labimotion 1.4.1 → 2.0.0.rc6

data/lib/labimotion/models/concerns/attachment_converter.rb

@@ -25,17 +25,18 @@ module Labimotion
       def exec_converter
         return if self.has_attribute?(:con_state) == false || self.con_state.nil? || self.con_state == Labimotion::ConState::NONE
 
-        return if attachable_id.nil? && self.con_state != Labimotion::ConState::WAIT
+        return if attachable_id.nil? && con_state != Labimotion::ConState::WAIT
 
+        current_user = User.find_by(id: created_by)
         case con_state
         when Labimotion::ConState::NMR
-          self.con_state = Labimotion::NmrMapper.process_ds(id)
+          self.con_state = Labimotion::NmrMapper.process_ds(id, current_user)
           update_column(:con_state, con_state)
         when Labimotion::ConState::WAIT
-          self.con_state = Labimotion::Converter.jcamp_converter(id)
+          self.con_state = Labimotion::Converter.jcamp_converter(id, current_user)
           update_column(:con_state, con_state)
         when Labimotion::ConState::CONVERTED
-          Labimotion::Converter.metadata(id)
+          Labimotion::Converter.metadata(id, current_user)
         end
       end
     end

data/lib/labimotion/models/concerns/datasetable.rb

@@ -42,6 +42,7 @@ module Labimotion
       props['identifier'] = klass.identifier if klass.identifier.present?
       props['uuid'] = uuid
       props['klass'] = 'Dataset'
+      props = Labimotion::VocabularyHandler.update_vocabularies(props, args[:current_user], args[:element])
 
       ds = Labimotion::Dataset.find_by(element_type: self.class.name, element_id: id)
       if ds.present? && (ds.klass_uuid != props['klass_uuid'] || ds.properties != props)

data/lib/labimotion/models/concerns/segmentable.rb

@@ -59,6 +59,8 @@ module Labimotion
         props['uuid'] = uuid
         props['klass'] = 'Segment'
         props = Labimotion::SampleAssociation.update_sample_association(props, args[:current_user_id])
+        current_user = User.find_by(id: args[:current_user_id])
+        props = Labimotion::VocabularyHandler.update_vocabularies(props, current_user, self)
         segment = Labimotion::Segment.where(element_type: self.class.name, element_id: self.id, segment_klass_id: seg['segment_klass_id']).order(id: :desc).first
         if segment.present? && (segment.klass_uuid != props['klass_uuid'] || segment.properties != props)
           segment.update!(properties_release: klass.properties_release, properties: props, uuid: uuid, klass_uuid: props['klass_uuid'])

data/lib/labimotion/models/element.rb

@@ -58,6 +58,9 @@ module Labimotion
     after_create :update_counter
     before_destroy :delete_attachment
 
+    def user_labels
+      tag&.taggable_data&.fetch('user_labels', nil)
+    end
 
     def attachments
       Attachment.where(attachable_id: self.id, attachable_type: self.class.name)

data/lib/labimotion/models/std_layer.rb

@@ -0,0 +1,9 @@
+# frozen_string_literal: true
+
+module Labimotion
+  class StdLayer < ApplicationRecord
+    acts_as_paranoid
+    self.table_name = :layers
+    has_many :layer_tracks, primary_key: 'identifier', foreign_key: 'identifier', class_name: 'Labimotion::StdLayersRevision'
+  end
+end

data/lib/labimotion/models/std_layers_revision.rb

@@ -0,0 +1,9 @@
+# frozen_string_literal: true
+
+module Labimotion
+  class StdLayersRevision < ApplicationRecord
+    acts_as_paranoid
+    self.table_name = :layer_tracks
+    belongs_to :layers, primary_key: 'identifier', foreign_key: 'identifier', class_name: 'Labimotion::StdLayer'
+  end
+end

