Class: Robot::Verification::Base

Inherits:
Object
  • Object
show all
Defined in:
app/models/robot/verification/base.rb

Overview

Base class for handling bed verification for picking robots

Direct Known Subclasses

SourceDestBeds, SourceDestControlBeds

Instance Attribute Summary collapse

Instance Method Summary collapse

Instance Attribute Details

#errors ⇒ Object (readonly)

rubocop:todo Metrics/ClassLength



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# File 'app/models/robot/verification/base.rb', line 5

has_metadata do
  # NOTE: The following attribute is not required for Microarray Genotyping.
  # I think this might be broken and suggests that there should be separate classes for project: one for
  # next-gen sequencing that includes this attribute in it's metadata, and one for microarray genotyping
  # that doesn't.
  include ProjectManager::Associations
  include BudgetDivision::Associations

  custom_attribute(:project_cost_code, required: true)
  custom_attribute(:funding_comments)
  custom_attribute(:collaborators)
  custom_attribute(:external_funding_source)
  custom_attribute(:sequencing_budget_cost_centre)
  custom_attribute(:project_funding_model, in: PROJECT_FUNDING_MODELS)
  custom_attribute(:gt_committee_tracking_id)

  before_validation do |record|
    record.project_cost_code = nil if record.project_cost_code.blank?
    record.project_funding_model = nil if record.project_funding_model.blank?
  end
end

Instance Method Details

#all_picks(batch, max_beds) ⇒ Object

Returns all pick information by destination_bed barcode }}

Examples:

{ 'DN3R' => {
 1 => [{'DN3R'=>1},{'DN1S'=>1, 'DN2T'=>2}, {}]

Parameters:

  • batch (Batch) —

    The batch to get the pick-list for

  • max_beds (Integer) —

    The max_beds for plates on the robot



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# File 'app/models/robot/verification/base.rb', line 66

has_metadata do
  # NOTE: The following attribute is not required for Microarray Genotyping.
  # I think this might be broken and suggests that there should be separate classes for project: one for
  # next-gen sequencing that includes this attribute in it's metadata, and one for microarray genotyping
  # that doesn't.
  include ProjectManager::Associations
  include BudgetDivision::Associations

  custom_attribute(:project_cost_code, required: true)
  custom_attribute(:funding_comments)
  custom_attribute(:collaborators)
  custom_attribute(:external_funding_source)
  custom_attribute(:sequencing_budget_cost_centre)
  custom_attribute(:project_funding_model, in: PROJECT_FUNDING_MODELS)
  custom_attribute(:gt_committee_tracking_id)

  before_validation do |record|
    record.project_cost_code = nil if record.project_cost_code.blank?
    record.project_funding_model = nil if record.project_funding_model.blank?
  end
end

#pick_number_to_expected_layout(batch, destination_plate_barcode, max_beds) ⇒ Object

Returns a hash of { pick_number => layout_data_object }, for a batch and a specific destination plate pick_number is a sequential number, starting at 1 layout_data_object is an array of hashes: 1st Element: Hash of destination plate barcodes and their sort position 2nd Element: Hash of source plate barcodes and their sort position 3rd Element: Hash of control plate barcodes and their sort position when appropriate. (nil otherwise) @example ['DN3R'=>1,'DN2T'=>2, {}] There will only be more than one pick if the number of source plates exceed the max plates allowed on the robot and therefore more than one pick is needed to transfer from all the wells onto the destination plate



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# File 'app/models/robot/verification/base.rb', line 52

has_metadata do
  # NOTE: The following attribute is not required for Microarray Genotyping.
  # I think this might be broken and suggests that there should be separate classes for project: one for
  # next-gen sequencing that includes this attribute in it's metadata, and one for microarray genotyping
  # that doesn't.
  include ProjectManager::Associations
  include BudgetDivision::Associations

  custom_attribute(:project_cost_code, required: true)
  custom_attribute(:funding_comments)
  custom_attribute(:collaborators)
  custom_attribute(:external_funding_source)
  custom_attribute(:sequencing_budget_cost_centre)
  custom_attribute(:project_funding_model, in: PROJECT_FUNDING_MODELS)
  custom_attribute(:gt_committee_tracking_id)

  before_validation do |record|
    record.project_cost_code = nil if record.project_cost_code.blank?
    record.project_funding_model = nil if record.project_funding_model.blank?
  end
end

#pick_numbers(batch, destination_plate_barcode, max_beds) ⇒ Array<String>

Note:

Added as I refactor the batches/_assets.html.erb page. Currently just wraps pick_number_to_expected_layout and as a result performs a lot of unnecessary work.

