labimotion 2.1.0.rc7 → 2.1.0.rc9

checksums.yaml

@@ -1,7 +1,7 @@
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+  data.tar.gz: 8eea6d130958617f8bf7cabe2c439c3053b768c93c292c41852f13d20116ca2b
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data/lib/labimotion/apis/generic_element_api.rb

@@ -1,5 +1,6 @@
 # frozen_string_literal: true
 
+require 'cgi'
 require 'labimotion/conf'
 require 'labimotion/libs/export_element'
 
@@ -138,7 +139,7 @@ module Labimotion
           env['api.format'] = :binary
           content_type 'application/vnd.openxmlformats-officedocument.wordprocessingml.document'
           el_filename = export.res_name
-          filename = URI.escape(el_filename)
+          filename = CGI.escape(el_filename)
           # header['Content-Disposition'] = "attachment; filename=abc.docx"
           header('Content-Disposition', "attachment; filename=\"#{filename}\"")
 

data/lib/labimotion/apis/generic_klass_api.rb

@@ -1,5 +1,6 @@
 # frozen_string_literal: true
 
+require 'cgi'
 require 'labimotion/version'
 require 'labimotion/libs/export_element'
 
@@ -20,7 +21,7 @@ module Labimotion
           entity.update_columns(identifier: SecureRandom.uuid) if entity&.identifier.nil?
           env['api.format'] = :binary
           content_type('application/json')
-          filename = URI.escape("LabIMotion_#{params[:klass]}_#{entity.label}-#{Time.new.strftime("%Y%m%d%H%M%S")}.json")
+          filename = CGI.escape("LabIMotion_#{params[:klass]}_#{entity.label}-#{Time.new.strftime("%Y%m%d%H%M%S")}.json")
           # header['Content-Disposition'] = "attachment; filename=abc.docx"
           header('Content-Disposition', "attachment; filename=\"#{filename}\"")
           "Labimotion::#{params[:klass]}Entity".constantize.represent(entity)

data/lib/labimotion/entities/element_revision_entity.rb

@@ -13,6 +13,8 @@ module Labimotion
       object.properties[Labimotion::Prop::LAYERS]&.keys.each do |key|
         field_sample_molecules = object.properties[Labimotion::Prop::LAYERS][key][Labimotion::Prop::FIELDS].select { |ss| ss['type'] == Labimotion::FieldType::DRAG_SAMPLE || ss['type'] == Labimotion::FieldType::DRAG_MOLECULE }
         field_sample_molecules.each do |field|
+          next unless field['value'].is_a?(Hash)
+
           idx = object.properties[Labimotion::Prop::LAYERS][key][Labimotion::Prop::FIELDS].index(field)
           sid = field.dig('value', 'el_id')
           next unless sid.present?

data/lib/labimotion/entities/eln_element_entity.rb

@@ -30,6 +30,8 @@ module Labimotion
           ss['type'] == Labimotion::FieldType::DRAG_SAMPLE || ss['type'] == Labimotion::FieldType::DRAG_MOLECULE
         end
         field_sample_molecules.each do |field|
+          next unless field['value'].is_a?(Hash)
+
           idx = object.properties[Labimotion::Prop::LAYERS][key][Labimotion::Prop::FIELDS].index(field)
           sid = field.dig('value', 'el_id')
           next unless sid.present?

data/lib/labimotion/entities/properties_entity.rb

@@ -58,6 +58,8 @@ module Labimotion
     end
 
     def update_sample_or_molecule_field(key, field, idx)
+      return unless field['value'].is_a?(Hash)
+
       sid = field.dig('value', 'el_id')
       return unless sid.present?
 
