Class: DataReleaseStudyType

Inherits:
ApplicationRecord show all
Extended by:
Attributable::Association::Target
Defined in:
app/models/data_release_study_type.rb

Overview

On Study creation the user selects a DataReleaseStudyType from a drop down list of pre-registered data release study types. The default option is determined by the #is_default flag in the database

This information is exposed:

  • In the warehouses, where it may be used by customers, NPG, or bioinformaticians
  • Via the V1 API. (Not aware of any uses here, but there may be)

It drives specific behaviours:

  • Shows the array express accession field on study edit page if #for_array_express is true
  • Determines if the tag is added to the study accession
  • Determines the list of valid delay reasons

See Also:

Defined Under Namespace

Modules: Associations

Instance Attribute Summary collapse

Class Method Summary collapse

Methods included from Attributable::Association::Target

default, extended, for_select_association

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

Instance Attribute Details

#for_array_express ⇒ Boolean

Determines if the study needs an ArrayExpress accession number and adds an tag to the study.xml. (This used to trigger generation of an ArrayExpress accession, but I'm not sure this is still the case)

Returns:

  • (Boolean) —

    True if the associated study needs ArrayExpress accession numbers



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# File 'app/models/data_release_study_type.rb', line 32

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

#is_assay_type ⇒ Boolean

Controls whether 'assay of no other use' as acceptable reason for a delay in data-release in app/views/shared/metadata/edit/_study.html.erb

Returns:

  • (Boolean) —

    True if 'assay of no other use' is a valid delay reason



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# File 'app/models/data_release_study_type.rb', line 32

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

#is_default ⇒ Boolean

Should be true for single option, sets it as the default DataReleaseStudyType

Returns:

  • (Boolean) —

    True if a default, false otherwise



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# File 'app/models/data_release_study_type.rb', line 32

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

Class Method Details

.default ⇒ DataReleaseStudyType

Returns the default DataReleaseStudyType according to the is_default flag.

Returns:



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# File 'app/models/data_release_study_type.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