labimotion 2.1.0.rc8 → 2.1.0.rc10

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA256:
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-  data.tar.gz: e7cc351ed12b84cc6dad32705bdb0297addb5a9400445c72cbb4fdf7417c8bb6
+  metadata.gz: 8d9456ffe5c3e059a5e8dfc78ca671f0565c051bad7473c91e609de05d43b4d1
+  data.tar.gz: d05ebbe88cd259e6c88fdc2d7948e5369646d6ec00260eb113db61ffcf29cc37
 SHA512:
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+  data.tar.gz: 0d0c5438dc13b8b9025311151938abdfaca59e1c5f89b29978f97bc406e109ce22fccefa38df57084a1d76a0b31bfdd1681483bcb116831e368019673389225e

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

@@ -36,6 +36,13 @@ module Labimotion
       Labimotion.log_exception(e)
     end
 
+    def sample_url
+      protocol = Rails.env.production? ? 'https' : 'http'
+      host = ENV['PUBLIC_URL'] || 'localhost:3000'
+      api = 'mydb/collection/all/sample'
+      "#{protocol}://#{host}/#{api}"
+    end
+
     def build_layers
       objs = []
       @properties[Labimotion::Prop::LAYERS]&.keys&.sort_by do |key|
@@ -183,7 +190,8 @@ module Labimotion
         name = val['el_name'].present? ? "Name: [#{val['el_name']}] \n" : ''
         ext = val['el_external_label'].present? ? "Ext. Label: [#{val['el_external_label']}] \n" : ''
         mass = val['el_molecular_weight'].present? ? "Mass: [#{val['el_molecular_weight']}] \n" : ''
-        "#{label}#{name}#{ext}#{mass}"
+        url = val['el_id'].present? ? "#{sample_url}/#{val['el_id']}" : ''
+        "#{label}#{name}#{ext}#{mass}#{url}"
       when Labimotion::FieldType::DRAG_MOLECULE
         val = sub_val[sub_field['id']]['value'] || {}
         smile = val['el_smiles'].present? ? "SMILES: [#{val['el_smiles']}] \n" : ''
@@ -194,7 +202,7 @@ module Labimotion
       when Labimotion::FieldType::SELECT
         sub_val[sub_field['id']]['value']
       when Labimotion::FieldType::SYSTEM_DEFINED
-        unit = Labimotion::Units::FIELDS.find { |o| o[:field] == sub_field['option_layers'] }&.fetch(:units, [])&.find { |u| u[:key] == sub_field['value_system'] }&.fetch(:label, '')
+        unit = Labimotion::Units::FIELDS.find { |o| o[:field] == sub_field['option_layers'] }&.fetch(:units, [])&.find { |u| u[:key] == sub_val[sub_field['id']]['value_system'] }&.fetch(:label, '')
         val = sub_val[sub_field['id']]['value'].to_s + ' ' + unit
         val = Sablon.content(:html, "<div>" + val + "</div>") if val.include? '<'
         val

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