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pulibrary / tigerdata-app / c4214121-fbbb-4bc6-b44a-565342302937

30 Jul 2025 08:03PM UTC coverage: 75.796% (+0.2%) from 75.625%
c4214121-fbbb-4bc6-b44a-565342302937

Pull #1666

circleci

hectorcorrea
Rubocop made me do it
Pull Request #1666: Refactor project creation in Mediaflux

0 of 3 new or added lines in 2 files covered. (0.0%)

28 existing lines in 2 files now uncovered.

2239 of 2954 relevant lines covered (75.8%)

317.46 hits per line

Source File
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73.51
/app/models/project.rb
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# frozen_string_literal: true
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class Project < ApplicationRecord
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  class ProjectCreateError < StandardError; end
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  validates_with ProjectValidator
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  has_many :provenance_events, dependent: :destroy
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  before_save do |project|
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    # Ensure that the metadata JSONB postgres field is persisted properly
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    project.metadata = project.metadata_model
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  end
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  # Valid project status described in ADR 7
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  # See `architecture-decisions/0007-valid-project-statuses.md`
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  PENDING_STATUS = "pending"
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  APPROVED_STATUS = "approved"
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  ACTIVE_STATUS = "active"
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  delegate :to_json, to: :metadata_json # field in the database
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  def create!(initial_metadata:, user:)
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    self.metadata_model = initial_metadata
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    if self.valid?
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      if initial_metadata.project_id == ProjectMetadata::DOI_NOT_MINTED
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        self.draft_doi(user: user)
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        self.save!
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        ProvenanceEvent.generate_submission_events(project: self, user: user)
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      else
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        self.save!
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      end
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      # return doi
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      self.metadata_model.project_id
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    else
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      nil
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    end
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  end
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  def approve!(current_user:)
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    request = Mediaflux::ProjectCreateServiceRequest.new(session_token: current_user.mediaflux_session, project: self)
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    request.resolve
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    if request.mediaflux_id.to_i == 0
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      raise ProjectCreateError.new("Error saving project #{self.id} to Mediaflux: #{request.response_error}. Debug output: #{request.debug_output}")
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    end
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    self.mediaflux_id = request.mediaflux_id
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    self.metadata_model.status = Project::APPROVED_STATUS
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    self.save!
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    debug_output = request.debug_output
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    # create provenance events:
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    # - one for approving the project and
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    # - another for changing the status of the project
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    # - another with debug information from the create project service
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    ProvenanceEvent.generate_approval_events(project: self, user: current_user, debug_output: debug_output)
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    self.mediaflux_id
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  end
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  def reload
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    super
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    @metadata_model = ProjectMetadata.new_from_hash(self.metadata)
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    self
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  end
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  def activate!(collection_id:, current_user:)
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    response = Mediaflux::AssetMetadataRequest.new(session_token: current_user.mediaflux_session, id: collection_id)
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    mediaflux_metadata = response.metadata # get the metadata of the collection from mediaflux
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    return unless mediaflux_metadata[:collection] == true # If the collection id exists
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    # check if the project doi in rails matches the project doi in mediaflux
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    return unless mediaflux_metadata[:project_id] == self.metadata_model.project_id
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    # activate a project by setting the status to 'active'
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    self.metadata_model.status = Project::ACTIVE_STATUS
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    # also read in the actual project directory
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    self.metadata_model.project_directory = mediaflux_metadata[:project_directory]
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    self.save!
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    ProvenanceEvent.generate_active_events(project: self, user: current_user)
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  end
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  def draft_doi(user: nil)
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    puldatacite = PULDatacite.new
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    self.metadata_model.project_id = puldatacite.draft_doi
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  end
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  # Ideally this method should return a ProjectMetadata object (like `metadata_model` does)
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  # but we'll keep them both while we are refactoring the code so that we don't break
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  # everything at once since `metadata` is used everywhere.
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  def metadata
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    @metadata_hash = (metadata_json || {}).with_indifferent_access
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  end
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  def metadata_model
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    @metadata_model ||= ProjectMetadata.new_from_hash(self.metadata)
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  end
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  def metadata_model=(new_metadata_model)
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    @metadata_model = new_metadata_model
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  end
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  def metadata=(metadata_model)
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    # Convert our metadata to a hash so it can be saved on our JSONB field
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    metadata_hash = JSON.parse(metadata_model.to_json)
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    self.metadata_json = metadata_hash
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  end
