labimotion 2.3.3 → 2.4.0.rc1

data/lib/labimotion/utils/mapper_utils.rb

@@ -6,18 +6,8 @@ require 'zip'
 require 'labimotion/constants'
 
 module Labimotion
-  # rubyzip 2.x does not detect encrypted entries and would inflate them as garbage
-  class EncryptedZipError < Zip::Error; end
-
   class MapperUtils
     class << self
-      # Read an entry and close its stream, so no handle on the stored file stays open
-      def read_entry(entry)
-        raise EncryptedZipError, "Encrypted zip entry: #{entry.name}" if entry.encrypted?
-
-        entry.get_input_stream(&:read)
-      end
-
       def load_config(config_json)
         JSON.parse(config_json)
       rescue JSON::ParserError => e
@@ -47,18 +37,7 @@ module Labimotion
       def extract_data_from_zip(zip_file_url, source_map)
         return nil if zip_file_url.nil?
 
-        # nil means nothing to map; errors are raised so the caller can record ERROR
         process_zip_file(zip_file_url, source_map)
-      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
@@ -188,12 +167,10 @@ module Labimotion
       def process_zip_file(zip_file_url, source_map)
         final_parameters = {}
 
-        # Never close: closing can rewrite the stored file in place
-        zip_file = Zip::File.new(zip_file_url)
-        source_map['sourceSelector'].each do |source_name|
-          result = process_source(zip_file, source_map[source_name], final_parameters)
-          # A BagIt zip is mapped by the converter instead
-          return result if result&.dig(:is_bagit)
+        Zip::File.open(zip_file_url) do |zip_file|
+          source_map['sourceSelector'].each do |source_name|
+            process_source(zip_file, source_map[source_name], final_parameters)
+          end
         end
 
         return { is_bagit: false, metadata: final_parameters } if final_parameters.present?
@@ -205,8 +182,6 @@ module Labimotion
         return if invalid_source_config?(source_config)
 
         zip_file.each do |entry|
-          next if entry.directory?
-
           if source_file?(entry, source_config)
             process_file_entry(entry, source_config, final_parameters)
           elsif bagit_metadata_file?(entry)
@@ -216,7 +191,7 @@ module Labimotion
       end
 
       def process_file_entry(entry, source_config, final_parameters)
-        file_content = read_entry(entry).force_encoding(Constants::File::ENCODING)
+        file_content = entry.get_input_stream.read.force_encoding(Constants::File::ENCODING)
         extracted_parameters = extract_parameters(file_content, source_config['parameters'])
         final_parameters.merge!(extracted_parameters) if extracted_parameters.present?
 

data/lib/labimotion/utils/prop.rb

@@ -1,7 +1,6 @@
 module Labimotion
   ## Converter State
   class Prop
-    CONVERTER_FIELD_UINT_PREFIX = '___unit___'.freeze
     LAYERS = 'layers'.freeze
     FIELDS = 'fields'.freeze
     SUBFIELDS = 'sub_fields'.freeze

