Class: SequenomQcPlate

Inherits:
Plate show all
Defined in:
app/models/sequenom_qc_plate.rb

Overview

Sequenom was a geneotyping process in which four 96 well parent plates were transferred onto a single 384 well plate prior to genotyping. The four plates were interlaced such that: A1: Plate 1, well A1 A2: Plate 2, well A1 B1: Plate 3, well A1 B2: Plate 4, well A1 The remaining methods allow legacy Sequenom plates to get viewed.

Constant Summary

Constants included from Metadata

Metadata::SECTION_FIELDS

Instance Attribute Summary collapse

Attributes included from AssetRefactor::Labware::Methods

#storage_location_service

Class Method Summary collapse

Instance Method Summary collapse

Methods inherited from Plate

#after_comment_addition, #all_submission_ids, #ancestor_of_purpose, #ancestors_of_purpose, #buffer_required?, #cherrypick_completed, #comments, #compatible_purposes, #convert_to, create_with_barcode!, #details, #find_well_by_name, #generate_barcode, #height, #iteration, #labware_type, #maps, #name_for_label, #number_of_blank_samples, #occupied_well_count, #plate_columns, plate_ids_from_requests, #plate_rows, #plate_type, #plate_type=, #priority, #related_studies, safe_sanger_barcode, #sanger_barcode=, #scored?, search_for_plates, #source_plate, #state, #stock_plate, #stock_plate?, #stock_role, #stock_wells, #subject_type, #submission_ids, #submission_ids_as_source, #submissions, #summary_hash, #team, #transition_to, #update_qc_values_with_parser, #update_volume, #valid_positions?, #well_hash, #width

Methods included from Metadata

#has_metadata, required_tags

Methods included from QcFile::Associations

#has_qc_files

Methods included from AssetRefactor::Labware::Methods

#labware, #labwhere_location, #scanned_in_date, #storage_location

Methods included from PlateCreation::CreationChild

included

Methods included from SubmissionPool::Association::Plate

included

Methods included from Plate::FluidigmBehaviour

#apply_fluidigm_data, included, #retrieve_fluidigm_data

Methods included from Asset::Ownership::Owned

#change_owner_to, included

Methods included from Barcode::Barcodeable

#aker_barcode, #aker_barcode=, #any_barcode_matching?, #barcode_format, #barcode_number, #cgap_barcode, #cgap_barcode=, #external_barcode, #external_barcode=, #external_identifier, #fluidigm_barcode, #fluidigm_barcode=, #generate_barcode, included, #infinium_barcode, #infinium_barcode=, #prefix, #primary_barcode, #printable_target, #sanger_barcode

Methods included from Transfer::State::PlateState

included

Methods included from Transfer::Associations

included

Methods included from Api::PlateIO::Extensions

included, #json_root

Methods inherited from Labware

#display_name, #generate_name, #human_barcode

Methods inherited from Asset

#add_parent, #ancestor_of_purpose, #asset_type_for_request_types, #assign_relationships, #barcode_number, #compatible_purposes, #contained_samples, #details, #external_identifier, #generate_barcode, #get_qc_result_value_for, #has_stock_asset?, #label, #label=, #original_stock_plates, #prefix, #printable?, #printable_target, #register_stock!, #request_types, #role, #source_plate, #spiked_in_buffer, #summary_hash, #type, #update_from_qc

Methods included from EventfulRecord

#has_many_events, #has_many_lab_events, #has_one_event_with_family

Methods included from Event::PlateEvents

#event_date, #fluidigm_stamp_date, #gel_qc_date, #pico_date, #qc_started_date, #sequenom_stamp_date

Methods inherited from ApplicationRecord

convert_labware_to_receptacle_for, find_by_id_or_name, find_by_id_or_name!

Methods included from Warren::BroadcastMessages

#broadcast, included, #queue_associated_for_broadcast, #queue_for_broadcast, #warren

Instance Attribute Details

#gender_check_bypassObject

Returns the value of attribute gender_check_bypass


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# File 'app/models/sequenom_qc_plate.rb', line 15

def gender_check_bypass
  @gender_check_bypass
end

#plate_prefixObject

Returns the value of attribute plate_prefix


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# File 'app/models/sequenom_qc_plate.rb', line 16

def plate_prefix
  @plate_prefix
end

#user_barcodeObject

Returns the value of attribute user_barcode


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# File 'app/models/sequenom_qc_plate.rb', line 17

def user_barcode
  @user_barcode
end

Class Method Details

.default_purposeObject


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# File 'app/models/sequenom_qc_plate.rb', line 21

def self.default_purpose
  PlatePurpose.create_with(size: default_plate_size).find_or_create_by!(name: 'Sequenom')
end

Instance Method Details

#source_platesObject


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# File 'app/models/sequenom_qc_plate.rb', line 25

def source_plates
  return [] if parents.empty?

  source_barcodes.map do |plate_barcode|
    if plate_barcode.blank?
      nil
    else
      parents.detect { |plate| plate.barcode_number == plate_barcode }
    end
  end
end