@@ -79,6 +81,8 @@ module Labimotion
     end
 
     def update_reaction_field(key, field, idx)
+      return unless field['value'].is_a?(Hash)
+
       sid = field.dig('value', 'el_id')
       return unless sid.present?
 

data/lib/labimotion/entities/segment_revision_entity.rb

@@ -12,6 +12,8 @@ module Labimotion
       object.properties[Labimotion::Prop::LAYERS]&.keys.each do |key|
         field_sample_molecules = object.properties[Labimotion::Prop::LAYERS][key][Labimotion::Prop::FIELDS].select { |ss| ss['type'] == Labimotion::FieldType::DRAG_SAMPLE || ss['type'] == Labimotion::FieldType::DRAG_MOLECULE }
         field_sample_molecules.each do |field|
+          next unless field['value'].is_a?(Hash)
+
           idx = object.properties[Labimotion::Prop::LAYERS][key][Labimotion::Prop::FIELDS].index(field)
           sid = field.dig('value', 'el_id')
           next unless sid.present?

data/lib/labimotion/helpers/converter_helpers.rb

@@ -2,12 +2,25 @@
 require 'grape'
 
 module Labimotion
-  ## ElementHelpers
+  ## ConverterHelpers
   module ConverterHelpers
     extend Grape::API::Helpers
 
-    def demo(params)
-      ### TODO: implement demo
+    # Update the general_description field in the container's extended_metadata
+    def self.update_general_description(container, current_user, date: nil, time: nil)
+      return unless container.present?
+
+      desc = container.extended_metadata['general_description']
+
+      general_desc = desc if desc.present? && desc.is_a?(Hash)
+      general_desc = JSON.parse(container.extended_metadata['general_description']) if desc.present? && desc.is_a?(String)
+      general_desc = {} unless general_desc.is_a?(Hash)
+      general_desc['creator'] = current_user.name if current_user.present?
+      general_desc['date'] = date if date.present?
+      general_desc['time'] = time if time.present?
+
+      container.extended_metadata['general_description'] = general_desc.to_json
+      container.save!
     end
   end
 end

data/lib/labimotion/libs/converter.rb

@@ -6,6 +6,7 @@ require 'json'
 require 'date'
 require 'labimotion/version'
 require 'labimotion/utils/utils'
+require 'labimotion/helpers/converter_helpers'
 
 # rubocop: disable Metrics/AbcSize
 # rubocop: disable Metrics/MethodLength
@@ -228,6 +229,19 @@ module Labimotion
     def self.update_ds(dataset, dsr, current_user = nil) # rubocop: disable Metrics/PerceivedComplexity
       layers = dataset.properties[Labimotion::Prop::LAYERS] || {}
       new_prop = dataset.properties
+
+      container = dataset.element
+
+      # Extract and update general description fields
+      general_dsr = dsr.select { |ds| ds[:layer] == 'general' }
+      if general_dsr.present?
+        date = general_dsr.find { |ds| ds[:field] == 'date' }&.dig(:value)
+        time = general_dsr.find { |ds| ds[:field] == 'time' }&.dig(:value)
+        Labimotion::ConverterHelpers.update_general_description(container, current_user, date: date, time: time)
+      else
+        Labimotion::ConverterHelpers.update_general_description(container, current_user)
+      end
+
       dsr.each do |ds|
         layer = layers[ds[:layer]]
         next if layer.blank? || layer[Labimotion::Prop::FIELDS].blank?

data/lib/labimotion/libs/export_element.rb

@@ -1,4 +1,5 @@
 # frozen_string_literal: true
+require 'ostruct'
 require 'export_table'
 require 'labimotion/version'
 require 'labimotion/utils/units'

data/lib/labimotion/libs/nmr_mapper.rb

@@ -4,6 +4,7 @@ require 'labimotion/libs/dataset_builder'
 require 'labimotion/version'
 require 'labimotion/utils/mapper_utils'
 require 'labimotion/utils/utils'
+require 'labimotion/helpers/converter_helpers'
 
 module Labimotion
   ## NmrMapper
@@ -61,6 +62,7 @@ module Labimotion
 
       def update_ds(_cid, obj, current_user, element)
         dataset = obj[:dataset]
+        process_general_description(obj, current_user, element)
         dataset.properties = process_prop(obj, current_user, element)
         dataset.save!
       end
@@ -106,6 +108,17 @@ module Labimotion
         new_prop
       end
 