data/lib/labimotion/models/vocabulary.rb

@@ -0,0 +1,12 @@
+# frozen_string_literal: true
+require 'labimotion/models/concerns/generic_klass_revisions'
+require 'labimotion/models/concerns/workflow'
+
+module Labimotion
+  class Vocabulary < ApplicationRecord
+    self.table_name = :vocabularies
+    acts_as_paranoid
+
+
+  end
+end

data/lib/labimotion/utils/mapper_utils.rb

@@ -0,0 +1,169 @@
+# frozen_string_literal: true
+
+require 'json'
+require 'time'
+require 'zip'
+require 'labimotion/constants'
+
+module Labimotion
+  class MapperUtils
+    class << self
+      def load_config(config_json)
+        JSON.parse(config_json)
+      rescue JSON::ParserError => e
+        Rails.logger.error "Error parsing JSON: #{e.message}"
+        nil
+      rescue Errno::ENOENT => e
+        Rails.logger.error "Config file not found at #{Constants::Mapper::NMR_CONFIG}: #{e.message}"
+        nil
+      rescue StandardError => e
+        Rails.logger.error "Unexpected error loading config: #{e.message}"
+        nil
+      end
+
+      def load_brucker_config
+        config = load_config(File.read(Constants::Mapper::NMR_CONFIG))
+        return if config.nil? || config['sourceMap'].nil?
+
+        source_selector = config['sourceMap']['sourceSelector']
+        return if source_selector.blank?
+
+        parameters = config['sourceMap']['parameters']
+        return if parameters.blank?
+
+        config
+      end
+
+      def extract_data_from_zip(zip_file_url, source_map)
+        return nil if zip_file_url.nil?
+
+        process_zip_file(zip_file_url, source_map)
+      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?
+
+        patterns = {
+          standard: build_parameter_pattern(parameter_names, :standard),
+          parm: build_parameter_pattern(parameter_names, :parm)
+        }
+
+        extracted_parameters = {}
+        begin
+          file_content.each_line do |line|
+            if (match = match_parameter(line, patterns))
+              value = clean_value(match[:value])
+              extracted_parameters[match[:param_name]] = value
+            end
+          end
+        rescue StandardError => e
+          Rails.logger.error "Error reading file content: #{e.message}"
+          return nil
+        end
+        extracted_parameters.compact_blank!
+        extracted_parameters
+      end
+
+      def format_timestamp(timestamp_str, give_format = nil)
+        return nil if timestamp_str.blank?
+
+        begin
+          timestamp = Integer(timestamp_str)
+          time_object = Time.at(timestamp).in_time_zone(Constants::DateTime::TIME_ZONE)
+          case give_format
+          when 'date'
+            time_object.strftime(Constants::DateTime::DATE_FORMAT)
+          when 'time'
+            time_object.strftime(Constants::DateTime::TIME_FORMAT)
+          else
+            time_object.strftime(Constants::DateTime::DATETIME_FORMAT)
+          end
+        rescue ArgumentError, TypeError => e
+          Rails.logger.error "Error parsing timestamp '#{timestamp_str}': #{e.message}"
+          nil
+        end
+      end
+
+      private
+
+      def build_parameter_pattern(parameter_names, format)
+        pattern = case format
+                  when :standard
+                    '^\\s*##?\\s*[$]?(?<param_name>%s)\\s*(?:=\\s*)?(?<value>.*?)\\s*$'
+                  when :parm
+                    '^\\s*(?<param_name>%s)\\s+(?<value>[^\\s].*?)(?:\\s+[A-Za-z]+)?\\s*$'
+                  end
+
+        param_regex = parameter_names.map { |p| "\\b#{Regexp.escape(p)}\\b" }.join('|')
+        Regexp.new(pattern % param_regex)
+      end
+
+      def match_parameter(line, patterns)
+        patterns.each_value do |pattern|
+          match = line.match(pattern)
+          return match if match
+        end
+        nil
+      end
+
+      def clean_value(value)
+        value = value.strip
+        value = value[1..-2].strip if value.start_with?('<') && value.end_with?('>')
+        value
+      end
+
+      def process_zip_file(zip_file_url, source_map)
+        final_parameters = {}
+
+        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?
+
+        nil
+      end
+
+      def process_source(zip_file, source_config, final_parameters)
+        return if invalid_source_config?(source_config)
+
+        zip_file.each do |entry|
+          if source_file?(entry, source_config)
+            process_file_entry(entry, source_config['parameters'], final_parameters)
+          elsif bagit_metadata_file?(entry)
+            return { is_bagit: true, metadata: nil }
+          end
+        end
+      end
+
+      def process_file_entry(entry, parameters, final_parameters)
+        file_content = entry.get_input_stream.read.force_encoding(Constants::File::ENCODING)
+        extracted_parameters = extract_parameters(file_content, parameters)
+        final_parameters.merge!(extracted_parameters) if extracted_parameters.present?
+      end
+
+      def invalid_source_config?(source_config)
+        source_config.nil? ||
+          source_config['file'].nil? ||
+          source_config['parameters'].nil?
+      end
+
+      def source_file?(entry, source_config)
+        entry.name.include?(source_config['file'])
+      end
+
+      def bagit_metadata_file?(entry)
+        entry.name.include?('metadata/') &&
+          entry.name.include?('converter.json')
+      end
+    end
+  end
+end

