b489533f-9066-4a1f-b488-40e1f0465f4b

Committed 04 Aug 2025 05:29PM UTC coverage: 75.6% (-1.5%) from 77.142%

Build # b489533f-9066-4a1f-b488-40e1f0465f4b

Build Type

Pull #1657

circleci

Committed by

JaymeeH

Commit Message

Merge branch 'i1632-save-data-users' of https://github.com/pulibrary/tiger-data-app into i1632-save-data-users

Pull Request Pull Request #1657: Add data users to a project after it is created in mediaflux

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5 existing lines in 2 files now uncovered.

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71.82

/app/models/project.rb

# frozen_string_literal: true
class Project < ApplicationRecord

  class ProjectCreateError < StandardError; end

  validates_with ProjectValidator
  has_many :provenance_events, dependent: :destroy
  before_save do |project|
    # Ensure that the metadata JSONB postgres field is persisted properly
    project.metadata = project.metadata_model
  end

  # Valid project status described in ADR 7
  # See `architecture-decisions/0007-valid-project-statuses.md`
  PENDING_STATUS = "pending"
  APPROVED_STATUS = "approved"
  ACTIVE_STATUS = "active"

  delegate :to_json, to: :metadata_json # field in the database

  def create!(initial_metadata:, user:)
    self.metadata_model = initial_metadata
    if self.valid?
      if initial_metadata.project_id == ProjectMetadata::DOI_NOT_MINTED
        self.draft_doi(user: user)
        self.save!
        ProvenanceEvent.generate_submission_events(project: self, user: user)
      else
        self.save!
      end
      # return doi
      self.metadata_model.project_id
    else
      nil
    end
  end

  def approve!(current_user:)
    request = Mediaflux::ProjectCreateServiceRequest.new(session_token: current_user.mediaflux_session, project: self)
    request.resolve

    if request.mediaflux_id.to_i == 0
      raise ProjectCreateError.new("Error saving project #{self.id} to Mediaflux: #{request.response_error}. Debug output: #{request.debug_output}")
    end

    self.mediaflux_id = request.mediaflux_id
    self.metadata_model.status = Project::APPROVED_STATUS
    self.save!

    debug_output = if request.mediaflux_id == 0
                     "Error saving project #{self.id} to Mediaflux: #{request.response_error}. Debug output: #{request.debug_output}"
                   else
                     "#{request.debug_output}"
                   end
    Rails.logger.error debug_output

    add_users_request = Mediaflux::ProjectUserAddRequest.new(session_token: current_user.mediaflux_session, project: self)
    add_users_request.resolve

    user_debug = "#{add_users_request.debug_output}"
    Rails.logger.error "Project #{self.id} users have been added to MediaFlux: #{user_debug}"

    # create provenance events:
    # - one for approving the project and
    # - another for changing the status of the project
    # - another with debug information from the create project service
    ProvenanceEvent.generate_approval_events(project: self, user: current_user, debug_output: debug_output)

    self.mediaflux_id
  end

  def reload
    super
    @metadata_model = ProjectMetadata.new_from_hash(self.metadata)
    self
  end

  def draft_doi(user: nil)
    puldatacite = PULDatacite.new
    self.metadata_model.project_id = puldatacite.draft_doi
  end

  # Ideally this method should return a ProjectMetadata object (like `metadata_model` does)
  # but we'll keep them both while we are refactoring the code so that we don't break
  # everything at once since `metadata` is used everywhere.
  def metadata
    @metadata_hash = (metadata_json || {}).with_indifferent_access
  end

  def metadata_model
    @metadata_model ||= ProjectMetadata.new_from_hash(self.metadata)
  end

  def metadata_model=(new_metadata_model)
    @metadata_model = new_metadata_model
  end

  def metadata=(metadata_model)
    # Convert our metadata to a hash so it can be saved on our JSONB field
    metadata_hash = JSON.parse(metadata_model.to_json)
    self.metadata_json = metadata_hash
  end

