Class: TagLayout

Inherits:
ApplicationRecord show all
Includes:
Asset::Ownership::ChangesOwner, Uuid::Uuidable
Defined in:
app/models/tag_layout.rb

Overview

Lays out the tags in the specified tag group in a particular pattern.

In pulldown they use only one set of tags and put them into wells in a particular pattern: by columns, or by rows. Depending on the size of the tag group that is used by the layout template it either repeats (for example, 8 tags in the group laid out in columns would repeat the tags across the plate), or it doesn't (for example, a 96 tag group would occupy an entire 96 well plate).

Defined Under Namespace

Modules: CombByRows, InColumns, InColumnsThenColumns, InColumnsThenRows, InInverseColumns, InInverseRows, InRows Classes: AsFixedGroupByPlate, AsGroupByPlate, CombinatorialSequential, DualIndexWalker, Quadrants, TemplateSubmission, WalkManualWellsByPools, WalkManualWellsOfPlate, WalkWellsByPools, WalkWellsOfPlate, Walker

Constant Summary collapse

DIRECTION_ALGORITHMS = 
{
  'column' => 'TagLayout::InColumns',
  'row' => 'TagLayout::InRows',
  'inverse column' => 'TagLayout::InInverseColumns',
  'inverse row' => 'TagLayout::InInverseRows',
  'column then row' => 'TagLayout::InColumnsThenRows',
  'column then column' => 'TagLayout::InColumnsThenColumns',
  'combinatorial by row' => 'TagLayout::CombByRows'
}.freeze
WALKING_ALGORITHMS = 
{
  'wells in pools' => 'TagLayout::WalkWellsByPools',
  'wells of plate' => 'TagLayout::WalkWellsOfPlate',
  'manual by pool' => 'TagLayout::WalkManualWellsByPools',
  'as group by plate' => 'TagLayout::AsGroupByPlate',
  'manual by plate' => 'TagLayout::WalkManualWellsOfPlate',
  'quadrants' => 'TagLayout::Quadrants',
  'as fixed group by plate' => 'TagLayout::AsFixedGroupByPlate',
  'combinatorial sequential' => 'TagLayout::CombinatorialSequential'
}.freeze

Instance Attribute Summary collapse

Instance Method Summary collapse

Methods included from Asset::Ownership::ChangesOwner

included

Methods included from Uuid::Uuidable

included, #unsaved_uuid!, #uuid

Methods inherited from ApplicationRecord

alias_association, convert_labware_to_receptacle_for, find_by_id_or_name, find_by_id_or_name!

Methods included from Squishify

extended

Methods included from Warren::Callback::ExceptExternallyManaged

#broadcast_except_externally_managed, included

Instance Attribute Details

#replace_tags ⇒ Object

When true, the layout replaces the existing tags of the aliquots. Without a tag2 group, it removes their existing tag2 instead of keeping it. Used when tags are added to aliquots that are already tagged, e.g. Ultima tags on Illumina libraries.



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# File 'app/models/tag_layout.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

#tags_per_well ⇒ Object

Returns the value of attribute tags_per_well.



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# File 'app/models/tag_layout.rb', line 12

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

#direction=(new_direction) ⇒ Object 



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# File 'app/models/tag_layout.rb', line 79

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

#direction_algorithm_module ⇒ Object 



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# File 'app/models/tag_layout.rb', line 91

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

#walking_by=(walk) ⇒ Object 



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# File 'app/models/tag_layout.rb', line 83

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

#wells_in_walking_order ⇒ Object 



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# File 'app/models/tag_layout.rb', line 87

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