data/lib/labimotion/utils/utils.rb

@@ -80,6 +80,28 @@ module Labimotion
       current_version
     end
 
+    def self.find_field(properties, field_path, separator = '.')
+      return if properties.nil? || field_path.nil?
+
+      layer_name, field_name = field_path.split(separator)
+      fields = properties.dig(Labimotion::Prop::LAYERS, layer_name, Labimotion::Prop::FIELDS)
+      return unless fields
+
+      fields.find { |f| f['field'] == field_name }
+    end
+
+    def self.find_options_val(field, properties)
+      return if field.nil? || properties.nil? || field['option_layers'].nil? || field['value'].nil?
+
+      option_layers = properties.dig(Labimotion::Prop::SEL_OPTIONS, field['option_layers'])
+      options = option_layers && option_layers['options']
+      return if options.nil?
+
+      sel_option = options.find { |o| o['key'] = field['value'] }
+      sel_option && sel_option['label']
+
+    end
+
     def self.pkg(pkg)
       pkg = {} if pkg.nil?
       pkg['eln'] = Chemotion::Application.config.version

data/lib/labimotion/version.rb

@@ -2,5 +2,5 @@
 
 ## Labimotion Version
 module Labimotion
-  VERSION = '1.4.1'
+  VERSION = '2.0.0.rc6'
 end

data/lib/labimotion.rb

@@ -1,8 +1,8 @@
 # In your_gem_name.rb or main Ruby file
 module Labimotion
-
   autoload :CONF, 'labimotion/conf'
   autoload :VERSION, 'labimotion/version'
+  autoload :Constants, 'labimotion/constants'
 
   def self.logger
     @@labimotion_logger ||= Logger.new(Rails.root.join('log/labimotion.log')) # rubocop:disable Style/ClassVars
@@ -13,15 +13,19 @@ module Labimotion
     Labimotion.logger.error(exception.backtrace.join("\n"))
   end
 
+  autoload :MapperUtils, 'labimotion/utils/mapper_utils'
   autoload :Utils, 'labimotion/utils/utils'
 
   ######## APIs
+  autoload :LabimotionAPI, 'labimotion/apis/labimotion_api'
   autoload :GenericKlassAPI, 'labimotion/apis/generic_klass_api'
   autoload :GenericElementAPI, 'labimotion/apis/generic_element_api'
   autoload :GenericDatasetAPI, 'labimotion/apis/generic_dataset_api'
   autoload :SegmentAPI, 'labimotion/apis/segment_api'
   autoload :LabimotionHubAPI, 'labimotion/apis/labimotion_hub_api'
   autoload :ConverterAPI, 'labimotion/apis/converter_api'
+  autoload :StandardLayerAPI, 'labimotion/apis/standard_layer_api'
+  autoload :VocabularyAPI, 'labimotion/apis/vocabulary_api'
 