  def title
    self.metadata_model.title
  end

  def departments
    unsorted = metadata_model.departments || []
    unsorted.sort
  end

  def project_directory
    metadata_model.project_directory || ""
  end

  def project_directory_parent_path
    # The tigerdata.project.create expectes every project to be under "tigerdata"
    Mediaflux::Connection.root
  end

  def project_directory_short
    project_directory
  end

  def status
    metadata_model.status
  end

  def pending?
    status == PENDING_STATUS
  end

  def in_mediaflux?
    mediaflux_id.present?
  end

  def self.users_projects(user)
    # See https://scalegrid.io/blog/using-jsonb-in-postgresql-how-to-effectively-store-index-json-data-in-postgresql/
    # for information on the @> operator
    uid = user.uid
    query_ro = '{"data_user_read_only":["' + uid + '"]}'
    query_rw = '{"data_user_read_write":["' + uid + '"]}'
    query = "(metadata_json @> ? :: jsonb) OR (metadata_json @> ? :: jsonb)"
    args = [query_ro, query_rw]
    if user.eligible_sponsor?
      query += "OR (metadata_json->>'data_sponsor' = ?)"
      args << uid
    end
    if user.eligible_manager?
      query += "OR (metadata_json->>'data_manager' = ?)"
      args << uid
    end
    Project.where( query, *args)
  end

  def self.sponsored_projects(sponsor)
    Project.where("metadata_json->>'data_sponsor' = ?", sponsor)
  end

  def self.managed_projects(manager)
    Project.where("metadata_json->>'data_manager' = ?", manager)
  end

  def self.pending_projects
    Project.where("mediaflux_id IS NULL")
  end

  def self.approved_projects
    Project.where("mediaflux_id IS NOT NULL")
  end

  def self.data_user_projects(user)
    # See https://scalegrid.io/blog/using-jsonb-in-postgresql-how-to-effectively-store-index-json-data-in-postgresql/
    # for information on the @> operator
    query_ro = '{"data_user_read_only":["' + user + '"]}'
    query_rw = '{"data_user_read_write":["' + user + '"]}'
    Project.where("(metadata_json @> ? :: jsonb) OR (metadata_json @> ? :: jsonb)", query_ro, query_rw)
  end

  def user_has_access?(user:)
    return true if user.eligible_sysadmin?
    metadata_model.data_sponsor == user.uid || metadata_model.data_manager == user.uid ||
    metadata_model.data_user_read_only.include?(user.uid) || metadata_model.data_user_read_write.include?(user.uid)
  end

  def created_by_user
    User.find_by(uid: metadata_model.created_by)
  end

  def to_xml
    ProjectShowPresenter.new(self).to_xml
  end

  # @return [String] XML representation of the <meta> element
  def mediaflux_meta_xml(user:)
    doc = ProjectMediaflux.document(project: self, user: user)
    doc.xpath("/response/reply/result/asset/meta").to_s
  end

  def mediaflux_metadata(session_id:)
    @mediaflux_metadata ||= begin
      accum_req = Mediaflux::AssetMetadataRequest.new(session_token: session_id, id: mediaflux_id)
      accum_req.metadata
    end
    @mediaflux_metadata
  end

  def asset_count(session_id:)
    values = mediaflux_metadata(session_id:)
    values.fetch(:total_file_count, 0)
  end

  def self.default_storage_unit
    "KB"
  end

  def self.default_storage_usage
    "0 #{default_storage_unit}"
  end

  def storage_usage(session_id:)
    values = mediaflux_metadata(session_id:)
    values.fetch(:quota_used, self.class.default_storage_usage) # if the storage is empty use the default
  end

  def storage_usage_raw(session_id:)
    values = mediaflux_metadata(session_id:)
    values.fetch(:quota_used_raw, 0) # if the storage raw is empty use zero
  end

  def self.default_storage_capacity
    "0 GB"
  end

  def storage_capacity(session_id:)
    values = mediaflux_metadata(session_id:)
    quota_value = values.fetch(:quota_allocation, '') #if quota does not exist, set value to an empty string
    if quota_value.blank?
      return self.class.default_storage_capacity
    else
      return quota_value
    end
  end

  def storage_capacity_raw(session_id:)
    values = mediaflux_metadata(session_id:)
    quota_value = values.fetch(:quota_allocation_raw, 0) #if quota does not exist, set value to 0
    quota_value
  end

