labimotion 2.3.0.rc6 → 2.3.1

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA256:
-  metadata.gz: 7f03974c2c4a8918a74bd6ff6ae9eb077e0ad38507f716b5fc952792d12bb3d3
-  data.tar.gz: f00fb94a263cb13172fea15710f616fa851ccfc233c576ede27a5b8cf23a9923
+  metadata.gz: 50d1572a0d16e5ac73fdf5aa6a22e5188c9fd2f008c671fc9705a310fbd090ac
+  data.tar.gz: 85631425352102b56f1c0c9998710c0e9af6c4f416b272cee3e05cffd6c4209e
 SHA512:
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-  data.tar.gz: ed06f0529322828dbf24473e0d3a7775800c8d960253491af35f0525c0586358e642faf05d71e8a36406cd8da3244304d8cde1e652a659f809d4537a15f8413d
+  metadata.gz: a8d4af5906da69a5ce49e100fb5ac4d63ea399bd4cc587af58dff73b2563eebe196d7658aa0257665b439be486b5f1d2bc851226bc265cd14b309e04120ae842
+  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/utils/units.rb

@@ -9,7 +9,7 @@ module Labimotion
       "default": "",
       "position": 10,
       "placeholder": "acceleration",
-      "units": [{ "key": "mm_s2", "label": "mm/s<sup>2</sup>" }]
+      "units": [{ "key": "mm_s2", "label": "mm/s²" }]
     },
     {
       "type": "numeric",
@@ -59,10 +59,10 @@ module Labimotion
       "position": 38,
       "placeholder": "areal density",
       "units": [
-        { "key": "kg_m2", "label": "kg m<sup>-2</sup>", "nm": 1 },
-        { "key": "t_m2", "label": "t m<sup>-2</sup>", "nm": 0.001 },
-        { "key": "kg_cm2", "label": "kg cm<sup>-2</sup>", "nm": 1e-4 },
-        { "key": "g_m2", "label": "g m<sup>-2</sup>", "nm": 1000 }
+        { "key": "kg_m2", "label": "kg m⁻²", "nm": 1 },
+        { "key": "t_m2", "label": "t m⁻²", "nm": 0.001 },
+        { "key": "kg_cm2", "label": "kg cm⁻²", "nm": 1e-4 },
+        { "key": "g_m2", "label": "g m⁻²", "nm": 1000 }
       ]
     },
     {
@@ -97,7 +97,7 @@ module Labimotion
       "position": 60,
       "placeholder": "concentration",
       "units": [
-        { "key": "ng_l", "label": "ng/L", "nm": 1000000 },
+        { "key": "ng_l", "label": "ng/L", "nm": 1000000000 },
         { "key": "mg_l", "label": "mg/L", "nm": 1000 },
         { "key": "g_l", "label": "g/L", "nm": 1 }
       ]
@@ -171,7 +171,7 @@ module Labimotion
       "position": 75,
       "placeholder": "density",
       "units": [
-        { "key": "g_cm3", "label": "g/cm<sup>3</sup>", "nm": 1 },
+        { "key": "g_cm3", "label": "g/cm³", "nm": 1 },
         { "key": "kg_l", "label": "kg/l", "nm": 1 }
       ]
     },
@@ -198,7 +198,8 @@ module Labimotion
         { "key": "d", "label": "d", "nm": 1 },
         { "key": "h", "label": "h", "nm": 24 },
         { "key": "min", "label": "m", "nm": 1440 },
-        { "key": "s", "label": "s", "nm": 86400 }
+        { "key": "s", "label": "s", "nm": 86400 },
+        { "key": "y", "label": "y", "nm": 0.0027378507871321013 }
       ]
     },
     {
@@ -280,7 +281,8 @@ module Labimotion
         { "key": "eV", "label": "eV", "nm": 6.241509e21 },
         { "key": "keV", "label": "keV", "nm": 6.241509e18 },
         { "key": "j", "label": "J", "nm": 1000 },
-        { "key": "k_j", "label": "kJ", "nm": 1 }
+        { "key": "k_j", "label": "kJ", "nm": 1 },
+        { "key": "kWh", "label": "kWh", "nm": 2.7777778e-4 }
       ]
     },
     {
@@ -357,9 +359,9 @@ module Labimotion
         { "key": "k_min", "label": "K/min", "nm": 1 },
         { "key": "k_s", "label": "K/s", "nm": 0.016666666666667 },
         { "key": "k_h", "label": "K/h", "nm": 60 },
-        { "key": "degc_min", "label": "°C min<sup>-1</sup>", "nm": 1 },
-        { "key": "degc_s", "label": "°C s<sup>-1</sup>", "nm": 0.016666666666667 },
-        { "key": "degc_h", "label": "°C h<sup>-1</sup>", "nm": 60 }
+        { "key": "degc_min", "label": "°C min⁻¹", "nm": 1 },