   ######## Entities
   autoload :PropertiesEntity, 'labimotion/entities/properties_entity'
@@ -43,6 +47,7 @@ module Labimotion
   autoload :ElementRevisionEntity, 'labimotion/entities/element_revision_entity'
   autoload :SegmentRevisionEntity, 'labimotion/entities/segment_revision_entity'
   ## autoload :DatasetRevisionEntity, 'labimotion/entities/dataset_revision_entity'
+  autoload :VocabularyEntity, 'labimotion/entities/vocabulary_entity'
 
   ######## Helpers
   autoload :GenericHelpers, 'labimotion/helpers/generic_helpers'
@@ -54,9 +59,11 @@ module Labimotion
   autoload :ConverterHelpers, 'labimotion/helpers/converter_helpers'
   autoload :SampleAssociationHelpers, 'labimotion/helpers/sample_association_helpers'
   autoload :RepositoryHelpers, 'labimotion/helpers/repository_helpers'
+  autoload :VocabularyHelpers, 'labimotion/helpers/vocabulary_helpers'
 
   ######## Libs
   autoload :Converter, 'labimotion/libs/converter'
+  autoload :DatasetBuilder, 'labimotion/libs/dataset_builder'
   autoload :NmrMapper, 'labimotion/libs/nmr_mapper'
   autoload :NmrMapperRepo, 'labimotion/libs/nmr_mapper_repo' ## for Chemotion Repository
   autoload :TemplateHub, 'labimotion/libs/template_hub'
@@ -64,6 +71,7 @@ module Labimotion
   autoload :SampleAssociation, 'labimotion/libs/sample_association'
   autoload :PropertiesHandler, 'labimotion/libs/properties_handler'
   autoload :AttachmentHandler, 'labimotion/libs/attachment_handler'
+  autoload :VocabularyHandler, 'labimotion/libs/vocabulary_handler'
 
   ######## Utils
   autoload :Prop, 'labimotion/utils/prop'
@@ -84,6 +92,7 @@ module Labimotion
   autoload :ElementKlass, 'labimotion/models/element_klass'
   autoload :SegmentKlass, 'labimotion/models/segment_klass'
   autoload :DatasetKlass, 'labimotion/models/dataset_klass'
+  autoload :Vocabulary, 'labimotion/models/vocabulary'
 
   autoload :ElementsRevision, 'labimotion/models/elements_revision'
   autoload :SegmentsRevision, 'labimotion/models/segments_revision'
@@ -97,6 +106,9 @@ module Labimotion
   autoload :ElementsElement, 'labimotion/models/elements_element'
   autoload :CollectionsElement, 'labimotion/models/collections_element'
 
+  autoload :StdLayer, 'labimotion/models/std_layer'
+  autoload :StdLayersRevision, 'labimotion/models/std_layers_revision'
+
   ######## Models/Concerns
   autoload :GenericKlassRevisions, 'labimotion/models/concerns/generic_klass_revisions'
   autoload :GenericRevisions, 'labimotion/models/concerns/generic_revisions'
@@ -104,6 +116,4 @@ module Labimotion
   autoload :Datasetable, 'labimotion/models/concerns/datasetable'
   autoload :AttachmentConverter, 'labimotion/models/concerns/attachment_converter.rb'
   autoload :LinkedProperties, 'labimotion/models/concerns/linked_properties'
-
-
 end

