMN = 'column'
+
+    # el_klass (permit-target key) => model class name
+    MODELS = {
+      'reaction' => '::Reaction',
+      'sample' => '::Sample',
+      'molecule' => '::Molecule',
+      'wellplate' => '::Wellplate',
+      'screen' => '::Screen',
+      'research_plan' => '::ResearchPlan',
+      'device_description' => '::DeviceDescription'
+    }.freeze
+
+    # Curated, scalar columns exposed per type: [column/method, label, unit_column?]
+    COLUMNS = {
+      'reaction' => [
+        %w[name Name], %w[short_label], ['status', 'Status'], ['role', 'Role'],
+        ['rxno', 'Reaction Type'], ['conditions', 'Conditions'],
+        ['duration', 'Duration'], %w[solvent Solvent]
+      ],
+      'sample' => [
+        %w[name Name], %w[short_label], ['external_label', 'External Label'],
+        ['sum_formula', 'Sum Formula'], ['molecular_mass', 'Molecular Mass'],
+        %w[purity Purity], %w[density Density],
+        ['real_amount_value', 'Real Amount', 'real_amount_unit'],
+        ['target_amount_value', 'Target Amount', 'target_amount_unit'],
+        %w[location Location]
+      ],
+      'molecule' => [
+        ['iupac_name', 'IUPAC Name'], ['sum_formular', 'Sum Formula'],
+        ['molecular_weight', 'Molecular Weight'],
+        ['exact_molecular_weight', 'Exact Molecular Weight'],
+        ['cano_smiles', 'Canonical SMILES'], ['melting_point', 'Melting Point'],
+        ['boiling_point', 'Boiling Point'], %w[density Density]
+      ],
+      'wellplate' => [
+        %w[name Name], %w[short_label], ['description', 'Description'],
+        %w[width Width], %w[height Height]
+      ],
+      'screen' => [
+        %w[name Name], ['description', 'Description'], %w[result Result],
+        %w[collaborator Collaborator], ['conditions', 'Conditions'],
+        %w[requirements Requirements]
+      ],
+      'research_plan' => [
+        %w[name Name], %w[short_label]
+      ],
+      'device_description' => [
+        %w[name Name], %w[short_label], ['serial_number', 'Serial Number'],
+        ['device_class', 'Device Class'], ['operation_mode', 'Operation Mode'],
+        ['application_name', 'Application Name'], ['vendor_url', 'Vendor URL'],
+        %w[institute Institute], %w[building Building], %w[room Room]
+      ]
+    }.freeze
+
+    # Property field types whose value is a scalar worth surfacing inline.
+    PROPERTY_TYPES = %w[
+      text textarea number integer select select-multi checkbox
+      datetime system-defined formula-field text-formula ontology-select
+    ].freeze
+
+    def initialize(el_klass, el_id, el_type = nil)
+      @el_klass = el_klass.to_s
+      @el_type = el_type.to_s
+      @el_id = el_id
+    end
+
+    # drag_element keeps the linked class in +el_klass+; drag_sample / drag_molecule
+    # keep it in +el_type+ (and may omit el_klass). Resolve one effective dispatch key.
+    def target_key
+      return @target_key if defined?(@target_key)
+
+      @target_key =
+        if MODELS.key?(@el_klass) || generic_klass?(@el_klass)
+          @el_klass
+        elsif MODELS.key?(@el_type)
+          @el_type
+        else
+          ''
+        end
+    end
+
+    def column_based?
+      MODELS.key?(target_key)
+    end
+
+    def generic?
+      generic_klass?(target_key)
+    end
+
+    def record
+      return @record if defined?(@record)
+
+      @record =
+        if column_based?
+          MODELS[target_key].safe_constantize&.find_by(id: @el_id)
+        elsif generic?
+          Labimotion::Element.find_by(id: @el_id)
+        end
+    end
+
+    # All attributes the user can pick, each with its current value.
+    def available
+      return generic_attributes if generic?
+      return column_attributes if column_based?
+
+      []
+    end
+
+    # Refresh the values/labels of a previously stored selection. Selections whose
+    # source attribute no longer exists are kept but flagged as missing; for an
+    # unknown/unsupported el_klass the selection is returned untouched.
+    def resolve(selected)
+      return selected unless selected.is_a?(Array)
+      return selected unless generic? || column_based?
+
+      index = available.index_by { |a| [a['source'], a['key']] }
+      selected.map do |attr|
+        next attr unless attr.is_a?(Hash)
+
+        index[[attr['source'], attr['key']]] || attr.merge('value' => nil, 'missing' => true)
+      end
+    end
+
+    private
+
+    def generic_klass?(name)
+      name.present? && !MODELS.key?(name) && Labimotion::ElementKlass.exists?(name: name)
+    end
+
+    def generic_attributes
+      el = record
+      return [] unless el&.properties.is_a?(Hash)
+
+      attrs = []
+      layers = el.properties[Labimotion::Prop::LAYERS] || {}
+      layers.values.sort_by { |layer| layer['position'] || 0 }.each do |layer|
+        (layer[Labimotion::Prop::FIELDS] || []).each do |field|
+          next unless PROPERTY_TYPES.include?(field['type'])
+
+          attr = {
+            'source' => SOURCE_PROPERTY,
+            'key' => "#{layer['key']}::#{field['field']}",
+            'label' => field['label'].presence || field['field'],
+            'type' => field['type'],
+            'value' => field['value'],
+            'group' => layer['label'].presence || layer['key']
+          }
+          attr['value_system'] = field['value_system'] if field['value_system'].present?
+          attrs << attr
+        end
+      end
+      attrs
+    end
+
+    def column_attributes
+      rec = record
+      return [] if rec.blank?
+
+      (COLUMNS[target_key] || []).filter_map do |col, label, unit_col|
+        next unless rec.respond_to?(col)
+
+        attr = {
+          'source' => SOURCE_COLUMN,
+          'key' => col,
+          'label' => label.presence || col.to_s.humanize,
+          'type' => SOURCE_COLUMN,
+          'value' => rec.public_send(col),
+          'group' => target_key
+        }
+        attr['value_system'] = rec.public_send(unit_col) if unit_col && rec.respond_to?(unit_col) && rec.public_send(unit_col).present?
+        attr
+      end
+    end
+  end
+end

