labimotion 2.0.0.rc6 → 2.0.0.rc8

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA256:
-  metadata.gz: b55a7bdf8c25fd127bd7a7bab35676d74e3f3523cb55e03516cc28d3e2df738c
-  data.tar.gz: a28bad0092a10adc3befb26c3803d5f969d40bf9e387a7015890c2f81cd3089e
+  metadata.gz: e53e20059dd2a04452a513beb5024c762f8596d5694874c67b58d64baaf0ce47
+  data.tar.gz: d6b10330fe1dbce975b54a799e5a25d4cb13202fcf7b0a909ae9204fa1442146
 SHA512:
-  metadata.gz: 94b3f84c3b2588b08f19c66bafdd17fb9eef3674040bd3dc0683132a4b5709c11f643e81afda2109741da24e4a38c6b407c4eff279c00c9292ef0942611c4ec8
-  data.tar.gz: 19082b803643920e698b9f14c1ce89b68aac5121a5adeab473d86c16c7129ba1d9e024e1bcec83b7c802ed79409183e1129967881295b66c363912652d563191
+  metadata.gz: 118380f7c4b0483f3ceb7b80d5aa324db7d3fcde3e0b7a5ee66a92a02528fd8e8b352072c79fce563c9955eedc7efcf199e1f1645d391736c54715993f8d4c1d
+  data.tar.gz: c23b0428e3854382643548c08abdd0b875efbcdc052b7b6dd7a612996781056679dc23ce09d46b99e844c1e69016bd17dc54d9dd6d99bbfe1d22a6ce9bd06c44

data/lib/labimotion/apis/vocabulary_api.rb

@@ -31,7 +31,7 @@ module Labimotion
             source_id: params[:source_id],
             layer_id: params[:layer_id],
             field_id: params[:name],
-            identifier: params[:source_id],
+            identifier: SecureRandom.uuid,
             created_by: current_user.id,
             properties: declared(params, include_missing: false),
           }

data/lib/labimotion/constants.rb

@@ -13,6 +13,10 @@ module Labimotion
       ENCODING = 'UTF-8'
     end
 
+    module CHMO
+      CV = 'Cyclic Voltammetry'
+    end
+
     module Mapper
       NMR_CONFIG = ::File.join(__dir__, 'libs', 'data', 'mapper', 'Source.json').freeze
       WIKI_CONFIG = ::File.join(__dir__, 'libs', 'data', 'mapper', 'Chemwiki.json').freeze

data/lib/labimotion/entities/vocabulary_entity.rb

@@ -11,9 +11,10 @@ module Labimotion
 
       case voc['source']
       when Labimotion::Prop::ELEMENT
-        if voc['identifier'] == 'element.name'
+        voc['source_name'] = ElementKlass.find_by(identifier: voc['source_id'])&.label
+        # if voc['identifier'] == 'element.name'
           # voc['source_name'] = ElementKlass.find_by(identifier: voc['source_id'])&.name
-        end
+        # end
       when Labimotion::Prop::SEGMENT
         voc['source_name'] = SegmentKlass.find_by(identifier: voc['source_id'])&.label
       when Labimotion::Prop::DATASET

data/lib/labimotion/helpers/element_helpers.rb

@@ -127,11 +127,12 @@ module Labimotion
         attributes['properties']['uuid'] = uuid
         attributes['uuid'] = uuid
         attributes['klass_uuid'] = properties['klass_uuid']
-        element.update(attributes)
+        element.update_columns(attributes)
       end
       element.save_segments(segments: params[:segments], current_user_id: current_user.id)
       element.reload
       element.properties = update_vocabularies(element.properties, current_user, element)
+      ## element.user_for_revision = current_user
       element.save!
       element
     rescue StandardError => e

data/lib/labimotion/libs/data/mapper/Chemwiki.json

@@ -1,6 +1,6 @@
 {
   "CHMO:0000025": {
-    "index": ["A", "B", "C", "Q1", "Q2", "Q3", "G", "H", "Q4", "Q5", "K", "L", "Q6", "N", "O", "P", "Q7", "R", "S", "T", "U", "V", "W", "X", "Q8", "Q9", "Q10"],
+    "index": ["A", "B", "C", "D", "Q2", "Q3", "G", "H", "Q4", "Q5", "K", "L", "Q6", "N", "O", "P", "Q7", "R", "S", "T", "U", "V", "W", "X", "Q8", "Q9", "Q10"],
     "mapper": {
       "A": {
         "sources": ["inchikey"]
@@ -11,6 +11,10 @@
       "C": {
         "sources": ["concentration"]
       },
+      "D": {
+        "sources": ["redox"],
+        "separator": ","
+      },
       "G": {
         "sources": ["solvent_volume"]
       },
@@ -54,10 +58,6 @@
       "X": {
         "sources": ["re"]
       },
-      "Q1": {
-        "sources": ["redox"],
-        "separator": ","
-      },
       "Q2": {
         "sources": ["solvent"]
       },
@@ -198,8 +198,8 @@
       },
       "redox": {
         "title": "Redox-Potential",
-        "param": "n/a",
-        "type": "string"
+        "param": 6,
+        "type": "spc"
       },
       "elect_molfile": {
         "title": "Electrolyte_inchikey",

data/lib/labimotion/libs/data/vocab/System.json

@@ -55,7 +55,7 @@
     "id": 4,
     "identifier": "user-name",
     "name": "creator",
-    "label": "creator",
+    "label": "Creator",
     "field_type": "text",
     "opid": 9,
     "term_id": "NCIT_C42628",

data/lib/labimotion/libs/export_dataset.rb

@@ -23,6 +23,7 @@ module Labimotion
       @analysis = @dataset&.element&.parent
       @element = @analysis&.root&.containable if @analysis.present?
       @element_type = @element.class.name if @element.present?
+      @spectra_values = []
     end
 
     def read
@@ -37,44 +38,12 @@ module Labimotion
       Labimotion.log_exception(e)
     end
 
-    def spectra
-      name_mapping = []
-      ## gds = Labimotion::Dataset.find_by(element_id: id, element_type: 'Container')
-      cds = Container.find(@id)
-      cds_csv = cds.attachments.where(aasm_state: 'csv').order(:filename)
-      csv_length = cds_csv.length
-      return if csv_length.zero?
-
-      cds_csv.each_with_index do |att, idx|
-        sheet_name = "Sheet#{idx+1}"
-        sheet = @xfile.workbook.add_worksheet(name: sheet_name)
-        name_mapping.push([sheet_name, att.filename])
-        File.open(att.attachment_url) do |fi|
-          fi.each_line do |line|
-            sheet.add_row(line.split(','))
-          end
-        end
-      end
-      return unless name_mapping.length > 1
-
-      first_sheet = @xfile.workbook.worksheets&.first
-      header_style = first_sheet&.styles.add_style(sz: 12, fg_color: 'FFFFFF', bg_color: '00008B', border: { style: :thick, color: 'FF777777', edges: [:bottom] })
-      first_sheet&.add_row(['Sheet name', 'File name'], style: header_style)
-      name_mapping&.each do |mapping|
-        next if mapping.length < 2
-
-        @xfile.workbook.worksheets&.first&.add_row([mapping[0].to_s, mapping[1].to_s])
-      end
-    rescue StandardError => e
-      Labimotion.log_exception(e)
-    end
-
     def export
       return if @dataset.nil? || @analysis.nil? || @element.nil?
 
       description
       dataset_info
-      # element_info
+      spectra_info
       chemwiki_info
     rescue StandardError => e
       Labimotion.log_exception(e)
@@ -83,6 +52,7 @@ module Labimotion
     private
 
     def chemwiki_info
+      @spectra_values
       config = Labimotion::MapperUtils.load_config(File.read(Constants::Mapper::WIKI_CONFIG))
       return if config.nil? || config[@ols_term_id].nil?
 
@@ -97,31 +67,45 @@ module Labimotion
 
       # sheet.column_info.each { |col| col.width = map_width }
 
-      array_header = []
-      array_data = []
-      map_index.each do |key|
-        mapper = map_mapper.dig(key)
-        next if mapper.nil? || mapper['sources'].nil? || !mapper.is_a?(Hash)
-
-        col_header = ''
-        col_value = ''
-        mapper['sources'].each_with_index do |source_key, idx|
-          source = map_source&.dig(source_key)
-          next if source.nil? || source['title'].nil?
-
-          col_header = source['title']
+      if @spectra_values.length == 0
+        @spectra_values.push([])
+      end
 
-          if col_value.present?
-            col_value += (mapper['separator'] || '') + source_data(source)
-          else
-            col_value = source_data(source)
+      @spectra_values.each_with_index do |spdata, idx|
+        array_header = []
+        array_data = []
+        map_index.each do |key|
+          mapper = map_mapper.dig(key)
+          next if mapper.nil? || mapper['sources'].nil? || !mapper.is_a?(Hash)
+
+          col_header = ''
+          col_value = ''
+          mapper['sources'].each_with_index do |source_key, idx|
+            source = map_source&.dig(source_key)
+            next if source.nil? || source['title'].nil?
+
+            col_header = source['title']
+
+            if col_value.present?
+              col_value += (mapper['separator'] || '') + source_data(source, spdata)
+            else
+              col_value = source_data(source, spdata)
+            end
           end
+          array_header.push(col_header || '')
+          array_data.push(col_value || '')
         end
-        array_header.push(col_header || '')
-        array_data.push(col_value || '')
+        if idx == 0
+          sheet.add_row(array_header)
+        end
+        sheet.add_row(array_data)
+
+        ## for Redox potential
+        last_row = sheet.rows.last
+        last_row.cells[3].type = :string
       end
-      sheet.add_row(array_header)
-      sheet.add_row(array_data)
+
+
     rescue StandardError => e
       Labimotion.log_exception(e)
     end
@@ -132,26 +116,28 @@ module Labimotion
 
       case field['type']
       when 'select'
+        return '' if field['value'].empty?
         Labimotion::Utils.find_options_val(field, properties) || field['value']
       else
         field['value']
       end
     end
 
-    def source_data(source)
+    def source_data(source, spdata)
       param = source['param']
       return '' if param.nil? || source['type'].nil?
 
       val = case source['type']
             when 'string'
               param
+            when 'spc'
+              spdata.length.positive? && param.is_a?(Integer) ? spdata.pluck(param).join(';') : ''
             when 'sample'
               @element.send(param) if @element.respond_to?(param)
             when 'molecule'
               @element.molecule.send(param) if @element_type == 'Sample' && @element&.molecule&.respond_to?(param)
             when 'dataset'
               field = Labimotion::Utils.find_field(@dataset.properties, param)
-              # (field && field['value']) || ''
               conv_value(field, @dataset.properties)
             end
       val || ''
@@ -170,8 +156,6 @@ module Labimotion
     end
 
     def ols_name
-      #name = @dataset.dataset_klass.label
-
       match = @label.match(/\((.*?)\)/)
       name = match && match.length > 1 ? match[1] : @label
 
@@ -212,54 +196,207 @@ module Labimotion
       name = ols_name
       return if name.nil?
 
+      sheet = create_dataset_sheet(name)
+      process_layers(sheet)
+    rescue StandardError => e
+      Labimotion.log_exception(e)
+    end
+
+    def create_dataset_sheet(name)
       sheet = @xfile.workbook.add_worksheet(name: name)
       sheet.add_row([@dataset.dataset_klass.label])
-      header_style = sheet.styles.add_style(sz: 12, fg_color: 'FFFFFF', bg_color: '00008B', border: { style: :thick, color: 'FF777777', edges: [:bottom] })
-      layer_style = sheet.styles.add_style(b: true, bg_color: 'CEECF5')
-      sheet.add_row(header, style: header_style)
+      sheet.add_row(header, style: create_header_style(sheet))
+      sheet
+    end
 
+    def process_layers(sheet)
       layers = @dataset.properties[Labimotion::Prop::LAYERS] || {}
       options = @dataset.properties[Labimotion::Prop::SEL_OPTIONS]
-      layer_keys = layers.keys.sort_by { |key| layers[key]['position'] }
-      layer_keys.each do |key|
+
+      sort_layers(layers).each do |key|
         layer = layers[key]
-        sheet.add_row([layer['label'], ' ', ' ', ' ', ' ', ' ', ' ', ' ', ' '], style: layer_style)
-        sorted_fields = layer[Labimotion::Prop::FIELDS].sort_by { |obj| obj['position'] }
-        sorted_fields.each do |field|
-          next if field['type'] == 'dummy'
-
-          type = field['type']
-          from_device = field['device'].present? ? 'Device' : ''
-          from_device = field['system'].present? ? 'Chemotion' : from_device
-          type = "#{field['type']}-#{field['option_layers']}" if field['type'] == Labimotion::FieldType::SELECT || field['type'] == Labimotion::FieldType::SYSTEM_DEFINED
-
-          show_value = field['value'] =~ /\A\d+,\d+\z/ ? field['value']&.gsub(',', '.') : field['value']
-          ols_short_form = (field['ontology'] && field['ontology']['short_form']) || ''
-          ols_label = (field['ontology'] && field['ontology']['label']) || ''
-          ols_iri = (field['ontology'] && field['ontology']['iri']) || ''
-          sheet.add_row([' ', field['label'], nil, field['value_system'], field['field'], type, from_device, field['dkey'], nil, ols_short_form, ols_label, ols_iri].freeze)
-
-          case field['type']
-          when Labimotion::FieldType::SELECT
-            sheet.rows.last.cells[2].type = :string
-            sheet.rows.last.cells[8].type = :string
-            show_value = opt_value(field, options) if show_value.present?
-          when Labimotion::FieldType::SYSTEM_DEFINED, Labimotion::FieldType::INTEGER
-            sheet.rows.last.cells[2].type = :float
-            sheet.rows.last.cells[8].type = :float
-          else
-            sheet.rows.last.cells[2].type = :string
-            sheet.rows.last.cells[8].type = :string
-          end
-          sheet.rows.last.cells[2].value = show_value
-          sheet.rows.last.cells[8].value = field['system'] || field['device']
-        end
-        # sheet.column_widths nil, nil, nil, nil, 0, 0, 0, 0, 0
+        add_layer_row(sheet, layer)
+        process_fields(sheet, layer, options)
+      end
+    end
+
+    def sort_layers(layers)
+      layers.keys.sort_by { |key| layers[key]['position'] }
+    end
+
+    def add_layer_row(sheet, layer)
+      layer_style = sheet.styles.add_style(b: true, bg_color: 'CEECF5')
+      sheet.add_row([layer['label']] + [' '] * 8, style: layer_style)
+    end
+
+    def process_fields(sheet, layer, options)
+      sorted_fields = sort_fields(layer)
+
+      sorted_fields.each do |field|
+        next if field['type'] == 'dummy'
+
+        add_field_row(sheet, field)
+        set_field_types(sheet, field, options)
       end
+    end
+
+    def sort_fields(layer)
+      layer[Labimotion::Prop::FIELDS].sort_by { |obj| obj['position'] }
+    end
+
+    def add_field_row(sheet, field)
+      type = determine_field_type(field)
+      from_device = determine_source(field)
+      show_value = format_value(field['value'])
+      ontology_data = extract_ontology_data(field)
+
+      row_data = [
+        ' ',
+        field['label'],
+        nil,
+        field['value_system'],
+        field['field'],
+        type,
+        from_device,
+        field['dkey'],
+        nil
+      ] + ontology_data
+
+      sheet.add_row(row_data.freeze)
+    end
+
+    def determine_field_type(field)
+      return "#{field['type']}-#{field['option_layers']}" if [
+        Labimotion::FieldType::SELECT,
+        Labimotion::FieldType::SYSTEM_DEFINED
+      ].include?(field['type'])
+
+      field['type']
+    end
+
+    def determine_source(field)
+      return 'Chemotion' if field['system'].present?
+      return 'Device' if field['device'].present?
+      ''
+    end
+
+    def format_value(value)
+      return value&.gsub(',', '.') if value =~ /\A\d+,\d+\z/
+      value
+    end
+
+    def extract_ontology_data(field)
+      ontology = field['ontology'] || {}
+      [
+        ontology['short_form'] || '',
+        ontology['label'] || '',
+        ontology['iri'] || ''
+      ]
+    end
+
+    def set_field_types(sheet, field, options)
+      last_row = sheet.rows.last
+
+      case field['type']
+      when Labimotion::FieldType::SELECT
+        set_select_field_type(last_row, field, options)
+      when Labimotion::FieldType::SYSTEM_DEFINED, Labimotion::FieldType::INTEGER
+        set_numeric_field_type(last_row)
+      else
+        set_string_field_type(last_row)
+      end
+
+      set_field_values(last_row, field)
+    end
+
+    def set_select_field_type(row, field, options)
+      row.cells[2].type = :string
+      row.cells[8].type = :string
+      row.cells[2].value = opt_value(field, options) if field['value'].present?
+    end
+
+    def set_numeric_field_type(row)
+      row.cells[2].type = :float
+      row.cells[8].type = :float
+    end
+
+    def set_string_field_type(row)
+      row.cells[2].type = :string
+      row.cells[8].type = :string
+    end
+
+    def set_field_values(row, field)
+      row.cells[8].value = field['system'] || field['device']
+    end
+
+    def spectra_info
+      name_mapping = process_csv_files
+      return if name_mapping.nil? || name_mapping.length <= 1
+
+      create_mapping_sheet(name_mapping)
     rescue StandardError => e
       Labimotion.log_exception(e)
     end
 
+    def process_csv_files
+      cds_csv = Container.find(@id).attachments.where(aasm_state: 'csv').order(:filename)
+      return if cds_csv.empty?
+
+      cds_csv.each_with_index.map do |att, index|
+        process_single_csv(att, index)
+      end.compact
+    end
+
+    def process_single_csv(attachment, index)
+      sheet_name = "Sheet#{index + 1}"
+      sheet = @xfile.workbook.add_worksheet(name: sheet_name)
+
+      File.open(attachment.attachment_url) do |file|
+        first_line = file.readline.chomp
+        next unless cv_spc?(first_line)
+
+        process_csv_content(first_line, file, sheet)
+      end
+      [sheet_name, attachment.filename]
+    end
+
+    def process_csv_content(first_line, file, sheet)
+      lines = []
+      file.each_line.with_index do |line, index|
+        line = first_line if index.zero?
+        row_data = line.split(',')
+        sheet.add_row(row_data)
+        lines << row_data if cv_data?(row_data, index)
+      end
+      @spectra_values << lines if lines.any?
+    end
+
+    def create_mapping_sheet(name_mapping)
+      first_sheet = @xfile.workbook.worksheets&.first
+      return unless first_sheet
+
+      header_style = create_header_style(first_sheet)
+      first_sheet.add_row(['Sheet name', 'File name'], style: header_style)
+
+      name_mapping.each do |sheet_name, filename|
+        first_sheet.add_row([sheet_name.to_s, filename.to_s])
+      end
+    end
+
+
+    def create_header_style(sheet)
+      sheet.styles.add_style(
+        sz: 12,
+        fg_color: 'FFFFFF',
+        bg_color: '00008B',
+        border: {
+          style: :thick,
+          color: 'FF777777',
+          edges: [:bottom]
+        }
+      )
+    end
+
     def opt_value(field, options)
       return nil if field.nil? || options.nil? || field['value']&.empty? || field['option_layers']&.empty?
       return nil unless opts = options.fetch(field['option_layers'], nil)&.fetch('options', nil)
@@ -271,6 +408,15 @@ module Labimotion
       field['value']
     end
 
+    def cv_spc?(first_line)
+      data = first_line.split(',')
+      data && data.length > 2 && data[2] == Constants::CHMO::CV
+    end
+
+    def cv_data?(data, idx)
+      data.length > 7 && idx > 7
+    end
+
     def header
       ['Layer Label', 'Field Label', 'Value', 'Unit', 'Name', 'Type', 'Source?', 'Source identifier', 'Source data', 'Ontology', 'Ontology Label', 'iri'].freeze
     end

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

@@ -43,6 +43,7 @@ module Labimotion
         released_by: released_by,
         uuid: uuid,
         version: version,
+        created_by: updated_by,
         properties_release: properties_release,
         released_at: released_at
       }

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

@@ -8,6 +8,8 @@ module Labimotion
       after_create :create_vault
       after_update :save_to_vault
       before_destroy :delete_attachments
+
+      ## attr_accessor :user_for_revision
     end
 
     def create_vault
@@ -19,6 +21,7 @@ module Labimotion
         uuid: uuid,
         klass_uuid: klass_uuid,
         properties: properties,
+        ## created_by: user_for_revision&.id,
         properties_release: properties_release
       }
       attributes["#{Labimotion::Utils.element_name_dc(self.class.name)}_id"] = id

data/lib/labimotion/utils/utils.rb

@@ -97,9 +97,8 @@ module Labimotion
       options = option_layers && option_layers['options']
       return if options.nil?
 
-      sel_option = options.find { |o| o['key'] = field['value'] }
+      sel_option = options.find { |o| o['key'] == field['value'] }
       sel_option && sel_option['label']
-
     end
 
     def self.pkg(pkg)

data/lib/labimotion/version.rb

@@ -2,5 +2,5 @@
 
 ## Labimotion Version
 module Labimotion
-  VERSION = '2.0.0.rc6'
+  VERSION = '2.0.0.rc8'
 end

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: labimotion
 version: !ruby/object:Gem::Version
-  version: 2.0.0.rc6
+  version: 2.0.0.rc8
 platform: ruby
 authors:
 - Chia-Lin Lin
@@ -9,7 +9,7 @@ authors:
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2025-02-21 00:00:00.000000000 Z
+date: 2025-02-28 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: rails