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: labimotion
 version: !ruby/object:Gem::Version
-  version: 1.4.1
+  version: 2.0.0.rc6
 platform: ruby
 authors:
 - Chia-Lin Lin
@@ -9,7 +9,7 @@ authors:
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2024-10-24 00:00:00.000000000 Z
+date: 2025-02-21 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: rails
@@ -38,11 +38,16 @@ files:
 - lib/labimotion/apis/generic_dataset_api.rb
 - lib/labimotion/apis/generic_element_api.rb
 - lib/labimotion/apis/generic_klass_api.rb
+- lib/labimotion/apis/labimotion_api.rb
 - lib/labimotion/apis/labimotion_hub_api.rb
 - lib/labimotion/apis/segment_api.rb
+- lib/labimotion/apis/standard_api.rb
+- lib/labimotion/apis/standard_layer_api.rb
+- lib/labimotion/apis/vocabulary_api.rb
 - lib/labimotion/collection/export.rb
 - lib/labimotion/collection/import.rb
 - lib/labimotion/conf.rb
+- lib/labimotion/constants.rb
 - lib/labimotion/entities/application_entity.rb
 - lib/labimotion/entities/dataset_entity.rb
 - lib/labimotion/entities/dataset_klass_entity.rb
@@ -58,6 +63,7 @@ files:
 - lib/labimotion/entities/segment_entity.rb
 - lib/labimotion/entities/segment_klass_entity.rb
 - lib/labimotion/entities/segment_revision_entity.rb
+- lib/labimotion/entities/vocabulary_entity.rb
 - lib/labimotion/helpers/converter_helpers.rb
 - lib/labimotion/helpers/dataset_helpers.rb
 - lib/labimotion/helpers/element_helpers.rb
@@ -67,14 +73,21 @@ files:
 - lib/labimotion/helpers/sample_association_helpers.rb
 - lib/labimotion/helpers/search_helpers.rb
 - lib/labimotion/helpers/segment_helpers.rb
+- lib/labimotion/helpers/vocabulary_helpers.rb
 - lib/labimotion/libs/attachment_handler.rb
 - lib/labimotion/libs/converter.rb
+- lib/labimotion/libs/data/mapper/Chemwiki.json
+- lib/labimotion/libs/data/mapper/Source.json
+- lib/labimotion/libs/data/vocab/Standard.json
+- lib/labimotion/libs/data/vocab/System.json
+- lib/labimotion/libs/dataset_builder.rb
 - lib/labimotion/libs/export_dataset.rb
 - lib/labimotion/libs/export_element.rb
 - lib/labimotion/libs/nmr_mapper.rb
 - lib/labimotion/libs/properties_handler.rb
 - lib/labimotion/libs/sample_association.rb
 - lib/labimotion/libs/template_hub.rb
+- lib/labimotion/libs/vocabulary_handler.rb
 - lib/labimotion/models/collections_element.rb
 - lib/labimotion/models/concerns/attachment_converter.rb
 - lib/labimotion/models/concerns/datasetable.rb
@@ -98,10 +111,14 @@ files:
 - lib/labimotion/models/segment_klass.rb
 - lib/labimotion/models/segment_klasses_revision.rb
 - lib/labimotion/models/segments_revision.rb
+- lib/labimotion/models/std_layer.rb
+- lib/labimotion/models/std_layers_revision.rb
+- lib/labimotion/models/vocabulary.rb
 - lib/labimotion/utils/con_state.rb
 - lib/labimotion/utils/export_utils.rb
 - lib/labimotion/utils/field_type.rb
 - lib/labimotion/utils/import_utils.rb
+- lib/labimotion/utils/mapper_utils.rb
 - lib/labimotion/utils/prop.rb
 - lib/labimotion/utils/search.rb
 - lib/labimotion/utils/serializer.rb
@@ -111,7 +128,10 @@ files:
 homepage: https://github.com/LabIMotion/labimotion
 licenses:
 - AGPL-3.0
-metadata: {}
+metadata:
+  homepage_uri: https://github.com/LabIMotion/labimotion
+  source_code_uri: https://github.com/LabIMotion/labimotion
+  bug_tracker_uri: https://github.com/LabIMotion/labimotion/discussions
 post_install_message: 
 rdoc_options: []
 require_paths:
@@ -123,9 +143,9 @@ required_ruby_version: !ruby/object:Gem::Requirement
       version: '0'
 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: