Class: WorkflowsController

Inherits:
ApplicationController show all
Includes:
Tasks::CherrypickHandler, Tasks::PlateTemplateHandler, Tasks::PlateTransferHandler, Tasks::SetDescriptorsHandler
Defined in:
app/controllers/workflows_controller.rb

Overview

Note:

A large amount of the task processing actually occurs within the controller. These methods are included via the various Handler modules.

Controls progress through the tasks in a Workflow as part of taking a Batch through a Pipeline

#stage is the main processing step, and responds to all HTTP methods. The currently active task is supplied by params

If params is nil it will render the page associated with the current Task using Task#render_task If params is present it will perform the current Task using Task#do_task before incrementing the stage and rendering the next task. If there are no further tasks present, it will redirect to the finish_batch page.

Constant Summary

Constants included from FlashTruncation

FlashTruncation::STRING_OVERHEAD

Instance Attribute Summary collapse

Instance Method Summary collapse

Methods included from Tasks::SetDescriptorsHandler

#render_set_descriptors_task

Methods included from Tasks::PlateTransferHandler

#do_plate_transfer_task, #find_or_create_target, #includes_for_plate_creation, #render_plate_transfer_task, #target_plate

Methods included from Tasks::PlateTemplateHandler

generate_spreadsheet, #render_plate_template_task

Methods included from Tasks::CherrypickHandler

#do_cherrypick_task, included, #render_cherrypick_task, #setup_input_params_for_pass_through

Methods inherited from ApplicationController

#block_api_access, #evil_parameter_hack!, #extract_header_info, #set_cache_disabled!

Methods included from AuthenticatedSystem

included

Methods included from FlashTruncation

#max_flash_size, #truncate_flash, #truncate_flash_array

Instance Attribute Details

#batch ⇒ Object

Returns the value of attribute batch.



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# File 'app/controllers/workflows_controller.rb', line 21

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

#plate_purpose_options ⇒ Object

Returns the value of attribute plate_purpose_options.



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# File 'app/controllers/workflows_controller.rb', line 21

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_layout ⇒ Object

Returns the value of attribute spreadsheet_layout.



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# File 'app/controllers/workflows_controller.rb', line 21

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

#render_task(task, params) ⇒ Object

Default render task activity, eg. from Task#render_task



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# File 'app/controllers/workflows_controller.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

#stage ⇒ Object

TODO: This needs to be made RESTful. 1: Routes need to be refactored to provide more sensible urls 2: We call them tasks in the code, and stages in the URL. They should be consistent 3: This endpoint currently does two jobs, executing the current task, and rendering the next 4: Some tasks rely on parameters passed in from the previous task. This isn't ideal, but it might be worth maintaining the behaviour until we solve the problems. 5: We need to improve the repeatability of tasks. 6: GET should be Idempotent. doing a task should be a POST rubocop:todo Metrics/PerceivedComplexity, Metrics/MethodLength, Metrics/AbcSize



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# File 'app/controllers/workflows_controller.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