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  def title
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    self.metadata_model.title
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  end
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  def departments
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    unsorted = metadata_model.departments || []
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    unsorted.sort
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  end
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  def project_directory
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    metadata_model.project_directory || ""
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  end
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  def project_directory_parent_path
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    # The tigerdata.project.create expectes every project to be under "tigerdata"
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    Mediaflux::Connection.root
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  end
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  def project_directory_short
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    project_directory
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  end
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  def status
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    metadata_model.status
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  end
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  def pending?
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    status == PENDING_STATUS
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  end
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  def in_mediaflux?
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    mediaflux_id.present?
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  end
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  def self.users_projects(user)
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    # See https://scalegrid.io/blog/using-jsonb-in-postgresql-how-to-effectively-store-index-json-data-in-postgresql/
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    # for information on the @> operator
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    uid = user.uid
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    query_ro = '{"data_user_read_only":["' + uid + '"]}'
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    query_rw = '{"data_user_read_write":["' + uid + '"]}'
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    query = "(metadata_json @> ? :: jsonb) OR (metadata_json @> ? :: jsonb)"
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    args = [query_ro, query_rw]
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    if user.eligible_sponsor?
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      query += "OR (metadata_json->>'data_sponsor' = ?)"
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      args << uid
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    end
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    if user.eligible_manager?
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      query += "OR (metadata_json->>'data_manager' = ?)"
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      args << uid
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    end
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    Project.where( query, *args)
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  end
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  def self.sponsored_projects(sponsor)
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    Project.where("metadata_json->>'data_sponsor' = ?", sponsor)
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  end
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  def self.managed_projects(manager)
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    Project.where("metadata_json->>'data_manager' = ?", manager)
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  end
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  def self.pending_projects
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    Project.where("mediaflux_id IS NULL")
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  end
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  def self.approved_projects
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    Project.where("mediaflux_id IS NOT NULL")
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  end
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  def self.data_user_projects(user)
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    # See https://scalegrid.io/blog/using-jsonb-in-postgresql-how-to-effectively-store-index-json-data-in-postgresql/
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    # for information on the @> operator
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    query_ro = '{"data_user_read_only":["' + user + '"]}'
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    query_rw = '{"data_user_read_write":["' + user + '"]}'
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    Project.where("(metadata_json @> ? :: jsonb) OR (metadata_json @> ? :: jsonb)", query_ro, query_rw)
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  end
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  def user_has_access?(user:)
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    return true if user.eligible_sysadmin?
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    metadata_model.data_sponsor == user.uid || metadata_model.data_manager == user.uid ||
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    metadata_model.data_user_read_only.include?(user.uid) || metadata_model.data_user_read_write.include?(user.uid)
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  end
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  def save_in_mediaflux(user:)
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UNCOV
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    ProjectMediaflux.save(project: self, user: user)
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  end
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  def created_by_user
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    User.find_by(uid: metadata_model.created_by)
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  end
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  def to_xml
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    ProjectShowPresenter.new(self).to_xml
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  end
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  # @return [String] XML representation of the <meta> element
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  def mediaflux_meta_xml(user:)
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    doc = ProjectMediaflux.document(project: self, user: user)
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    doc.xpath("/response/reply/result/asset/meta").to_s
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  end
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  def mediaflux_metadata(session_id:)
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    @mediaflux_metadata ||= begin
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      accum_req = Mediaflux::AssetMetadataRequest.new(session_token: session_id, id: mediaflux_id)
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      accum_req.metadata
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    end
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    @mediaflux_metadata
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  end
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  def asset_count(session_id:)
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    values = mediaflux_metadata(session_id:)
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    values.fetch(:total_file_count, 0)
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  end
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  def self.default_storage_unit
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    "KB"
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  end
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  def self.default_storage_usage
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    "0 #{default_storage_unit}"
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  end
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  def storage_usage(session_id:)
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    values = mediaflux_metadata(session_id:)
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    values.fetch(:quota_used, self.class.default_storage_usage) # if the storage is empty use the default
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  end
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  def storage_usage_raw(session_id:)
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    values = mediaflux_metadata(session_id:)
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    values.fetch(:quota_used_raw, 0) # if the storage raw is empty use zero
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  end
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  def self.default_storage_capacity
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    "0 GB"
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  end
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  def storage_capacity(session_id:)
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    values = mediaflux_metadata(session_id:)
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    quota_value = values.fetch(:quota_allocation, '') #if quota does not exist, set value to an empty string
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    if quota_value.blank?
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      return self.class.default_storage_capacity
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    else
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      return quota_value
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    end
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  end
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  def storage_capacity_raw(session_id:)
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    values = mediaflux_metadata(session_id:)
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    quota_value = values.fetch(:quota_allocation_raw, 0) #if quota does not exist, set value to 0
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    quota_value
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  end
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  # Fetches the first n files
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  def file_list(session_id:, size: 10)
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    return { files: [] } if mediaflux_id.nil?
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    query_req = Mediaflux::QueryRequest.new(session_token: session_id, collection: mediaflux_id, deep_search: true, aql_query: "type!='application/arc-asset-collection'")
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    iterator_id = query_req.result
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    iterator_req = Mediaflux::IteratorRequest.new(session_token: session_id, iterator: iterator_id, size: size)
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    results = iterator_req.result
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    # Destroy _after_ fetching the first set of results from iterator_req.
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    # This call is required since it possible that we have read less assets than
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    # what the collection has but we are done with the iterator.
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    Mediaflux::IteratorDestroyRequest.new(session_token: session_id, iterator: iterator_id).resolve
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    results
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  end
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  # Fetches the entire file list to a file
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  def file_list_to_file(session_id:, filename:)
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    return { files: [] } if mediaflux_id.nil?
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    query_req = Mediaflux::QueryRequest.new(session_token: session_id, collection: mediaflux_id, deep_search: true,  aql_query: "type!='application/arc-asset-collection'")
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    iterator_id = query_req.result
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    start_time = Time.zone.now
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    prefix = "file_list_to_file #{session_id[0..7]} #{self.metadata_model.project_id}"
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    log_elapsed(start_time, prefix, "STARTED")
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    File.open(filename, "w") do |file|
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      page_number = 0
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      # file header
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      file.write("ID, PATH, NAME, COLLECTION?, LAST_MODIFIED, SIZE\r\n")
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      loop do
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        iterator_start_time = Time.zone.now
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        page_number += 1
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        iterator_req = Mediaflux::IteratorRequest.new(session_token: session_id, iterator: iterator_id, size: 1000)
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        iterator_resp = iterator_req.result
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        log_elapsed(iterator_start_time, prefix, "FETCHED page #{page_number} from iterator")
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        lines = files_from_iterator(iterator_resp)
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        file.write(lines.join("\r\n") + "\r\n")
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        break if iterator_resp[:complete] || iterator_req.error?
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      end
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      log_elapsed(start_time, prefix, "ENDED")
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    end
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    # Destroy _after_ fetching the results from iterator_req
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    # This call is technically not necessary since Mediaflux automatically deletes the iterator
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    # once we have ran through it and by now we have. But it does not hurt either.
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    Mediaflux::IteratorDestroyRequest.new(session_token: session_id, iterator: iterator_id).resolve
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  end
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  private
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    def files_from_iterator(iterator_resp)
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      lines = []
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      iterator_resp[:files].each do |asset|
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        lines << "#{asset.id}, #{asset.path_only}, #{asset.name}, #{asset.collection}, #{asset.last_modified}, #{asset.size}"
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      end
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      lines
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    end
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    def project_directory_pathname
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      # allow the directory to be modified by changes in the metadata_json
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      @project_directory_pathname = nil if @original_directory.present? && @original_directory != metadata_model.project_directory
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      @project_directory_pathname ||= begin
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        @original_directory = metadata_model.project_directory
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        Pathname.new(@original_directory)
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      end
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    end
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    # Ensure that the project directory is a valid path
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    def safe_directory(directory)
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      Project.safe_directory(directory)
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    end
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    def log_elapsed(start_time, prefix, message)
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      elapsed_time = Time.zone.now - start_time
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      timing_info = "#{format('%.2f', elapsed_time)} s"
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      Rails.logger.info "#{prefix}: #{message}, #{timing_info}"
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    end
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end
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