labimotion 2.3.0 → 2.3.1

checksums.yaml

@@ -1,7 +1,7 @@
 ---
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-  data.tar.gz: 1da451215fba4042ea72906285df462080d212a31017d55a3f0d9d43c970b91b
+  metadata.gz: 50d1572a0d16e5ac73fdf5aa6a22e5188c9fd2f008c671fc9705a310fbd090ac
+  data.tar.gz: 85631425352102b56f1c0c9998710c0e9af6c4f416b272cee3e05cffd6c4209e
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+  data.tar.gz: 57e90440bc487d8fc950bb408e5c8794fa0566bad76d3a731f3cc92460623234a4893fdd1f6e61ed9f2730a1ec2b045b78ff940556fa49f6e92a6bc73c7475e6

data/lib/labimotion/constants.rb

@@ -28,5 +28,11 @@ module Labimotion
       DATASET = 'DatasetKlass'
       ALL = [ELEMENT, SEGMENT, DATASET].freeze
     end
+
+    module Tpa
+      # Segments and layers sent along with reaction variations to a third-party
+      # app (see ExportTpaSegments), as segment-klass label => layer keys.
+      SEGMENT_LAYERS = { 'Mol interactions' => %w[binding_props bind_partners].freeze }.freeze
+    end
   end
 end

data/lib/labimotion/libs/converter.rb

@@ -29,7 +29,10 @@ module Labimotion
       dsr = []
       ols = nil
       Zip::File.open(att.attachment_attacher.file.url) do |zip_file|
-        res = Labimotion::Converter.collect_metadata(zip_file, current_user) if att.filename.split('.')&.last == 'zip'
+        if att.filename.split('.')&.last == 'zip'
+          res = Labimotion::Converter.collect_metadata(zip_file, current_user)
+          Labimotion::Converter.collect_reaction_converter_metadata(att, zip_file)
+        end
         ols = res[:o] unless res&.dig(:o).nil?
         dsr.push(res[:d]) unless res&.dig(:d).nil?
       end
@@ -93,6 +96,33 @@ module Labimotion
       { a: oa, f: folder }
     end
 
+    def self.collect_reaction_converter_metadata(oat, zip_file)
+      zip_file.each do |entry|
+        next unless entry.name == 'metadata/reaction_variation.json'
+
+        # Create temp file
+        tmp_file = Tempfile.new(['reaction_variation', '.json'])
+        tmp_file.binmode
+
+        # Write ZIP entry content into temp file
+        entry.extract(tmp_file.path) { true }
+
+        # Create attachment
+        att = Attachment.create!(
+          filename: 'reaction_variation.json',
+          file_path: tmp_file.path,
+          content_type: 'application/json',
+          attachable_id: oat.attachable_id,
+          attachable_type: 'Container',
+          con_state: Labimotion::ConState::CONVERTED,
+          created_by: oat.created_by,
+          created_for: oat.created_for
+        )
+
+        att.save! if att.valid?
+      end
+    end
+
     def self.collect_metadata(zip_file, current_user = {}) # rubocop: disable Metrics/PerceivedComplexity
       dsr = []
       ols = nil