+      def process_general_description(obj, current_user, element)
+        container = obj[:dataset]&.element
+        return unless container.present?
+
+        dt = obj[:metadata]&.dig('DATE')
+        date = Labimotion::MapperUtils.format_timestamp(dt, 'date') if dt.present?
+        time = Labimotion::MapperUtils.format_timestamp(dt, 'time') if dt.present?
+
+        Labimotion::ConverterHelpers.update_general_description(container, current_user, date: date, time: time)
+      end
+
       def process_prop(obj, current_user, element)
         new_prop = obj[:dataset].properties
         new_prop

data/lib/labimotion/libs/properties_handler.rb

@@ -8,9 +8,9 @@ module Labimotion
       def check_val(field, type)
         case type
         when Labimotion::FieldType::DRAG_SAMPLE, Labimotion::FieldType::DRAG_ELEMENT
-          return field.dig('value', 'el_id').present?
+          return field['value'].is_a?(Hash) && field.dig('value', 'el_id').present?
         when Labimotion::FieldType::UPLOAD
-          return field.dig('value', 'files')&.length&.positive?
+          return field['value'].is_a?(Hash) && field.dig('value', 'files')&.length&.positive?
         when Labimotion::FieldType::TABLE
           return field[Labimotion::Prop::SUBFIELDS]&.length&.positive? && field['sub_values']&.length&.positive?
         end

data/lib/labimotion/libs/sample_association.rb

@@ -79,6 +79,7 @@ module Labimotion
         field_samples.each do |field|
           idx = properties[Labimotion::Prop::LAYERS][key][Labimotion::Prop::FIELDS].index(field)
           return if field.is_a?(String) || properties.is_a?(String)
+          next unless field['value'].is_a?(Hash)
 
           sid = field.dig('value', 'el_id')
           next if sid.blank?
@@ -102,7 +103,8 @@ module Labimotion
         field_elements = layer[Labimotion::Prop::FIELDS].select { |ss| ss['type'] == Labimotion::FieldType::DRAG_ELEMENT }
         field_elements.each do |field|
           idx = properties[Labimotion::Prop::LAYERS][key][Labimotion::Prop::FIELDS].index(field)
-          next if field['value'].is_a?(String)
+          return if field.is_a?(String) || properties.is_a?(String)
+          next unless field['value'].is_a?(Hash)
 
           sid = field.dig('value', 'el_id')
           next if element.nil? || sid.blank? || sid == element.id

data/lib/labimotion/utils/serializer.rb

@@ -37,6 +37,8 @@ module Labimotion
         # layer = object.properties[key]
         field_sample_molecules = object.properties[Labimotion::Prop::LAYERS][key][Labimotion::Prop::FIELDS].select { |ss| Labimotion::FieldType::DRAG_ALL.include?(ss['type']) }
         field_sample_molecules.each do |field|
+          next unless field['value'].is_a?(Hash)
+
           idx = object.properties[Labimotion::Prop::LAYERS][key][Labimotion::Prop::FIELDS].index(field)
           sid = field.dig('value') != '' && field.dig('value', 'el_id')
           next unless sid.present?

data/lib/labimotion/version.rb

@@ -2,5 +2,5 @@
 
 ## Labimotion Version
 module Labimotion
-  VERSION = '2.1.0.rc7'
+  VERSION = '2.1.0.rc9'
 end

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: labimotion
 version: !ruby/object:Gem::Version
-  version: 2.1.0.rc7
+  version: 2.1.0.rc9
 platform: ruby
 authors:
 - Chia-Lin Lin
@@ -9,7 +9,7 @@ authors:
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2025-10-30 00:00:00.000000000 Z
+date: 2025-11-03 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: caxlsx
@@ -175,6 +175,9 @@ required_ruby_version: !ruby/object:Gem::Requirement
   - - ">="
     - !ruby/object:Gem::Version
       version: '2.7'
+  - - "<"
+    - !ruby/object:Gem::Version
+      version: '3.4'
 required_rubygems_version: !ruby/object:Gem::Requirement
   requirements:
   - - ">"