data/lib/labimotion/version.rb

@@ -2,5 +2,5 @@
 
 ## Labimotion Version
 module Labimotion
-  VERSION = '2.3.0.rc1'
+  VERSION = '2.4.0.rc1'
 end

data/lib/labimotion.rb

@@ -89,6 +89,7 @@ module Labimotion
   autoload :ExportDataset, 'labimotion/libs/export_dataset'
   autoload :SampleAssociation, 'labimotion/libs/sample_association'
   autoload :PropertiesHandler, 'labimotion/libs/properties_handler'
+  autoload :LinkedElement, 'labimotion/libs/linked_element'
   autoload :AttachmentHandler, 'labimotion/libs/attachment_handler'
   autoload :VocabularyHandler, 'labimotion/libs/vocabulary_handler'
   autoload :XlsxExporter, 'labimotion/libs/xlsx_exporter'

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: labimotion
 version: !ruby/object:Gem::Version
-  version: 2.3.0.rc1
+  version: 2.4.0.rc1
 platform: ruby
 authors:
 - Chia-Lin Lin
@@ -118,6 +118,7 @@ files:
 - lib/labimotion/libs/dataset_builder.rb
 - lib/labimotion/libs/export_dataset.rb
 - lib/labimotion/libs/export_element.rb
+- lib/labimotion/libs/linked_element.rb
 - lib/labimotion/libs/nmr_mapper.rb
 - lib/labimotion/libs/properties_handler.rb
 - lib/labimotion/libs/sample_association.rb