Class: BulkSubmission

Inherits:
Object
  • Object
show all
Extended by:
ActiveModel::Naming
Includes:
ActiveModel::AttributeMethods, ActiveModel::Conversion, ActiveModel::Validations, ManifestUtil, Submission::AssetSubmissionFinder, Submission::ValidationsByTemplateName
Defined in:
app/models/bulk_submission.rb

Overview

A bulk submission is created through the upload of a spreadsheet (csv) It contains the information for setting up one or more submissions, allowing for the quick request of multiple pieces of work simultaneously. Bulk Submissions are not currently persisted.

Constant Summary collapse

DEFAULT_ENCODING =

This is the default output from excel

'Windows-1252'
COMMON_FIELDS =

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

[
  # Needed to construct the submission ...
  'template name',
  'study id',
  'study name',
  'project id',
  'project name',
  'submission name',
  'user login',
  # Needed to identify the assets and what happens to them ...
  'asset group id',
  'asset group name',
  'fragment size from',
  'fragment size to',
  'pcr cycles',
  'primer panel',
  'read length',
  'library type',
  'bait library',
  'bait library name',
  'comments',
  'number of lanes',
  'pre-capture plex level',
  'pre-capture group',
  'gigabases expected',
  'priority',
  'flowcell type',
  'scrna core number of pools',
  'scrna core cells per chip well',
  '% phix requested',
  'low diversity',
  'ot recipe',
  'wafer size'
].freeze
ALIAS_FIELDS = 
{ 'plate barcode' => 'barcode', 'tube barcode' => 'barcode' }.freeze

Constants included from Submission::ValidationsByTemplateName

Submission::ValidationsByTemplateName::HEADER_BARCODE, Submission::ValidationsByTemplateName::HEADER_CELLS_PER_CHIP_WELL, Submission::ValidationsByTemplateName::HEADER_NUMBER_OF_POOLS, Submission::ValidationsByTemplateName::HEADER_PLATE_WELLS, Submission::ValidationsByTemplateName::HEADER_PROJECT_NAME, Submission::ValidationsByTemplateName::HEADER_STUDY_NAME, Submission::ValidationsByTemplateName::HEADER_TEMPLATE_NAME, Submission::ValidationsByTemplateName::SAMPLES_PER_POOL, Submission::ValidationsByTemplateName::SCRNA_CORE_CDNA_PREP_GEM_X_5P

Constants included from Submission::ScrnaCoreCdnaPrepFeasibilityValidator

Submission::ScrnaCoreCdnaPrepFeasibilityValidator::I18N_SCOPE_SCRNA_CORE_CDNA_PREP_FEASIBILITY_VALIDATOR

Constants included from Submission::ScrnaCoreCdnaPrepFeasibilityCalculator

Submission::ScrnaCoreCdnaPrepFeasibilityCalculator::ALLOWANCE_BANDS, Submission::ScrnaCoreCdnaPrepFeasibilityCalculator::HEADER_BARCODE, Submission::ScrnaCoreCdnaPrepFeasibilityCalculator::HEADER_CELLS_PER_CHIP_WELL, Submission::ScrnaCoreCdnaPrepFeasibilityCalculator::HEADER_NUMBER_OF_POOLS, Submission::ScrnaCoreCdnaPrepFeasibilityCalculator::HEADER_PLATE_WELL, Submission::ScrnaCoreCdnaPrepFeasibilityCalculator::SCRNA_CORE_CDNA_PREP_GEM_X_5P

Instance Attribute Summary collapse

Instance Method Summary collapse

Methods included from ManifestUtil

#filter_end_of_header, #is_end_of_header?

Methods included from Submission::ValidationsByTemplateName

#apply_additional_validations_by_template_name, #apply_number_of_samples_per_pool_validation, #group_rows_by_study_and_project, #submission_template_name, #validate_consistent_column_value

Methods included from Submission::ScrnaCoreCdnaPrepFeasibilityValidator

#validate_required_headers, #validate_scrna_core_cdna_prep_feasibility

Methods included from Submission::ScrnaCoreCdnaPrepFeasibilityCalculator

#calculate_allowance_bands, #calculate_chip_loading_volume, #calculate_resuspension_volume, #calculate_total_cells_in_300ul, #calculate_volume_needed

Methods included from Submission::AssetSubmissionFinder

#find_all_assets_by_name_including_samples!, #find_tubes_including_samples_for!, #find_wells_including_samples_for!, #is_plate?, #is_tube?

Constructor Details

#initialize(attrs = {}) ⇒ BulkSubmission

Returns a new instance of BulkSubmission.



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# File 'app/models/bulk_submission.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

Instance Attribute Details

#encoding ⇒ Object

Returns the value of attribute encoding.



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# File 'app/models/bulk_submission.rb', line 37

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

#spreadsheet ⇒ Object

Returns the value of attribute spreadsheet.



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# File 'app/models/bulk_submission.rb', line 37

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

#add_study_to_assets(assets, study) ⇒ Object 



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# File 'app/models/bulk_submission.rb', line 333

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

#assign_value_if_source_present(source_obj, source_key, target_obj, target_key) ⇒ Object

Assigns a value from the source object to the target object if the source value is present.

Parameters:

  • source_obj (Hash) —

    The source object containing the value to be assigned.

  • source_key (String, Symbol) —

    The key to look up the value in the source object.

  • target_obj (Hash) —

    The target object where the value will be assigned.

  • target_key (String, Symbol) —

    The key to assign the value in the target object.



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# File 'app/models/bulk_submission.rb', line 343

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

#calculated_request_options_by_template_name(details) ⇒ Hash

This method checks the 'template name' from the provided details and, if applicable, adds additional request options. Currently, it supports the SCRNA_CORE_CDNA_PREP_GEM_X_5P template by including an allowance_band value.

The allowance_band values are determined based on the study and project name.

Parameters:

  • details (Hash) —

    The submission details, which should include:

    • 'template name' (String) for validation.
    • 'study name' (String) and 'project name' (String) for extracting the corresponding allowance_band value.

Returns:

  • (Hash) —

    The request options to be added, e.g., { 'allowance_band' => '2 pool attempts, 2 counts' }.



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# File 'app/models/bulk_submission.rb', line 383

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

#completed_submissions ⇒ Object

This is used to present a list of successes



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# File 'app/models/bulk_submission.rb', line 504

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

#extract_request_options(details) ⇒ Object 



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# File 'app/models/bulk_submission.rb', line 347

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

#find_template(template_name) ⇒ Object

Returns the SubmissionTemplate and checks that it is valid

Raises:

  • (StandardError) 


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# File 'app/models/bulk_submission.rb', line 495

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

#id ⇒ Object 



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# File 'app/models/bulk_submission.rb', line 48

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

#persisted? ⇒ Boolean

Returns:

  • (Boolean) 


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# File 'app/models/bulk_submission.rb', line 44

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

#prepare_order(details) ⇒ Object

Returns an order for the given details rubocop:todo Metrics/PerceivedComplexity, Metrics/MethodLength, Metrics/AbcSize



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# File 'app/models/bulk_submission.rb', line 391

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

#process ⇒ Object

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



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# File 'app/models/bulk_submission.rb', line 150

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

#process_file ⇒ Object

rubocop:todo Metrics/MethodLength



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# File 'app/models/bulk_submission.rb', line 69

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

#shared_options!(rows) ⇒ Object

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



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# File 'app/models/bulk_submission.rb', line 317

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

#submission_structure ⇒ Object

Process CSV into a structure this creates an array containing a hash for each distinct "submission name" "submission name" => array of orders where each order is a hash of headers to values (grouped by "asset group name") rubocop:todo Metrics/PerceivedComplexity, Metrics/MethodLength, Metrics/AbcSize



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# File 'app/models/bulk_submission.rb', line 279

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

#translate(header) ⇒ Object 



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# File 'app/models/bulk_submission.rb', line 262

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_header? ⇒ Boolean

Returns:

  • (Boolean) 


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# File 'app/models/bulk_submission.rb', line 125

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

#warnings ⇒ ActiveModel::Errors

Returns the warnings collection for the BulkSubmission object. Initialises the warnings collection if it does not exist yet. The collection is used for showing informative warning messages to the user after the bulk submission has been processed successfully.

Returns:

  • (ActiveModel::Errors) —

    the warnings collection



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# File 'app/models/bulk_submission.rb', line 62

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