Returns an array of all pick numbers associated with the corresponding batch and plate_barcode

Parameters:

  • batch (Batch) —

    The Batch to get pick numbers for

  • destination_plate_barcode (String) —

    The barcode of the destination plate

  • max_beds (Integer) —

    The max_beds for plates on the robot

Returns:

  • (Array<String>) —

    Array of pick numbers associated with the batch/plate



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# File 'app/models/robot/verification/base.rb', line 39

has_metadata do
  # NOTE: The following attribute is not required for Microarray Genotyping.
  # I think this might be broken and suggests that there should be separate classes for project: one for
  # next-gen sequencing that includes this attribute in it's metadata, and one for microarray genotyping
  # that doesn't.
  include ProjectManager::Associations
  include BudgetDivision::Associations

  custom_attribute(:project_cost_code, required: true)
  custom_attribute(:funding_comments)
  custom_attribute(:collaborators)
  custom_attribute(:external_funding_source)
  custom_attribute(:sequencing_budget_cost_centre)
  custom_attribute(:project_funding_model, in: PROJECT_FUNDING_MODELS)
  custom_attribute(:gt_committee_tracking_id)

  before_validation do |record|
    record.project_cost_code = nil if record.project_cost_code.blank?
    record.project_funding_model = nil if record.project_funding_model.blank?
  end
end

#record_plate_types(plate_types_params) ⇒ Object

rubocop:enable Metrics/AbcSize, Metrics/MethodLength, Metrics/PerceivedComplexity



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# File 'app/models/robot/verification/base.rb', line 112

has_metadata do
  # NOTE: The following attribute is not required for Microarray Genotyping.
  # I think this might be broken and suggests that there should be separate classes for project: one for
  # next-gen sequencing that includes this attribute in it's metadata, and one for microarray genotyping
  # that doesn't.
  include ProjectManager::Associations
  include BudgetDivision::Associations

  custom_attribute(:project_cost_code, required: true)
  custom_attribute(:funding_comments)
  custom_attribute(:collaborators)
  custom_attribute(:external_funding_source)
  custom_attribute(:sequencing_budget_cost_centre)
  custom_attribute(:project_funding_model, in: PROJECT_FUNDING_MODELS)
  custom_attribute(:gt_committee_tracking_id)

  before_validation do |record|
    record.project_cost_code = nil if record.project_cost_code.blank?
    record.project_funding_model = nil if record.project_funding_model.blank?
  end
end

#valid_submission?(params) ⇒ Boolean

rubocop:todo Metrics/PerceivedComplexity, Metrics/MethodLength, Metrics/AbcSize

Returns:

  • (Boolean) 


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# File 'app/models/robot/verification/base.rb', line 76

has_metadata do
  # NOTE: The following attribute is not required for Microarray Genotyping.
  # I think this might be broken and suggests that there should be separate classes for project: one for
  # next-gen sequencing that includes this attribute in it's metadata, and one for microarray genotyping
  # that doesn't.
  include ProjectManager::Associations
  include BudgetDivision::Associations

  custom_attribute(:project_cost_code, required: true)
  custom_attribute(:funding_comments)
  custom_attribute(:collaborators)
  custom_attribute(:external_funding_source)
  custom_attribute(:sequencing_budget_cost_centre)
  custom_attribute(:project_funding_model, in: PROJECT_FUNDING_MODELS)
  custom_attribute(:gt_committee_tracking_id)

  before_validation do |record|
    record.project_cost_code = nil if record.project_cost_code.blank?
    record.project_funding_model = nil if record.project_funding_model.blank?
  end
end

#validate_barcode_params(barcode_hash) ⇒ Object

rubocop:todo Metrics/PerceivedComplexity, Metrics/MethodLength, Metrics/AbcSize



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# File 'app/models/robot/verification/base.rb', line 8

has_metadata do
  # NOTE: The following attribute is not required for Microarray Genotyping.
  # I think this might be broken and suggests that there should be separate classes for project: one for
  # next-gen sequencing that includes this attribute in it's metadata, and one for microarray genotyping
  # that doesn't.
  include ProjectManager::Associations
  include BudgetDivision::Associations

  custom_attribute(:project_cost_code, required: true)
  custom_attribute(:funding_comments)
  custom_attribute(:collaborators)
  custom_attribute(:external_funding_source)
  custom_attribute(:sequencing_budget_cost_centre)
  custom_attribute(:project_funding_model, in: PROJECT_FUNDING_MODELS)
  custom_attribute(:gt_committee_tracking_id)

  before_validation do |record|
    record.project_cost_code = nil if record.project_cost_code.blank?
    record.project_funding_model = nil if record.project_funding_model.blank?
  end
end