data/lib/labimotion/libs/export_tpa_segments.rb

@@ -0,0 +1,53 @@
+# frozen_string_literal: true
+
+require 'labimotion/constants'
+
+module Labimotion
+  ## ExportTpaSegments
+  # Builds the `segment` section of the reaction-variations payload handed to a
+  # third-party app (TPA). Segment values are element-wide -- one set per
+  # element, not per variation -- so they travel once, next to the variations.
+  #
+  # Only the segments and layers named in `segment_layers` (by default
+  # Constants::Tpa::SEGMENT_LAYERS) are exported, each field reduced to what the
+  # app needs:
+  #
+  #   { "<segment klass label>" => { "<layer key>" => { "<field>" => { label:, value:, unit:, type: } } } }
+  #
+  # A segment the element does not carry, or a layer its segment does not carry,
+  # is left out.
+  class ExportTpaSegments
+    # Mirrors Labimotion::Prop::LAYERS / ::FIELDS. Held locally because
+    # requiring `labimotion/utils/prop` here would race the gem's autoload.
+    LAYERS = 'layers'
+    FIELDS = 'fields'
+
+    class << self
+      def call(element, segment_layers: Labimotion::Constants::Tpa::SEGMENT_LAYERS)
+        segment_layers.each_with_object({}) do |(segment_label, layer_keys), payload|
+          segment = element.segments.detect { |s| s.segment_klass&.label == segment_label }
+          next unless segment
+
+          payload[segment_label] = layers(segment, layer_keys)
+        end
+      end
+
+      private
+
+      def layers(segment, layer_keys)
+        stored = segment.properties&.dig(LAYERS) || {}
+        Array(layer_keys).each_with_object({}) do |layer_key, acc|
+          layer = stored[layer_key]
+          acc[layer_key] = fields(layer) if layer
+        end
+      end
+
+      def fields(layer)
+        Array(layer[FIELDS]).to_h do |field|
+          [field['field'],
+           { label: field['label'], value: field['value'], unit: field['value_system'], type: field['type'] }]
+        end
+      end
+    end
+  end
+end

data/lib/labimotion/libs/nmr_mapper.rb

@@ -41,9 +41,10 @@ module Labimotion
 
       def process(att)
         config = Labimotion::MapperUtils.load_brucker_config
-        return if config.nil?
-
         attacher = att&.attachment_attacher
+        return Labimotion::MapperUtils.check_if_bagit(attacher&.file&.url) if config.nil?
+
+
         extracted_data = Labimotion::MapperUtils.extract_data_from_zip(attacher&.file&.url, config['sourceMap'])
         return if extracted_data.nil?
 

data/lib/labimotion/utils/mapper_utils.rb

@@ -46,6 +46,22 @@ module Labimotion
         nil
       end
 
+      def check_if_bagit(zip_file_url)
+        return nil if zip_file_url.nil?
+        Zip::File.open(zip_file_url) do |zip_file|
+          zip_file.each do |entry|
+            return { is_bagit: true, metadata: nil } if bagit_metadata_file?(entry)
+          end
+        end
+
+      rescue Zip::Error => e
+        Rails.logger.error "Zip file error: #{e.message}"
+        nil
+      rescue StandardError => e
+        Rails.logger.error "Unexpected error extracting metadata: #{e.message}"
+        nil
+      end
+
       def extract_parameters(file_content, parameter_names)
         return nil if file_content.blank? || parameter_names.blank?
 

data/lib/labimotion/version.rb

@@ -2,5 +2,5 @@
 
 ## Labimotion Version
 module Labimotion
-  VERSION = '2.3.0'
+  VERSION = '2.3.1'
 end

data/lib/labimotion.rb

@@ -96,6 +96,7 @@ module Labimotion
   autoload :ElementVariationHeader, 'labimotion/libs/element_variation_header'
   autoload :ExportElementVariations, 'labimotion/libs/export_element_variations'
   autoload :ImportElementVariations, 'labimotion/libs/import_element_variations'
+  autoload :ExportTpaSegments, 'labimotion/libs/export_tpa_segments'
 
   ######## Utils
   autoload :Prop, 'labimotion/utils/prop'

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: labimotion
 version: !ruby/object:Gem::Version
-  version: 2.3.0
+  version: 2.3.1
 platform: ruby
 authors:
 - Chia-Lin Lin
@@ -9,7 +9,7 @@ authors:
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2026-08-26 00:00:00.000000000 Z
+date: 2026-09-15 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: caxlsx
@@ -135,6 +135,7 @@ files:
 - lib/labimotion/libs/export_dataset.rb
 - lib/labimotion/libs/export_element.rb
 - lib/labimotion/libs/export_element_variations.rb
+- lib/labimotion/libs/export_tpa_segments.rb
 - lib/labimotion/libs/import_element_variations.rb
 - lib/labimotion/libs/nmr_mapper.rb
 - lib/labimotion/libs/properties_handler.rb