Class: StudyType

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

Overview

Note:

Study::Metadata#study_type_valid? has hard-coded validation to prevent the 'Not specified' study type from being used. This should probably be updated to use the #valid_for_creation flag. I'm also not sure of having 'Not specified' be a specific database entry, although it has been assigned to several historic studies so does at least allow a not_nil constraint.

On Study creation the user selects a StudyType from a drop down list of pre-registered study types.

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)
  • As <STUDY_TYPE existing_study_type="..." /> during study accessioning with the EBI

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

#vaild_type ⇒ Boolean

Returns Indicates the study type is recognised by the EBI. If false the accessioned study will contain <STUDY_TYPE existing_study_type="Other" new_study_type="<study_type.name>"/> instead of <STUDY_TYPE existing_study_type="<study_type.name>"/>.

Returns:

  • (Boolean) —

    Indicates the study type is recognised by the EBI. If false the accessioned study will contain <STUDY_TYPE existing_study_type="Other" new_study_type="<study_type.name>"/> instead of <STUDY_TYPE existing_study_type="<study_type.name>"/>



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# File 'app/models/study_type.rb', line 28

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_for_creation ⇒ Boolean

Returns Indicates a study can be created with this option (determines if it appears in the dropdown).

Returns:

  • (Boolean) —

    Indicates a study can be created with this option (determines if it appears in the dropdown)



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# File 'app/models/study_type.rb', line 28

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

.include?(studytype_name) ⇒ Boolean

Returns:

  • (Boolean) 


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# File 'app/models/study_type.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