+        { "key": "degc_s", "label": "°C s⁻¹", "nm": 0.016666666666667 },
+        { "key": "degc_h", "label": "°C h⁻¹", "nm": 60 }
       ]
     },
     {
@@ -394,7 +396,23 @@ module Labimotion
       "units": [
         { "key": "g", "label": "g", "nm": 1 },
         { "key": "mg", "label": "mg", "nm": 1000 },
-        { "key": "ug", "label": "µg", "nm": 1000000 }
+        { "key": "ug", "label": "µg", "nm": 1000000 },
+        { "key": "kg", "label": "kg", "nm": 0.001 }
+      ]
+    },
+    {
+      "type": "numeric",
+      "field": "mass_flow",
+      "label": "Mass flow",
+      "default": "",
+      "position": 121,
+      "placeholder": "mass flow",
+      "units": [
+        { "key": "g_min", "label": "g/min", "nm": 1 },
+        { "key": "kg_h", "label": "kg/h", "nm": 0.06 },
+        { "key": "kg_s", "label": "kg/s", "nm": 0.000016666666666667 },
+        { "key": "g_s", "label": "g/s", "nm": 0.016666666666667 },
+        { "key": "mg_s", "label": "mg/s", "nm": 16.666666666667 }
       ]
     },
     {
@@ -416,8 +434,8 @@ module Labimotion
       "position": 125,
       "placeholder": "mass loading",
       "units": [
-        { "key": "g_cm2", "label": "g cm<sup>-2</sup>", "nm": 1 },
-        { "key": "mg_cm2", "label": "mg cm<sup>-2</sup>", "nm": 1000 }
+        { "key": "g_cm2", "label": "g cm⁻²", "nm": 1 },
+        { "key": "mg_cm2", "label": "mg cm⁻²", "nm": 1000 }
       ]
     },
     {
@@ -440,7 +458,7 @@ module Labimotion
       "position": 127,
       "placeholder": "molar conductivity",
       "units": [
-        { "key": "s_cm2_mol", "label": "S cm<sup>2</sup> mol<sup>-1</sup>", "nm": 1 }
+        { "key": "s_cm2_mol", "label": "S cm² mol⁻¹", "nm": 1 }
       ]
     },
     {
@@ -492,6 +510,7 @@ module Labimotion
         { "key": "atm", "label": "atm", "nm": 1 },
         { "key": "pa", "label": "Pa", "nm": 101325 },
         { "key": "kpa", "label": "kPa", "nm": 101.325 },
+        { "key": "mpa", "label": "MPa", "nm": 0.101325 },
         { "key": "hpa", "label": "hPa", "nm": 1013.25 },
         { "key": "torr", "label": "Torr", "nm": 760 },
         { "key": "bar", "label": "bar", "nm": 1.01325 },
@@ -530,8 +549,8 @@ module Labimotion
       "position": 150,
       "placeholder": "Reaction rate",
       "units": [
-        { "key": "mol_lmin", "label": "mol L<sup>-1</sup> min<sup>-1</sup>", "nm": 1 },
-        { "key": "mol_lsec", "label": "mol L<sup>-1</sup> s<sup>-1</sup>", "nm": 0.016666666666667 }
+        { "key": "mol_lmin", "label": "mol L⁻¹ min⁻¹", "nm": 1 },
+        { "key": "mol_lsec", "label": "mol L⁻¹ s⁻¹", "nm": 0.016666666666667 }
       ]
     },
     {
@@ -558,6 +577,22 @@ module Labimotion
         { "key": "v_s", "label": "V/s", "nm": 1 }
       ]
     },
+    {
+      "type": "numeric",
+      "field": "space_time_yield",
+      "label": "Space-time yield",
+      "default": "",
+      "position": 156,
+      "placeholder": "space-time yield",
+      "units": [
+        { "key": "kg_m3_d", "label": "kg/(m³*d)", "nm": 1 },
+        { "key": "kg_m3_h", "label": "kg/(m³*h)", "nm": 0.041666666666667 },
+        { "key": "g_l_h", "label": "g/(L*h)", "nm": 0.041666666666667 },
+        { "key": "mg_ml_h", "label": "mg/(mL*h)", "nm": 0.041666666666667 },
+        { "key": "g_l_min", "label": "g/(L*min)", "nm": 0.00069444444444444 },
+        { "key": "g_m3_s", "label": "g/(m³*s)", "nm": 0.011574074074074 }
+      ]
+    },
     {
       "type": "numeric",
       "field": "specific_current",
@@ -568,9 +603,9 @@ module Labimotion
       "units": [
         { "key": "ma_g", "label": "mA/g", "nm": 1000, "unit_type": "mass" },
