sanger/sequencescape

# frozen_string_literal: true
# Despite name controls rendering of warehouse messages for {Study}
# Historically used to be v0.5 API
class Api::StudyIO < Api::Base
  module Extensions
    module ClassMethods
      def render_class
        Api::StudyIO
      end
    end

    def self.included(base)
      base.class_eval do
        extend ClassMethods

        scope :including_associations_for_json,
              -> do
                includes(
                  [
                    :uuid_object,
                    {
                      study_metadata: %i[faculty_sponsor reference_genome study_type data_release_study_type],
                      roles: :users
                    }
                  ]
                )
              end
      end
    end

    def render_class
      Api::StudyIO
    end
  end

  renders_model(::Study)

  map_attribute_to_json_attribute(:uuid)
  map_attribute_to_json_attribute(:id)
  map_attribute_to_json_attribute(:name)
  map_attribute_to_json_attribute(:ethically_approved)
  map_attribute_to_json_attribute(:state)
  map_attribute_to_json_attribute(:created_at)
  map_attribute_to_json_attribute(:updated_at)

  extra_json_attributes do |object, json_attributes|
    json_attributes['abbreviation'] = object.abbreviation

    object.roles.each do |role|
      role_key = role.name.downcase.gsub(/\s+/, '_')
      json_attributes[role_key] ||= []
      role.user_role_bindings.each do |user_role|
        json_attributes[role_key] << {
          login: user_role.user.login,
          email: user_role.user.email,
          name: user_role.user.name
        }
        json_attributes['updated_at'] = [json_attributes['updated_at'], user_role.updated_at].compact.max
      end
    end
  end

  with_association(:study_metadata) do
    with_association(:faculty_sponsor, lookup_by: :name) { map_attribute_to_json_attribute(:name, 'sac_sponsor') }

    with_association(:reference_genome, lookup_by: :name) { map_attribute_to_json_attribute(:name, 'reference_genome') }
    map_attribute_to_json_attribute(:prelim_id, 'prelim_id')
    map_attribute_to_json_attribute(:study_ebi_accession_number, 'accession_number')
    map_attribute_to_json_attribute(:study_description, 'description')
    map_attribute_to_json_attribute(:study_abstract, 'abstract')
    with_association(:study_type, lookup_by: :name) { map_attribute_to_json_attribute(:name, 'study_type') }

    map_attribute_to_json_attribute(:study_project_id, 'ena_project_id')
    map_attribute_to_json_attribute(:study_study_title, 'study_title')
    map_attribute_to_json_attribute(:study_sra_hold, 'study_visibility')

    map_attribute_to_json_attribute(:contaminated_human_dna)
    map_attribute_to_json_attribute(:contains_human_dna)
    map_attribute_to_json_attribute(:commercially_available)
    with_association(:data_release_study_type, lookup_by: :name) do
      map_attribute_to_json_attribute(:name, 'data_release_sort_of_study')
    end
    map_attribute_to_json_attribute(:remove_x_and_autosomes?, 'remove_x_and_autosomes')
    map_attribute_to_json_attribute(:separate_y_chromosome_data)

    map_attribute_to_json_attribute(:data_release_strategy)
    map_attribute_to_json_attribute(:ega_dac_accession_number)
    map_attribute_to_json_attribute(:array_express_accession_number)
    map_attribute_to_json_attribute(:ega_policy_accession_number)

    map_attribute_to_json_attribute(:data_release_timing)
    map_attribute_to_json_attribute(:data_release_delay_period)
    map_attribute_to_json_attribute(:data_release_delay_reason)

    map_attribute_to_json_attribute(:data_access_group)

    map_attribute_to_json_attribute(:bam, 'alignments_in_bam')
    map_attribute_to_json_attribute(:prelim_id)
    map_attribute_to_json_attribute(:hmdmc_approval_number, 'hmdmc_number')
    map_attribute_to_json_attribute(:s3_email_list)
    map_attribute_to_json_attribute(:data_deletion_period)
    map_attribute_to_json_attribute(:contaminated_human_data_access_group)
    with_association(:program, lookup_by: :id) { map_attribute_to_json_attribute(:name, 'programme') }
  end
end