labimotion 2.0.0.rc2 → 2.0.0.rc6

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 = '2.0.0.rc2'
+  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
@@ -13,6 +13,7 @@ module Labimotion
     Labimotion.logger.error(exception.backtrace.join("\n"))
   end
 
+  autoload :MapperUtils, 'labimotion/utils/mapper_utils'
   autoload :Utils, 'labimotion/utils/utils'
 
   ######## APIs
@@ -62,6 +63,7 @@ module Labimotion
 
   ######## 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'
@@ -114,6 +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: 2.0.0.rc2
+  version: 2.0.0.rc6
 platform: ruby
 authors:
 - Chia-Lin Lin
@@ -9,7 +9,7 @@ authors:
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2024-12-18 00:00:00.000000000 Z
+date: 2025-02-21 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: rails
@@ -47,6 +47,7 @@ files:
 - 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
@@ -75,8 +76,11 @@ files:
 - 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
@@ -114,6 +118,7 @@ files:
 - 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