data/lib/labimotion/utils/units.rb

@@ -9,7 +9,7 @@ module Labimotion
       "default": "",
       "position": 10,
       "placeholder": "acceleration",
-      "units": [{ "key": "mm_s2", "label": "mm/s²" }]
+      "units": [{ "key": "mm_s2", "label": "mm/s<sup>2</sup>" }]
     },
     {
       "type": "numeric",
@@ -59,10 +59,10 @@ module Labimotion
       "position": 38,
       "placeholder": "areal density",
       "units": [
-        { "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 }
+        { "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 }
       ]
     },
     {
@@ -97,7 +97,7 @@ module Labimotion
       "position": 60,
       "placeholder": "concentration",
       "units": [
-        { "key": "ng_l", "label": "ng/L", "nm": 1000000000 },
+        { "key": "ng_l", "label": "ng/L", "nm": 1000000 },
         { "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/cm³", "nm": 1 },
+        { "key": "g_cm3", "label": "g/cm<sup>3</sup>", "nm": 1 },
         { "key": "kg_l", "label": "kg/l", "nm": 1 }
       ]
     },
@@ -198,8 +198,7 @@ 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": "y", "label": "y", "nm": 0.0027378507871321013 }
+        { "key": "s", "label": "s", "nm": 86400 }
       ]
     },
     {
@@ -281,8 +280,7 @@ 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": "kWh", "label": "kWh", "nm": 2.7777778e-4 }
+        { "key": "k_j", "label": "kJ", "nm": 1 }
       ]
     },
     {
@@ -359,9 +357,9 @@ 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⁻¹", "nm": 1 },
-        { "key": "degc_s", "label": "°C s⁻¹", "nm": 0.016666666666667 },
-        { "key": "degc_h", "label": "°C h⁻¹", "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 }
       ]
     },
     {
@@ -396,23 +394,7 @@ module Labimotion
       "units": [
         { "key": "g", "label": "g", "nm": 1 },
         { "key": "mg", "label": "mg", "nm": 1000 },
-        { "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 }
+        { "key": "ug", "label": "µg", "nm": 1000000 }
       ]
     },
     {
@@ -434,8 +416,8 @@ module Labimotion
       "position": 125,
       "placeholder": "mass loading",
       "units": [
-        { "key": "g_cm2", "label": "g cm⁻²", "nm": 1 },
-        { "key": "mg_cm2", "label": "mg cm⁻²", "nm": 1000 }
+        { "key": "g_cm2", "label": "g cm<sup>-2</sup>", "nm": 1 },
+        { "key": "mg_cm2", "label": "mg cm<sup>-2</sup>", "nm": 1000 }
       ]
     },
     {
@@ -458,7 +440,7 @@ module Labimotion
       "position": 127,
       "placeholder": "molar conductivity",
       "units": [
-        { "key": "s_cm2_mol", "label": "S cm² mol⁻¹", "nm": 1 }
+        { "key": "s_cm2_mol", "label": "S cm<sup>2</sup> mol<sup>-1</sup>", "nm": 1 }
       ]
     },
     {
@@ -510,7 +492,6 @@ 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 },
@@ -549,8 +530,8 @@ module Labimotion
       "position": 150,
       "placeholder": "Reaction rate",
       "units": [
-        { "key": "mol_lmin", "label": "mol L⁻¹ min⁻¹", "nm": 1 },
-        { "key": "mol_lsec", "label": "mol L⁻¹ s⁻¹", "nm": 0.016666666666667 }
+        { "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 }
       ]
     },
     {
@@ -577,22 +558,6 @@ 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",
@@ -603,9 +568,9 @@ 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/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" }
+        { "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" }
       ]
     },
     {
@@ -628,7 +593,7 @@ module Labimotion
       "position": 158,
       "placeholder": "Specific surface area",
       "units": [
-        { "key": "m2_g", "label": "m²/g", "nm": 1 }
+        { "key": "m2_g", "label": "m<sup>2</sup>/g", "nm": 1 }
       ]
     },
     {
@@ -638,7 +603,7 @@ module Labimotion
       "default": "",
       "position": 160,
       "placeholder": "Specific Volume",
-      "units": [{ "key": "cm3_g", "label": "cm³/g", "nm": 1 }]
+      "units": [{ "key": "cm3_g", "label": "cm<sup>3</sup>/g", "nm": 1 }]
     },
     {
       "type": "numeric",
@@ -677,10 +642,10 @@ module Labimotion
       "position": 170,
       "placeholder": "surface",
       "units": [
-        { "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 }
+        { "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 }
       ]
     },
     {
@@ -717,8 +682,8 @@ module Labimotion
       "position": 186,
       "placeholder": "tensile stress",
       "units": [
-        { "key": "n_cm2", "label": "N cm⁻²", "nm": 1 },
-        { "key": "n_mm2", "label": "N mm⁻²", "nm": 0.01 }
+        { "key": "n_cm2", "label": "N cm<sup>-2</sup>", "nm": 1 },
+        { "key": "n_mm2", "label": "N mm<sup>-2</sup>", "nm": 0.01 }
       ]
     },
     {
@@ -728,7 +693,7 @@ module Labimotion
       "default": "",
       "position": 190,
       "placeholder": "Turnover number",
-      "units": [{ "key": "1_s", "label": "1/s", "nm": 1 }, { "key": "1_m", "label": "1/min", "nm": 60 }]
+      "units": [{ "key": "1_s", "label": "1/s", "nm": 1 }, { "key": "1_m", "label": "1/m", "nm": 60 }]
     },
     {
       "type": "numeric",
@@ -749,7 +714,7 @@ module Labimotion
       "default": "",
       "position": 205,
       "placeholder": "Kinematic Viscosity",
-      "units": [{ "key": "m2_s", "label": "m²/s", "nm": 1 }]
+      "units": [{ "key": "m2_s", "label": "m<sup>2</sup>/s", "nm": 1 }]
     },
     {
       "type": "numeric",
@@ -802,6 +767,6 @@ 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 = '2.3.3'
+  VERSION = '2.4.0.rc1'
 end

data/lib/labimotion.rb

@@ -13,11 +13,6 @@ module Labimotion
     Labimotion.logger.error(exception.backtrace.join("\n"))
   end
 
-  # Report a rescued exception to Sentry, if the host app uses it
-  def self.report_exception(exception)
-    Sentry.capture_exception(exception) if defined?(Sentry)
-  end
-
   autoload :MapperUtils, 'labimotion/utils/mapper_utils'
   autoload :Utils, 'labimotion/utils/utils'
 
@@ -94,16 +89,10 @@ module Labimotion
   autoload :ExportDataset, 'labimotion/libs/export_dataset'
   autoload :SampleAssociation, 'labimotion/libs/sample_association'
   autoload :PropertiesHandler, 'labimotion/libs/properties_handler'
-  autoload :KlassVersion, 'labimotion/libs/klass_version'
-  autoload :ReleaseMetadata, 'labimotion/libs/release_metadata'
+  autoload :LinkedElement, 'labimotion/libs/linked_element'
   autoload :AttachmentHandler, 'labimotion/libs/attachment_handler'
   autoload :VocabularyHandler, 'labimotion/libs/vocabulary_handler'
   autoload :XlsxExporter, 'labimotion/libs/xlsx_exporter'
-  autoload :ElementVariationColumnSet, 'labimotion/libs/element_variation_column_set'
-  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: 2.3.3
+  version: 2.4.0.rc1
 platform: ruby
 authors:
 - Chia-Lin Lin
@@ -9,7 +9,7 @@ authors:
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2026-10-19 00:00:00.000000000 Z
+date: 2026-07-03 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: caxlsx
@@ -45,20 +45,6 @@ dependencies:
     - - "<"
       - !ruby/object:Gem::Version
         version: '8.0'
-- !ruby/object:Gem::Dependency
-  name: roo
-  requirement: !ruby/object:Gem::Requirement
-    requirements:
-    - - "~>"
-      - !ruby/object:Gem::Version
-        version: '2.10'
-  type: :runtime
-  prerelease: false
-  version_requirements: !ruby/object:Gem::Requirement
-    requirements:
-    - - "~>"
-      - !ruby/object:Gem::Version
-        version: '2.10'
 description: 
 email:
 - chia-lin.lin@kit.edu
@@ -130,17 +116,11 @@ files:
 - lib/labimotion/libs/data/vocab/Standard.json
 - lib/labimotion/libs/data/vocab/System.json
 - lib/labimotion/libs/dataset_builder.rb
-- lib/labimotion/libs/element_variation_column_set.rb
-- lib/labimotion/libs/element_variation_header.rb
 - 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/klass_version.rb
+- lib/labimotion/libs/linked_element.rb
 - lib/labimotion/libs/nmr_mapper.rb
 - lib/labimotion/libs/properties_handler.rb
-- lib/labimotion/libs/release_metadata.rb
 - lib/labimotion/libs/sample_association.rb
 - lib/labimotion/libs/template_hub.rb
 - lib/labimotion/libs/template_matcher.rb
@@ -225,9 +205,9 @@ required_ruby_version: !ruby/object:Gem::Requirement
       version: '3.4'
 required_rubygems_version: !ruby/object:Gem::Requirement
   requirements:
-  - - ">="
+  - - ">"
     - !ruby/object:Gem::Version
-      version: '0'
+      version: 1.3.1
 requirements: []
 rubygems_version: 3.1.6
 signing_key: