labimotion 1.0.19 → 1.1.0
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checksums.yaml
CHANGED
@@ -1,7 +1,7 @@
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---
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SHA256:
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metadata.gz:
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data.tar.gz:
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metadata.gz: 0c374697be6dd59785865b85ea34a92de6d9e87d8d0fe9d5416b5b58c5f18f11
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data.tar.gz: 11b8842141477f92d08e50c0fc55c29f82c7a098dc8c08ed9be610b9d037c0ae
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SHA512:
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metadata.gz:
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data.tar.gz:
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metadata.gz: 0ebbb6edd334c5f13bbf3196cc7f5b56510019925f516abb35404b0943c9546e21fd16227ffebe5365955d9202b7201b795fac019c72050d0a59f902d4aa70ca
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data.tar.gz: eded51a9e589660b0a6dcf20187eb715e946448fa9a047263176212c0136d0a648c9015d50a3de0ae06ea39ba6942fcfc23e00b085aecaa583e8faa57e67f1ee
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@@ -19,7 +19,7 @@ module Labimotion
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get do
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list = "Labimotion::#{params[:klass]}".constantize.where(is_active: true).where.not(released_at: nil)
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list = list.where(is_generic: true) if params[:klass] == 'ElementKlass'
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entities = Labimotion::GenericPublicEntity.represent(list, displayed: params[:with_props])
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entities = Labimotion::GenericPublicEntity.represent(list, displayed: params[:with_props], root: 'list')
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rescue StandardError => e
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Labimotion.log_exception(e, current_user)
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[]
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@@ -20,7 +20,10 @@ module Labimotion
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def self.process_ds(id, current_user = {})
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att = Attachment.find_by(id: id, con_state: Labimotion::ConState::CONVERTED)
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-
return if att.nil? || att.attachable_id.nil? || att.attachable_type != 'Container'
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return if att.nil? || att.attachable_id.nil? || att.attachable_type != 'Container' || att.filename.split('.')&.last != 'zip'
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eln_ds = Container.find_by(id: att.attachable_id, container_type: 'dataset')
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return if eln_ds.nil? || eln_ds.parent.nil? || eln_ds.parent&.container_type != 'analysis'
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dsr = []
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ols = nil
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@@ -40,6 +40,8 @@ module Labimotion
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header_style = sheet.styles.add_style(sz: 12, fg_color: 'FFFFFF', bg_color: '00008B', border: { style: :thick, color: 'FF777777', edges: [:bottom] })
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sheet.add_row(['File name', res_name(id)])
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sheet.add_row(['Time', Time.now.strftime("%Y-%m-%d %H:%M:%S %Z")] )
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sheet.add_row(['(This file is automatically generated by the system.)'])
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sheet.add_row([''])
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sheet.add_row([''])
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sheet.add_row(['Fields description of sheet:' + ds.dataset_klass.label])
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sheet.add_row(['Fields', 'Field description'], style: header_style)
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@@ -49,13 +51,11 @@ module Labimotion
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sheet.add_row(['Unit', 'The unit of the field'])
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sheet.add_row(['Name', 'The key of the field, can be used to identify the field'])
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sheet.add_row(['Type', 'The type of the field'])
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sheet.add_row(['
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sheet.add_row(['
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sheet.add_row(['
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sheet.add_row([''])
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sheet.add_row(['Source?', '[Device] from device, [Chemotion] from Chemotion'])
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sheet.add_row(['Source identifier', 'The source identifier'])
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sheet.add_row(['Source data', 'The data from Device or Chemotion, cannot be modified once a generic dataset is created'])
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sheet.add_row([''])
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sheet.add_row([''])
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sheet.add_row(['', '(This file is automatically generated by the system.)'])
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end
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def export(id)
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@@ -84,29 +84,41 @@ module Labimotion
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next if field['type'] == 'dummy'
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type = field['type']
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from_device = field['device'].present? ? '
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from_device = field['system'].present? ? '
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from_device = field['device'].present? ? 'Device' : ''
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from_device = field['system'].present? ? 'Chemotion' : from_device
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type = "#{field['type']}-#{field['option_layers']}" if field['type'] == 'select' || field['type'] == 'system-defined'
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show_value = field['value'] =~ /\A\d+,\d+\z/ ? field['value']&.gsub(',', '.') : field['value']
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sheet.add_row([' ', field['label'],
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sheet.add_row([' ', field['label'], nil, field['value_system'], field['field'], type, from_device, field['dkey'], nil].freeze)
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if %w[system-defined integer].include? field['type']
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sheet.rows.last.cells[2].type = :integer
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sheet.rows.last.cells[8].type = :integer
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else
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sheet.rows.last.cells[2].type = :string
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sheet.rows.last.cells[8].type = :string
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end
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sheet.rows.last.cells[2].value = show_value
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sheet.rows.last.cells[8].value = field['system'] || field['device']
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end
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# sheet.column_widths nil, nil, nil, nil, 0, 0, 0, 0, 0
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end
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end
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def spectra(id)
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name_mapping = []
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wb = @xfile.workbook
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gds = Labimotion::Dataset.find_by(element_id: id, element_type: 'Container')
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cds = Container.find(id)
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cds_csv = cds.attachments.where(aasm_state: 'csv')
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cds_csv = cds.attachments.where(aasm_state: 'csv').order(:filename)
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csv_length = cds_csv.length
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return if csv_length.zero?
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cds_csv.each_with_index do |att, idx|
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name = name.slice(0, (25 - csv_length.to_s.length - 1))
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sheet_name = "#{name}_#{idx}"
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sheet_name = "Sheet#{idx+1}"
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sheet = @xfile.workbook.add_worksheet(name: sheet_name)
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name_mapping.push([sheet_name, att.filename])
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if Labimotion::IS_RAILS5 == true
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File.open(att.store.path) do |fi|
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@@ -122,10 +134,22 @@ module Labimotion
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end
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end
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end
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if name_mapping.length > 1
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first_sheet = @xfile.workbook.worksheets&.first
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header_style = first_sheet&.styles.add_style(sz: 12, fg_color: 'FFFFFF', bg_color: '00008B', border: { style: :thick, color: 'FF777777', edges: [:bottom] })
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first_sheet&.add_row(['Sheet name', 'File name'], style: header_style)
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name_mapping&.each do |mapping|
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next if mapping.length < 2
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@xfile.workbook.worksheets&.first&.add_row([mapping[0].to_s, mapping[1].to_s])
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end
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end
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end
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def header
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['Layer Label', 'Field Label', 'Value', 'Unit', 'Name', 'Type', '
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['Layer Label', 'Field Label', 'Value', 'Unit', 'Name', 'Type', 'Source?', 'Source identifier', 'Source data'].freeze
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end
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def read
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att = Attachment.find_by(id: id, con_state: Labimotion::ConState::NMR)
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return if att.nil?
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if
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result = is_brucker_binary(id)
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if result[:is_bagit] == true
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att.update_column(:con_state, Labimotion::ConState::CONVERTED)
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Labimotion::Converter.metadata(id)
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Labimotion::ConState::COMPLETED
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elsif result[:metadata] == nil
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Labimotion::ConState::NONE
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else
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data = process(att, id, content)
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@@ -29,7 +33,9 @@ module Labimotion
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zip_file.each do |entry|
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if entry.name.include?('/pdata/') && entry.name.include?('parm.txt')
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metadata = entry.get_input_stream.read.force_encoding('UTF-8')
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return metadata
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return { is_bagit: false, metadata: metadata }
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elsif entry.name.include?('metadata/') && entry.name.include?('converter.json')
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return { is_bagit: true, metadata: nil }
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end
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end
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end
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zip_file.each do |entry|
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if entry.name.include?('/pdata/') && entry.name.include?('parm.txt')
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metadata = entry.get_input_stream.read.force_encoding('UTF-8')
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return metadata
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return { is_bagit: false, metadata: metadata }
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elsif entry.name.include?('metadata/') && entry.name.include?('converter.json')
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return { is_bagit: true, metadata: nil }
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end
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end
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end
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end
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end
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nil
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{ is_bagit: false, metadata: nil }
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end
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def self.process(att, id, content)
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data/lib/labimotion/version.rb
CHANGED
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## Labimotion Version
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module Labimotion
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IS_RAILS5 = false
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VERSION_REPO = '0.3.1'
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VERSION = Labimotion::VERSION_REPO if Labimotion::IS_RAILS5 == true
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VERSION = Labimotion::VERSION_ELN if Labimotion::IS_RAILS5 == false
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VERSION = '1.1.0'
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end
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data/lib/labimotion.rb
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end
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def self.log_exception(exception, current_user = nil)
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Labimotion.logger.error("version: #{Labimotion::VERSION};
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Labimotion.logger.error("version: #{Labimotion::VERSION}; (#{current_user&.id}) \n Exception: #{exception.message}")
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Labimotion.logger.error(exception.backtrace.join("\n"))
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end
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metadata
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--- !ruby/object:Gem::Specification
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name: labimotion
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version: !ruby/object:Gem::Version
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version: 1.0
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version: 1.1.0
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platform: ruby
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authors:
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- Chia-Lin Lin
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autorequire:
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bindir: bin
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cert_chain: []
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date:
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date: 2024-01-12 00:00:00.000000000 Z
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dependencies:
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- !ruby/object:Gem::Dependency
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name: rails
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@@ -116,7 +116,7 @@ required_rubygems_version: !ruby/object:Gem::Requirement
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- !ruby/object:Gem::Version
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version: '0'
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requirements: []
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rubygems_version: 3.
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rubygems_version: 3.1.6
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signing_key:
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specification_version: 4
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summary: Chemotion LabIMotion
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