         { "key": "a_g", "label": "A/g", "nm": 1, "unit_type": "mass" },
-        { "key": "ma_cm2", "label": "mA/cm<sup>2</sup>", "nm": 1000, "unit_type": "area" },
-        { "key": "a_cm2", "label": "A/cm<sup>2</sup>", "nm": 1, "unit_type": "area" },
-        { "key": "a_mm2", "label": "A/mm<sup>2</sup>", "nm": 0.01, "unit_type": "area" }
+        { "key": "ma_cm2", "label": "mA/cm²", "nm": 1000, "unit_type": "area" },
+        { "key": "a_cm2", "label": "A/cm²", "nm": 1, "unit_type": "area" },
+        { "key": "a_mm2", "label": "A/mm²", "nm": 0.01, "unit_type": "area" }
       ]
     },
     {
@@ -593,7 +628,7 @@ module Labimotion
       "position": 158,
       "placeholder": "Specific surface area",
       "units": [
-        { "key": "m2_g", "label": "m<sup>2</sup>/g", "nm": 1 }
+        { "key": "m2_g", "label": "m²/g", "nm": 1 }
       ]
     },
     {
@@ -603,7 +638,7 @@ module Labimotion
       "default": "",
       "position": 160,
       "placeholder": "Specific Volume",
-      "units": [{ "key": "cm3_g", "label": "cm<sup>3</sup>/g", "nm": 1 }]
+      "units": [{ "key": "cm3_g", "label": "cm³/g", "nm": 1 }]
     },
     {
       "type": "numeric",
@@ -642,10 +677,10 @@ module Labimotion
       "position": 170,
       "placeholder": "surface",
       "units": [
-        { "key": "a_2", "label": "A<sup>2</sup>", "nm": 1.0e16 },
-        { "key": "um_2", "label": "µm<sup>2</sup>", "nm": 1.0e8 },
-        { "key": "mm_2", "label": "mm<sup>2</sup>", "nm": 100 },
-        { "key": "cm_2", "label": "cm<sup>2</sup>", "nm": 1 }
+        { "key": "a_2", "label": "A²", "nm": 1.0e16 },
+        { "key": "um_2", "label": "µm²", "nm": 1.0e8 },
+        { "key": "mm_2", "label": "mm²", "nm": 100 },
+        { "key": "cm_2", "label": "cm²", "nm": 1 }
       ]
     },
     {
@@ -682,8 +717,8 @@ module Labimotion
       "position": 186,
       "placeholder": "tensile stress",
       "units": [
-        { "key": "n_cm2", "label": "N cm<sup>-2</sup>", "nm": 1 },
-        { "key": "n_mm2", "label": "N mm<sup>-2</sup>", "nm": 0.01 }
+        { "key": "n_cm2", "label": "N cm⁻²", "nm": 1 },
+        { "key": "n_mm2", "label": "N mm⁻²", "nm": 0.01 }
       ]
     },
     {
@@ -693,7 +728,7 @@ module Labimotion
       "default": "",
       "position": 190,
       "placeholder": "Turnover number",
-      "units": [{ "key": "1_s", "label": "1/s", "nm": 1 }, { "key": "1_m", "label": "1/m", "nm": 60 }]
+      "units": [{ "key": "1_s", "label": "1/s", "nm": 1 }, { "key": "1_m", "label": "1/min", "nm": 60 }]
     },
     {
       "type": "numeric",
@@ -714,7 +749,7 @@ module Labimotion
       "default": "",
       "position": 205,
       "placeholder": "Kinematic Viscosity",
-      "units": [{ "key": "m2_s", "label": "m<sup>2</sup>/s", "nm": 1 }]
+      "units": [{ "key": "m2_s", "label": "m²/s", "nm": 1 }]
     },
     {
       "type": "numeric",
@@ -767,6 +802,6 @@ module Labimotion
         { "key": "m3", "label": "m³", "nm": 0.000001 }
       ]
     }
-    ]
+  ]
   end
 end

data/lib/labimotion/version.rb

@@ -2,5 +2,5 @@
 
 ## Labimotion Version
 module Labimotion
-  VERSION = '2.3.0.rc6'
+  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.rc6
+  version: 2.3.1
 platform: ruby
 authors:
 - Chia-Lin Lin
@@ -9,7 +9,7 @@ authors:
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2026-07-23 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
@@ -222,9 +223,9 @@ required_ruby_version: !ruby/object:Gem::Requirement
       version: '3.4'
 required_rubygems_version: !ruby/object:Gem::Requirement
   requirements:
-  - - ">"
+  - - ">="
     - !ruby/object:Gem::Version
-      version: 1.3.1
+      version: '0'
 requirements: []
 rubygems_version: 3.1.6
 signing_key: