cace366a-ffad-45f1-9b60-678e607fa527

Committed 14 May 2024 02:21PM UTC coverage: 60.862% (-35.0%) from 95.908%

Build # cace366a-ffad-45f1-9b60-678e607fa527

Build Type

push

circleci

Committed by

jrgriffiniii

Commit Message

wip

Run Details

1 of 3 new or added lines in 2 files covered. (33.33%)

1194 existing lines in 57 files now uncovered.

2076 of 3411 relevant lines covered (60.86%)

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74.73

/app/models/work.rb

# frozen_string_literal: true

# rubocop:disable Metrics/ClassLength
class Work < ApplicationRecord
  # Errors for cases where there is no valid Group
  class InvalidGroupError < ::ArgumentError; end

  has_many :work_activity, -> { order(updated_at: :desc) }, dependent: :destroy
  has_many :user_work, -> { order(updated_at: :desc) }, dependent: :destroy
  has_many :upload_snapshots, -> { order(updated_at: :desc) }, dependent: :destroy

  belongs_to :group, class_name: "Group"
  belongs_to :curator, class_name: "User", foreign_key: "curator_user_id", optional: true

  attribute :work_type, :string, default: "DATASET"
  attribute :profile, :string, default: "DATACITE"

  attr_accessor :user_entered_doi

  alias state_history user_work

  delegate :valid_to_submit, :valid_to_draft, :valid_to_approve, :valid_to_complete, to: :work_validator

  include AASM

  aasm column: :state do
    state :none, initial: true
    state :draft, :awaiting_approval, :approved, :withdrawn, :deletion_marker

    event :draft, after: :draft_doi do
      transitions from: :none, to: :draft, guard: :valid_to_draft
    end

    event :complete_submission do
      transitions from: :draft, to: :awaiting_approval, guard: :valid_to_complete
    end

    event :request_changes do
      transitions from: :awaiting_approval, to: :awaiting_approval, guard: :valid_to_submit
    end

    event :approve do
      transitions from: :awaiting_approval, to: :approved, guard: :valid_to_approve, after: :publish
    end

    event :withdraw do
      transitions from: [:draft, :awaiting_approval, :approved], to: :withdrawn
    end

    event :resubmit do
      transitions from: :withdrawn, to: :draft
    end

    event :remove do
      transitions from: :withdrawn, to: :deletion_marker
    end

    after_all_events :track_state_change
  end

  def state=(new_state)
    new_state_sym = new_state.to_sym
    valid_states = self.class.aasm.states.map(&:name)
    raise(StandardError, "Invalid state '#{new_state}'") unless valid_states.include?(new_state_sym)
    aasm_write_state_without_persistence(new_state_sym)
  end

  ##
  # Is this work editable by a given user?
  # A work is editable when:
  # * it is being edited by the person who made it
  # * it is being edited by a group admin of the group where is resides
  # * it is being edited by a super admin
  # @param [User]
  # @return [Boolean]
  def editable_by?(user)
    submitted_by?(user) || administered_by?(user)
  end

  def editable_in_current_state?(user)
    # anyone with edit privleges can edit a work while it is in draft
    return editable_by?(user) if draft?

    # Only admisitrators can edit a work in other states
    administered_by?(user)
  end

  def submitted_by?(user)
    created_by_user_id == user.id
  end

  def administered_by?(user)
    user.has_role?(:group_admin, group)
  end

  class << self
    def find_by_doi(doi)
      prefix = "10.34770/"
      doi = "#{prefix}#{doi}" unless doi.blank? || doi.start_with?(prefix)
      Work.find_by!("metadata @> ?", JSON.dump(doi:))
    end

    def find_by_ark(ark)
      prefix = "ark:/"
      ark = "#{prefix}#{ark}" unless ark.blank? || ark.start_with?(prefix)
      Work.find_by!("metadata @> ?", JSON.dump(ark:))
    end

    delegate :resource_type_general_values, to: PDCMetadata::Resource
  end

  include Rails.application.routes.url_helpers

  before_save do |work|
    # Ensure that the metadata JSONB postgres field is persisted properly
    work.metadata = JSON.parse(work.resource.to_json)
  end

  after_save do |work|
    if work.approved?
      work.reload
    end
  end

  validate do |_work|
    work_validator.valid?
  end

  # Overload ActiveRecord.reload method
  # https://apidock.com/rails/ActiveRecord/Base/reload
  #
  # NOTE: Usually `after_save` is a better place to put this kind of code:
  #
  #   after_save do |work|
  #     work.resource = nil
  #   end
  #
  # but that does not work in this case because the block points to a different
  # memory object for `work` than the we want we want to reload.
  def reload(options = nil)
    super
    # Force `resource` to be reloaded
    @resource = nil
    self
  end

  def title
    resource.main_title
  end

  def uploads_attributes
    return [] if approved? # once approved we no longer allow the updating of uploads via the application
    uploads.map do |upload|
      {
        id: upload.id,
        key: upload.key,
        filename: upload.filename.to_s,
        created_at: upload.created_at,
        url: upload.url
      }
    end
  end

  def form_attributes
    {
      uploads: uploads_attributes
    }
  end

  def draft_doi
    return if resource.doi.present?
    resource.doi = datacite_service.draft_doi
    save!
  end

  # Return the DOI formatted as a URL, so it can be used as a link on display pages
  # @return [String] A url formatted version of the DOI
  def doi_url
    return "https://doi.org/#{doi}" unless doi.starts_with?("https://doi.org")
    doi
  end

  def created_by_user
    User.find(created_by_user_id)
  rescue ActiveRecord::RecordNotFound
    nil
  end

  def resource=(resource)
    @resource = resource
    # Ensure that the metadata JSONB postgres field is persisted properly
    self.metadata = JSON.parse(resource.to_json)
  end

  def resource
    @resource ||= PDCMetadata::Resource.new_from_jsonb(metadata)
  end

  def url
    return unless persisted?

    @url ||= url_for(self)
  end

  def files_location_upload?
    files_location.blank? || files_location == "file_upload"
  end

  def files_location_cluster?
    files_location == "file_cluster"
  end

  def files_location_other?
    files_location == "file_other"
  end

  def change_curator(curator_user_id, current_user)
    if curator_user_id == "no-one"
      clear_curator(current_user)
    else
      update_curator(curator_user_id, current_user)
    end
  end

  def clear_curator(current_user)
    # Update the curator on the Work
    self.curator_user_id = nil
    save!

    # ...and log the activity
    WorkActivity.add_work_activity(id, "Unassigned existing curator", current_user.id, activity_type: WorkActivity::SYSTEM)
  end

  def update_curator(curator_user_id, current_user)
    # Update the curator on the Work
    self.curator_user_id = curator_user_id
    save!

    # ...and log the activity
    new_curator = User.find(curator_user_id)

    work_url = "[#{title}](#{Rails.application.routes.url_helpers.work_url(self)})"

    # Troubleshooting https://github.com/pulibrary/pdc_describe/issues/1783
    if work_url.include?("/describe/describe/")
      Rails.logger.error("URL #{work_url} included /describe/describe/ and was fixed. See https://github.com/pulibrary/pdc_describe/issues/1783")
      work_url = work_url.gsub("/describe/describe/", "/describe/")
    end

    message = if curator_user_id.to_i == current_user.id
                "Self-assigned @#{current_user.uid} as curator for work #{work_url}"
              else
                "Set curator to @#{new_curator.uid} for work #{work_url}"
              end
    WorkActivity.add_work_activity(id, message, current_user.id, activity_type: WorkActivity::SYSTEM)
  end

  def add_message(message, current_user_id)
    WorkActivity.add_work_activity(id, message, current_user_id, activity_type: WorkActivity::MESSAGE)
  end

  def add_provenance_note(date, note, current_user_id, change_label = "")
    WorkActivity.add_work_activity(id, { note:, change_label: }.to_json, current_user_id, activity_type: WorkActivity::PROVENANCE_NOTES, created_at: date)
    # WorkActivity.add_work_activity(id, note, current_user_id, activity_type: WorkActivity::PROVENANCE_NOTES, created_at: date)
  end

  def log_changes(resource_compare, current_user_id)
    return if resource_compare.identical?
    WorkActivity.add_work_activity(id, resource_compare.differences.to_json, current_user_id, activity_type: WorkActivity::CHANGES)
  end

  def log_file_changes(current_user_id)
    return if changes.count == 0
    WorkActivity.add_work_activity(id, changes.to_json, current_user_id, activity_type: WorkActivity::FILE_CHANGES)
  end

  def activities
    WorkActivity.activities_for_work(id, WorkActivity::MESSAGE_ACTIVITY_TYPES + WorkActivity::CHANGE_LOG_ACTIVITY_TYPES)
  end

  def new_notification_count_for_user(user_id)
    WorkActivityNotification.joins(:work_activity)
                            .where(user_id:, read_at: nil)
                            .where(work_activity: { work_id: id })
                            .count
  end

  # Marks as read the notifications for the given user_id in this work.
  # In practice, the user_id is the id of the current user and therefore this method marks the current's user
  # notifications as read.
  def mark_new_notifications_as_read(user_id)
    activities.each do |activity|
      unread_notifications = WorkActivityNotification.where(user_id:, work_activity_id: activity.id, read_at: nil)
      unread_notifications.each do |notification|
        notification.read_at = Time.now.utc
        notification.save
      end
    end
  end

  def current_transition
    aasm.current_event.to_s.humanize.delete("!")
  end

  # Retrieve the S3 file uploads associated with the Work
  # @return [Array<S3File>]
  def uploads
    return post_curation_uploads if approved?

    pre_curation_uploads
  end

  # Retrieve the S3 file uploads named "README"
  # @return [Array<S3File>]
  def readme_uploads
    uploads.select { |s3_file| s3_file.filename.include?("README") }
  end

  # Retrieve the S3 file uploads which are research artifacts proper (not README or other files providing metadata/documentation)
  # @return [Array<S3File>]
  def artifact_uploads
    uploads.reject { |s3_file| s3_file.filename.include?("README") }
  end

  # Returns the list of files for the work with some basic information about each of them.
  # This method is much faster than `uploads` because it does not return the actual S3File
  # objects to the client, instead it returns just a few selected data elements.
  def file_list
    s3_files = approved? ? post_curation_uploads : pre_curation_uploads
    files_info = s3_files.map do |s3_file|
      {
        "safe_id": s3_file.safe_id,
        "filename": s3_file.filename,
        "filename_display": s3_file.filename_display,
        "last_modified": s3_file.last_modified,
        "last_modified_display": s3_file.last_modified_display,
        "size": s3_file.size,
        "display_size": s3_file.display_size,
        "url": s3_file.url
      }
    end
    files_info
  end

  def total_file_size
    @total_file_size ||= begin
      total_size = 0
      file_list.each do |file|
        total_size += file[:size]
      end
      total_size
    end
  end

  # Fetches the data from S3 directly bypassing ActiveStorage
  def pre_curation_uploads
    s3_query_service.client_s3_files.sort_by(&:filename)
  end

  # Accesses post-curation S3 Bucket Objects
  def post_curation_s3_resources
    if approved?
      s3_resources
    else
      []
    end
  end

  # Returns the files in post-curation for the work
  def post_curation_uploads(force_post_curation: false)
    if force_post_curation
      # Always use the post-curation data regardless of the work's status
      post_curation_s3_query_service = S3QueryService.new(self, "postcuration")
      post_curation_s3_query_service.data_profile.fetch(:objects, [])
    else
      # Return the list based of files honoring the work status
      post_curation_s3_resources
    end
  end

  def s3_files
    pre_curation_uploads
  end

  def s3_client
    s3_query_service.client
  end

  delegate :bucket_name, :prefix, to: :s3_query_service
  delegate :doi_attribute_url, :curator_or_current_uid, to: :datacite_service

  # Generates the S3 Object key
  # @return [String]
  def s3_object_key
    "#{doi}/#{id}"
  end

  # Transmit a HEAD request for the S3 Bucket directory for this Work
  # @param bucket_name location to be checked to be found
  # @return [Aws::S3::Types::HeadObjectOutput]
  def find_post_curation_s3_dir(bucket_name:)
    # TODO: Directories really do not exists in S3
    #      if we really need this check then we need to do something else to check the bucket
    s3_client.head_object({
                            bucket: bucket_name,
                            key: s3_object_key
                          })
    true
  rescue Aws::S3::Errors::NotFound
    nil
  end

  # Generates the JSON serialized expression of the Work
  # @param args [Array<Hash>]
  # @option args [Boolean] :force_post_curation Force the request of AWS S3
  #   Resources, clearing the in-memory cache
  # @return [String]
  def as_json(*args)
    files = files_as_json(*args)

    # to_json returns a string of serialized JSON.
    # as_json returns the corresponding hash.
    {
      "resource" => resource.as_json,
      "files" => files,
      "group" => group.as_json.except("id"),
      "embargo_date" => embargo_date_as_json,
      "created_at" => format_date_for_solr(created_at),
      "updated_at" => format_date_for_solr(updated_at)
    }
  end

  # Format the date for Apache Solr
  # @param date [ActiveSupport::TimeWithZone]
  # @return [String]
  def format_date_for_solr(date)
    date.strftime("%Y-%m-%dT%H:%M:%SZ")
  end

  def pre_curation_uploads_count
    s3_query_service.file_count
  end

  delegate :ark, :doi, :resource_type, :resource_type=, :resource_type_general, :resource_type_general=,
           :to_xml, to: :resource

  # S3QueryService object associated with this Work
  # @return [S3QueryService]
  def s3_query_service
    mode = approved? ? "postcuration" : "precuration"
    @s3_query_service ||= S3QueryService.new(self, mode)
  end

  def past_snapshots
    UploadSnapshot.where(work: self)
  end

  # Build or find persisted UploadSnapshot models for this Work
  # @param [integer] user_id optional user to assign the snapshot to
  # @return [UploadSnapshot]
  def reload_snapshots(user_id: nil)
    work_changes = []
    s3_files = pre_curation_uploads
    s3_filenames = s3_files.map(&:filename)

    upload_snapshot = latest_snapshot

    upload_snapshot.snapshot_deletions(work_changes, s3_filenames)

    upload_snapshot.snapshot_modifications(work_changes, s3_files)

    # Create WorkActivity models with the set of changes
    unless work_changes.empty?
      new_snapshot = UploadSnapshot.new(work: self, url: s3_query_service.prefix)
      new_snapshot.store_files(s3_files)
      new_snapshot.save!
      WorkActivity.add_work_activity(id, work_changes.to_json, user_id, activity_type: WorkActivity::FILE_CHANGES)
    end
  end

  def self.presenter_class
    WorkPresenter
  end

  def presenter
    self.class.presenter_class.new(work: self)
  end

  def changes
    @changes ||= []
  end

  def track_change(action, filename)
    changes << { action:, filename: }
  end

  # rubocop:disable Naming/PredicateName
  def has_rights?(rights_id)
    resource.rights_many.index { |rights| rights.identifier == rights_id } != nil
  end
  # rubocop:enable Naming/PredicateName

  # This is the solr id / work show page in PDC Discovery
  def pdc_discovery_url
    "https://datacommons.princeton.edu/discovery/catalog/doi-#{doi.tr('/', '-').tr('.', '-')}"
  end

  # Determine whether or not the Work is under active embargo
  # @return [Boolean]
  def embargoed?
    return false if embargo_date.blank?

    current_date = Time.zone.now
    embargo_date >= current_date
  end

  def upload_count
    @upload_count ||= s3_query_service.count_objects
  end

  protected

    def work_validator
      @work_validator ||= WorkValidator.new(self)
    end

    # This must be protected, NOT private for ActiveRecord to work properly with this attribute.
    #   Protected will still keep others from setting the metatdata, but allows ActiveRecord the access it needs
    def metadata=(metadata)
      super
      @resource = PDCMetadata::Resource.new_from_jsonb(metadata)
    end

  private

    def publish(user)
      datacite_service.publish_doi(user)
      update_ark_information
      publish_precurated_files(user)
      save!
    end

    # Update EZID (our provider of ARKs) with the new information for this work.
    def update_ark_information
      # We only want to update the ark url under certain conditions.
      # Set this value in config/update_ark_url.yml
      if Rails.configuration.update_ark_url
        if ark.present?
          Ark.update(ark, datacite_service.doi_attribute_url)
        end
      end
    end

    def track_state_change(user, state = aasm.to_state)
      uw = UserWork.new(user_id: user.id, work_id: id, state:)
      uw.save!
      WorkActivity.add_work_activity(id, "marked as #{state.to_s.titleize}", user.id, activity_type: WorkActivity::SYSTEM)
      WorkStateTransitionNotification.new(self, user.id).send
    end

    # Request S3 Bucket Objects associated with this Work
    # @return [Array<S3File>]
    def s3_resources
      data_profile = s3_query_service.data_profile
      data_profile.fetch(:objects, [])
    end
    alias pre_curation_s3_resources s3_resources

    def s3_object_persisted?(s3_file)
      uploads_keys = uploads.map(&:key)
      uploads_keys.include?(s3_file.key)
    end

    def publish_precurated_files(user)
      # We need to explicitly check the to post-curation bucket here.
      s3_post_curation_query_service = S3QueryService.new(self, "postcuration")

      s3_dir = find_post_curation_s3_dir(bucket_name: s3_post_curation_query_service.bucket_name)
      raise(StandardError, "Attempting to publish a Work with an existing S3 Bucket directory for: #{s3_object_key}") unless s3_dir.nil?

      # Copy the pre-curation S3 Objects to the post-curation S3 Bucket...
      s3_query_service.publish_files(user)
    end

    def latest_snapshot
      return upload_snapshots.first unless upload_snapshots.empty?

      UploadSnapshot.new(work: self, files: [])
    end

    def datacite_service
      @datacite_service ||= PULDatacite.new(self)
    end

    def files_as_json(*args)
      return [] if embargoed?

      force_post_curation = args.any? { |arg| arg[:force_post_curation] == true }

      # Pre-curation files are not accessible externally,
      # so we are not interested in listing them in JSON.
      post_curation_uploads(force_post_curation:).map do |upload|
        {
          "filename": upload.filename,
          "size": upload.size,
          "display_size": upload.display_size,
          "url": upload.globus_url
        }
      end
    end

    def embargo_date_as_json
      if embargo_date.present?
        embargo_datetime = embargo_date.to_datetime
        embargo_date_iso8601 = embargo_datetime.iso8601
        # Apache Solr timestamps require the following format:
        # 1972-05-20T17:33:18Z
        # https://solr.apache.org/guide/solr/latest/indexing-guide/date-formatting-math.html
        embargo_date_iso8601.gsub(/\+.+$/, "Z")
      end
    end
end
# rubocop:enable Metrics/ClassLength

1	# frozen_string_literal: true
2
3	# rubocop:disable Metrics/ClassLength
4	class Work < ApplicationRecord	1✔
5	# Errors for cases where there is no valid Group
6	class InvalidGroupError < ::ArgumentError; end	1✔
7
8	has_many :work_activity, -> { order(updated_at: :desc) }, dependent: :destroy	33✔
9	has_many :user_work, -> { order(updated_at: :desc) }, dependent: :destroy	2✔
10	has_many :upload_snapshots, -> { order(updated_at: :desc) }, dependent: :destroy	24✔
11
12	belongs_to :group, class_name: "Group"	1✔
13	belongs_to :curator, class_name: "User", foreign_key: "curator_user_id", optional: true	1✔
14
15	attribute :work_type, :string, default: "DATASET"	1✔
16	attribute :profile, :string, default: "DATACITE"	1✔
17
18	attr_accessor :user_entered_doi	1✔
19
20	alias state_history user_work	1✔
21
22	delegate :valid_to_submit, :valid_to_draft, :valid_to_approve, :valid_to_complete, to: :work_validator	1✔
23
24	include AASM	1✔
25
26	aasm column: :state do	1✔
27	state :none, initial: true	1✔
28	state :draft, :awaiting_approval, :approved, :withdrawn, :deletion_marker	1✔
29
30	event :draft, after: :draft_doi do	1✔
31	transitions from: :none, to: :draft, guard: :valid_to_draft	1✔
32	end
33
34	event :complete_submission do	1✔
35	transitions from: :draft, to: :awaiting_approval, guard: :valid_to_complete	1✔
36	end
37
38	event :request_changes do	1✔
39	transitions from: :awaiting_approval, to: :awaiting_approval, guard: :valid_to_submit	1✔
40	end
41
42	event :approve do	1✔
43	transitions from: :awaiting_approval, to: :approved, guard: :valid_to_approve, after: :publish	1✔
44	end
45
46	event :withdraw do	1✔
47	transitions from: [:draft, :awaiting_approval, :approved], to: :withdrawn	1✔
48	end
49
50	event :resubmit do	1✔
51	transitions from: :withdrawn, to: :draft	1✔
52	end
53
54	event :remove do	1✔
55	transitions from: :withdrawn, to: :deletion_marker	1✔
56	end
57
58	after_all_events :track_state_change	1✔
59	end
60
61	def state=(new_state)	1✔
62	new_state_sym = new_state.to_sym	38✔
63	valid_states = self.class.aasm.states.map(&:name)	38✔
64	raise(StandardError, "Invalid state '#{new_state}'") unless valid_states.include?(new_state_sym)	38✔
65	aasm_write_state_without_persistence(new_state_sym)	38✔
66	end
67
68	##
69	# Is this work editable by a given user?
70	# A work is editable when:
71	# * it is being edited by the person who made it
72	# * it is being edited by a group admin of the group where is resides
73	# * it is being edited by a super admin
74	# @param [User]
75	# @return [Boolean]
76	def editable_by?(user)	1✔
77	submitted_by?(user) \|\| administered_by?(user)	76✔
78	end
79
80	def editable_in_current_state?(user)	1✔
81	# anyone with edit privleges can edit a work while it is in draft
82	return editable_by?(user) if draft?	41✔
83
84	# Only admisitrators can edit a work in other states
85	administered_by?(user)	3✔
86	end
87
88	def submitted_by?(user)	1✔
89	created_by_user_id == user.id	76✔
90	end
91
92	def administered_by?(user)	1✔
93	user.has_role?(:group_admin, group)	15✔
94	end
95
96	class << self	1✔
97	def find_by_doi(doi)	1✔
98	prefix = "10.34770/"	1✔
99	doi = "#{prefix}#{doi}" unless doi.blank? \|\| doi.start_with?(prefix)	1✔
100	Work.find_by!("metadata @> ?", JSON.dump(doi:))	1✔
101	end
102
103	def find_by_ark(ark)	1✔
104	prefix = "ark:/"	30✔
105	ark = "#{prefix}#{ark}" unless ark.blank? \|\| ark.start_with?(prefix)	30✔
106	Work.find_by!("metadata @> ?", JSON.dump(ark:))	30✔
107	end
108
109	delegate :resource_type_general_values, to: PDCMetadata::Resource	1✔
110	end
111
112	include Rails.application.routes.url_helpers	1✔
113
114	before_save do \|work\|	1✔
115	# Ensure that the metadata JSONB postgres field is persisted properly
116	work.metadata = JSON.parse(work.resource.to_json)	57✔
117	end
118
119	after_save do \|work\|	1✔
120	if work.approved?	57✔
121	work.reload	3✔
122	end
123	end
124
125	validate do \|_work\|	1✔
126	work_validator.valid?	58✔
127	end
128
129	# Overload ActiveRecord.reload method
130	# https://apidock.com/rails/ActiveRecord/Base/reload
131	#
132	# NOTE: Usually `after_save` is a better place to put this kind of code:
133	#
134	# after_save do \|work\|
135	# work.resource = nil
136	# end
137	#
138	# but that does not work in this case because the block points to a different
139	# memory object for `work` than the we want we want to reload.
140	def reload(options = nil)	1✔
141	super	6✔
142	# Force `resource` to be reloaded
143	@resource = nil	6✔
144	self	6✔
145	end
146
147	def title	1✔
148	resource.main_title	17✔
149	end
150
151	def uploads_attributes	1✔
152	return [] if approved? # once approved we no longer allow the updating of uploads via the application	20✔
153	uploads.map do \|upload\|	18✔
154	{
155	id: upload.id,	4✔
156	key: upload.key,
157	filename: upload.filename.to_s,
158	created_at: upload.created_at,
159	url: upload.url
160	}
161	end
162	end
163
164	def form_attributes	1✔
165	{
166	uploads: uploads_attributes	20✔
167	}
168	end
169
170	def draft_doi	1✔
171	return if resource.doi.present?	2✔
172	resource.doi = datacite_service.draft_doi	1✔
173	save!	1✔
174	end
175
176	# Return the DOI formatted as a URL, so it can be used as a link on display pages
177	# @return [String] A url formatted version of the DOI
178	def doi_url	1✔
UNCOV 179	return "https://doi.org/#{doi}" unless doi.starts_with?("https://doi.org")	×
180	doi	×
181	end
182
183	def created_by_user	1✔
184	User.find(created_by_user_id)	38✔
185	rescue ActiveRecord::RecordNotFound
UNCOV 186	nil	×
187	end
188
189	def resource=(resource)	1✔
190	@resource = resource	43✔
191	# Ensure that the metadata JSONB postgres field is persisted properly
192	self.metadata = JSON.parse(resource.to_json)	43✔
193	end
194
195	def resource	1✔
196	@resource \|\|= PDCMetadata::Resource.new_from_jsonb(metadata)	2,650✔
197	end
198
199	def url	1✔
200	return unless persisted?	×
201
202	@url \|\|= url_for(self)	×
203	end
204
205	def files_location_upload?	1✔
UNCOV 206	files_location.blank? \|\| files_location == "file_upload"	×
207	end
208
209	def files_location_cluster?	1✔
210	files_location == "file_cluster"	11✔
211	end
212
213	def files_location_other?	1✔
214	files_location == "file_other"	11✔
215	end
216
217	def change_curator(curator_user_id, current_user)	1✔
UNCOV 218	if curator_user_id == "no-one"	×
UNCOV 219	clear_curator(current_user)	×
220	else
UNCOV 221	update_curator(curator_user_id, current_user)	×
222	end
223	end
224
225	def clear_curator(current_user)	1✔
226	# Update the curator on the Work
UNCOV 227	self.curator_user_id = nil	×
UNCOV 228	save!	×
229
230	# ...and log the activity
UNCOV 231	WorkActivity.add_work_activity(id, "Unassigned existing curator", current_user.id, activity_type: WorkActivity::SYSTEM)	×
232	end
233
234	def update_curator(curator_user_id, current_user)	1✔
235	# Update the curator on the Work
UNCOV 236	self.curator_user_id = curator_user_id	×
UNCOV 237	save!	×
238
239	# ...and log the activity
UNCOV 240	new_curator = User.find(curator_user_id)	×
241
UNCOV 242	work_url = "[#{title}](#{Rails.application.routes.url_helpers.work_url(self)})"	×
243
244	# Troubleshooting https://github.com/pulibrary/pdc_describe/issues/1783
UNCOV 245	if work_url.include?("/describe/describe/")	×
246	Rails.logger.error("URL #{work_url} included /describe/describe/ and was fixed. See https://github.com/pulibrary/pdc_describe/issues/1783")	×
247	work_url = work_url.gsub("/describe/describe/", "/describe/")	×
248	end
249
UNCOV 250	message = if curator_user_id.to_i == current_user.id	×
UNCOV 251	"Self-assigned @#{current_user.uid} as curator for work #{work_url}"	×
252	else
UNCOV 253	"Set curator to @#{new_curator.uid} for work #{work_url}"	×
254	end
UNCOV 255	WorkActivity.add_work_activity(id, message, current_user.id, activity_type: WorkActivity::SYSTEM)	×
256	end
257
258	def add_message(message, current_user_id)	1✔
UNCOV 259	WorkActivity.add_work_activity(id, message, current_user_id, activity_type: WorkActivity::MESSAGE)	×
260	end
261
262	def add_provenance_note(date, note, current_user_id, change_label = "")	1✔
263	WorkActivity.add_work_activity(id, { note:, change_label: }.to_json, current_user_id, activity_type: WorkActivity::PROVENANCE_NOTES, created_at: date)	10✔
264	# WorkActivity.add_work_activity(id, note, current_user_id, activity_type: WorkActivity::PROVENANCE_NOTES, created_at: date)
265	end
266
267	def log_changes(resource_compare, current_user_id)	1✔
268	return if resource_compare.identical?	10✔
269	WorkActivity.add_work_activity(id, resource_compare.differences.to_json, current_user_id, activity_type: WorkActivity::CHANGES)	9✔
270	end
271
272	def log_file_changes(current_user_id)	1✔
273	return if changes.count == 0	1✔
274	WorkActivity.add_work_activity(id, changes.to_json, current_user_id, activity_type: WorkActivity::FILE_CHANGES)	1✔
275	end
276
277	def activities	1✔
278	WorkActivity.activities_for_work(id, WorkActivity::MESSAGE_ACTIVITY_TYPES + WorkActivity::CHANGE_LOG_ACTIVITY_TYPES)	11✔
279	end
280
281	def new_notification_count_for_user(user_id)	1✔
282	WorkActivityNotification.joins(:work_activity)	3✔
283	.where(user_id:, read_at: nil)
284	.where(work_activity: { work_id: id })
285	.count
286	end
287
288	# Marks as read the notifications for the given user_id in this work.
289	# In practice, the user_id is the id of the current user and therefore this method marks the current's user
290	# notifications as read.
291	def mark_new_notifications_as_read(user_id)	1✔
292	activities.each do \|activity\|	11✔
293	unread_notifications = WorkActivityNotification.where(user_id:, work_activity_id: activity.id, read_at: nil)	15✔
294	unread_notifications.each do \|notification\|	15✔
295	notification.read_at = Time.now.utc	1✔
296	notification.save	1✔
297	end
298	end
299	end
300
301	def current_transition	1✔
UNCOV 302	aasm.current_event.to_s.humanize.delete("!")	×
303	end
304
305	# Retrieve the S3 file uploads associated with the Work
306	# @return [Array<S3File>]
307	def uploads	1✔
308	return post_curation_uploads if approved?	36✔
309
310	pre_curation_uploads	34✔
311	end
312
313	# Retrieve the S3 file uploads named "README"
314	# @return [Array<S3File>]
315	def readme_uploads	1✔
UNCOV 316	uploads.select { \|s3_file\| s3_file.filename.include?("README") }	×
317	end
318
319	# Retrieve the S3 file uploads which are research artifacts proper (not README or other files providing metadata/documentation)
320	# @return [Array<S3File>]
321	def artifact_uploads	1✔
NEW 322	uploads.reject { \|s3_file\| s3_file.filename.include?("README") }	×
323	end
324
325	# Returns the list of files for the work with some basic information about each of them.
326	# This method is much faster than `uploads` because it does not return the actual S3File
327	# objects to the client, instead it returns just a few selected data elements.
328	def file_list	1✔
329	s3_files = approved? ? post_curation_uploads : pre_curation_uploads	40✔
330	files_info = s3_files.map do \|s3_file\|	40✔
331	{
332	"safe_id": s3_file.safe_id,	6✔
333	"filename": s3_file.filename,
334	"filename_display": s3_file.filename_display,
335	"last_modified": s3_file.last_modified,
336	"last_modified_display": s3_file.last_modified_display,
337	"size": s3_file.size,
338	"display_size": s3_file.display_size,
339	"url": s3_file.url
340	}
341	end
342	files_info	40✔
343	end
344
345	def total_file_size	1✔
346	@total_file_size \|\|= begin	11✔
347	total_size = 0	11✔
348	file_list.each do \|file\|	11✔
349	total_size += file[:size]	1✔
350	end
351	total_size	11✔
352	end
353	end
354
355	# Fetches the data from S3 directly bypassing ActiveStorage
356	def pre_curation_uploads	1✔
357	s3_query_service.client_s3_files.sort_by(&:filename)	72✔
358	end
359
360	# Accesses post-curation S3 Bucket Objects
361	def post_curation_s3_resources	1✔
362	if approved?	5✔
363	s3_resources	4✔
364	else
365	[]	1✔
366	end
367	end
368
369	# Returns the files in post-curation for the work
370	def post_curation_uploads(force_post_curation: false)	1✔
371	if force_post_curation	5✔
372	# Always use the post-curation data regardless of the work's status
UNCOV 373	post_curation_s3_query_service = S3QueryService.new(self, "postcuration")	×
UNCOV 374	post_curation_s3_query_service.data_profile.fetch(:objects, [])	×
375	else
376	# Return the list based of files honoring the work status
377	post_curation_s3_resources	5✔
378	end
379	end
380
381	def s3_files	1✔
382	pre_curation_uploads	×
383	end
384
385	def s3_client	1✔
UNCOV 386	s3_query_service.client	×
387	end
388
389	delegate :bucket_name, :prefix, to: :s3_query_service	1✔
390	delegate :doi_attribute_url, :curator_or_current_uid, to: :datacite_service	1✔
391
392	# Generates the S3 Object key
393	# @return [String]
394	def s3_object_key	1✔
UNCOV 395	"#{doi}/#{id}"	×
396	end
397
398	# Transmit a HEAD request for the S3 Bucket directory for this Work
399	# @param bucket_name location to be checked to be found
400	# @return [Aws::S3::Types::HeadObjectOutput]
401	def find_post_curation_s3_dir(bucket_name:)	1✔
402	# TODO: Directories really do not exists in S3
403	# if we really need this check then we need to do something else to check the bucket
UNCOV 404	s3_client.head_object({	×
405	bucket: bucket_name,
406	key: s3_object_key
407	})
UNCOV 408	true	×
409	rescue Aws::S3::Errors::NotFound
UNCOV 410	nil	×
411	end
412
413	# Generates the JSON serialized expression of the Work
414	# @param args [Array<Hash>]
415	# @option args [Boolean] :force_post_curation Force the request of AWS S3
416	# Resources, clearing the in-memory cache
417	# @return [String]
418	def as_json(*args)	1✔
419	files = files_as_json(*args)	1✔
420
421	# to_json returns a string of serialized JSON.
422	# as_json returns the corresponding hash.
423	{
424	"resource" => resource.as_json,	1✔
425	"files" => files,
426	"group" => group.as_json.except("id"),
427	"embargo_date" => embargo_date_as_json,
428	"created_at" => format_date_for_solr(created_at),
429	"updated_at" => format_date_for_solr(updated_at)
430	}
431	end
432
433	# Format the date for Apache Solr
434	# @param date [ActiveSupport::TimeWithZone]
435	# @return [String]
436	def format_date_for_solr(date)	1✔
437	date.strftime("%Y-%m-%dT%H:%M:%SZ")	2✔
438	end
439
440	def pre_curation_uploads_count	1✔
UNCOV 441	s3_query_service.file_count	×
442	end
443
444	delegate :ark, :doi, :resource_type, :resource_type=, :resource_type_general, :resource_type_general=,	1✔
445	:to_xml, to: :resource
446
447	# S3QueryService object associated with this Work
448	# @return [S3QueryService]
449	def s3_query_service	1✔
450	mode = approved? ? "postcuration" : "precuration"	117✔
451	@s3_query_service \|\|= S3QueryService.new(self, mode)	117✔
452	end
453
454	def past_snapshots	1✔
455	UploadSnapshot.where(work: self)	×
456	end
457
458	# Build or find persisted UploadSnapshot models for this Work
459	# @param [integer] user_id optional user to assign the snapshot to
460	# @return [UploadSnapshot]
461	def reload_snapshots(user_id: nil)	1✔
UNCOV 462	work_changes = []	×
UNCOV 463	s3_files = pre_curation_uploads	×
UNCOV 464	s3_filenames = s3_files.map(&:filename)	×
465
UNCOV 466	upload_snapshot = latest_snapshot	×
467
UNCOV 468	upload_snapshot.snapshot_deletions(work_changes, s3_filenames)	×
469
UNCOV 470	upload_snapshot.snapshot_modifications(work_changes, s3_files)	×
471
472	# Create WorkActivity models with the set of changes
UNCOV 473	unless work_changes.empty?	×
UNCOV 474	new_snapshot = UploadSnapshot.new(work: self, url: s3_query_service.prefix)	×
UNCOV 475	new_snapshot.store_files(s3_files)	×
UNCOV 476	new_snapshot.save!	×
UNCOV 477	WorkActivity.add_work_activity(id, work_changes.to_json, user_id, activity_type: WorkActivity::FILE_CHANGES)	×
478	end
479	end
480
481	def self.presenter_class	1✔
482	WorkPresenter	18✔
483	end
484
485	def presenter	1✔
486	self.class.presenter_class.new(work: self)	18✔
487	end
488
489	def changes	1✔
490	@changes \|\|= []	14✔
491	end
492
493	def track_change(action, filename)	1✔
494	changes << { action:, filename: }	1✔
495	end
496
497	# rubocop:disable Naming/PredicateName
498	def has_rights?(rights_id)	1✔
499	resource.rights_many.index { \|rights\| rights.identifier == rights_id } != nil	351✔
500	end
501	# rubocop:enable Naming/PredicateName
502
503	# This is the solr id / work show page in PDC Discovery
504	def pdc_discovery_url	1✔
505	"https://datacommons.princeton.edu/discovery/catalog/doi-#{doi.tr('/', '-').tr('.', '-')}"	22✔
506	end
507
508	# Determine whether or not the Work is under active embargo
509	# @return [Boolean]
510	def embargoed?	1✔
511	return false if embargo_date.blank?	23✔
512
UNCOV 513	current_date = Time.zone.now	×
UNCOV 514	embargo_date >= current_date	×
515	end
516
517	def upload_count	1✔
518	@upload_count \|\|= s3_query_service.count_objects	131✔
519	end
520
521	protected	1✔
522
523	def work_validator	1✔
524	@work_validator \|\|= WorkValidator.new(self)	63✔
525	end
526
527	# This must be protected, NOT private for ActiveRecord to work properly with this attribute.
528	# Protected will still keep others from setting the metatdata, but allows ActiveRecord the access it needs
529	def metadata=(metadata)	1✔
530	super	100✔
531	@resource = PDCMetadata::Resource.new_from_jsonb(metadata)	100✔
532	end
533
534	private	1✔
535
536	def publish(user)	1✔
UNCOV 537	datacite_service.publish_doi(user)	×
UNCOV 538	update_ark_information	×
UNCOV 539	publish_precurated_files(user)	×
UNCOV 540	save!	×
541	end
542
543	# Update EZID (our provider of ARKs) with the new information for this work.
544	def update_ark_information	1✔
545	# We only want to update the ark url under certain conditions.
546	# Set this value in config/update_ark_url.yml
UNCOV 547	if Rails.configuration.update_ark_url	×
UNCOV 548	if ark.present?	×
UNCOV 549	Ark.update(ark, datacite_service.doi_attribute_url)	×
550	end
551	end
552	end
553
554	def track_state_change(user, state = aasm.to_state)	1✔
555	uw = UserWork.new(user_id: user.id, work_id: id, state:)	3✔
556	uw.save!	3✔
557	WorkActivity.add_work_activity(id, "marked as #{state.to_s.titleize}", user.id, activity_type: WorkActivity::SYSTEM)	3✔
558	WorkStateTransitionNotification.new(self, user.id).send	3✔
559	end
560
561	# Request S3 Bucket Objects associated with this Work
562	# @return [Array<S3File>]
563	def s3_resources	1✔
564	data_profile = s3_query_service.data_profile	4✔
565	data_profile.fetch(:objects, [])	4✔
566	end
567	alias pre_curation_s3_resources s3_resources	1✔
568
569	def s3_object_persisted?(s3_file)	1✔
570	uploads_keys = uploads.map(&:key)	×
571	uploads_keys.include?(s3_file.key)	×
572	end
573
574	def publish_precurated_files(user)	1✔
575	# We need to explicitly check the to post-curation bucket here.
UNCOV 576	s3_post_curation_query_service = S3QueryService.new(self, "postcuration")	×
577
UNCOV 578	s3_dir = find_post_curation_s3_dir(bucket_name: s3_post_curation_query_service.bucket_name)	×
UNCOV 579	raise(StandardError, "Attempting to publish a Work with an existing S3 Bucket directory for: #{s3_object_key}") unless s3_dir.nil?	×
580
581	# Copy the pre-curation S3 Objects to the post-curation S3 Bucket...
UNCOV 582	s3_query_service.publish_files(user)	×
583	end
584
585	def latest_snapshot	1✔
UNCOV 586	return upload_snapshots.first unless upload_snapshots.empty?	×
587
UNCOV 588	UploadSnapshot.new(work: self, files: [])	×
589	end
590
591	def datacite_service	1✔
592	@datacite_service \|\|= PULDatacite.new(self)	1✔
593	end
594
595	def files_as_json(*args)	1✔
596	return [] if embargoed?	1✔
597
598	force_post_curation = args.any? { \|arg\| arg[:force_post_curation] == true }	2✔
599
600	# Pre-curation files are not accessible externally,
601	# so we are not interested in listing them in JSON.
602	post_curation_uploads(force_post_curation:).map do \|upload\|	1✔
603	{
UNCOV 604	"filename": upload.filename,	×
605	"size": upload.size,
606	"display_size": upload.display_size,
607	"url": upload.globus_url
608	}
609	end
610	end
611
612	def embargo_date_as_json	1✔
613	if embargo_date.present?	1✔
UNCOV 614	embargo_datetime = embargo_date.to_datetime	×
UNCOV 615	embargo_date_iso8601 = embargo_datetime.iso8601	×
616	# Apache Solr timestamps require the following format:
617	# 1972-05-20T17:33:18Z
618	# https://solr.apache.org/guide/solr/latest/indexing-guide/date-formatting-math.html
UNCOV 619	embargo_date_iso8601.gsub(/\+.+$/, "Z")	×
620	end
621	end
622	end
623	# rubocop:enable Metrics/ClassLength

pulibrary / pdc_describe / cace366a-ffad-45f1-9b60-678e607fa527

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