  # Fetches the first n files
  def file_list(session_id:, size: 10)
    return { files: [] } if mediaflux_id.nil?

    query_req = Mediaflux::QueryRequest.new(session_token: session_id, collection: mediaflux_id, deep_search: true, aql_query: "type!='application/arc-asset-collection'")
    iterator_id = query_req.result

    iterator_req = Mediaflux::IteratorRequest.new(session_token: session_id, iterator: iterator_id, size: size)
    results = iterator_req.result

    # Destroy _after_ fetching the first set of results from iterator_req.
    # This call is required since it possible that we have read less assets than
    # what the collection has but we are done with the iterator.
    Mediaflux::IteratorDestroyRequest.new(session_token: session_id, iterator: iterator_id).resolve

    results
  end

  # Fetches the entire file list to a file
  def file_list_to_file(session_id:, filename:)
    return { files: [] } if mediaflux_id.nil?

    query_req = Mediaflux::QueryRequest.new(session_token: session_id, collection: mediaflux_id, deep_search: true,  aql_query: "type!='application/arc-asset-collection'")
    iterator_id = query_req.result

    start_time = Time.zone.now
    prefix = "file_list_to_file #{session_id[0..7]} #{self.metadata_model.project_id}"
    log_elapsed(start_time, prefix, "STARTED")

    File.open(filename, "w") do |file|
      page_number = 0
      # file header
      file.write("ID, PATH, NAME, COLLECTION?, LAST_MODIFIED, SIZE\r\n")
      loop do
        iterator_start_time = Time.zone.now
        page_number += 1
        iterator_req = Mediaflux::IteratorRequest.new(session_token: session_id, iterator: iterator_id, size: 1000)
        iterator_resp = iterator_req.result
        log_elapsed(iterator_start_time, prefix, "FETCHED page #{page_number} from iterator")
        lines = files_from_iterator(iterator_resp)
        file.write(lines.join("\r\n") + "\r\n")
        break if iterator_resp[:complete] || iterator_req.error?
      end
      log_elapsed(start_time, prefix, "ENDED")
    end

    # Destroy _after_ fetching the results from iterator_req
    # This call is technically not necessary since Mediaflux automatically deletes the iterator
    # once we have ran through it and by now we have. But it does not hurt either.
    Mediaflux::IteratorDestroyRequest.new(session_token: session_id, iterator: iterator_id).resolve
  end


  private

    def files_from_iterator(iterator_resp)
      lines = []
      iterator_resp[:files].each do |asset|
        lines << "#{asset.id}, #{asset.path_only}, #{asset.name}, #{asset.collection}, #{asset.last_modified}, #{asset.size}"
      end
      lines
    end

    def project_directory_pathname
      # allow the directory to be modified by changes in the metadata_json
      @project_directory_pathname = nil if @original_directory.present? && @original_directory != metadata_model.project_directory

      @project_directory_pathname ||= begin
        @original_directory = metadata_model.project_directory
        Pathname.new(@original_directory)
      end
    end

    # Ensure that the project directory is a valid path
    def safe_directory(directory)
      Project.safe_directory(directory)
    end

    def log_elapsed(start_time, prefix, message)
      elapsed_time = Time.zone.now - start_time
      timing_info = "#{format('%.2f', elapsed_time)} s"
      Rails.logger.info "#{prefix}: #{message}, #{timing_info}"
    end
end

1	# frozen_string_literal: true
2	class Project < ApplicationRecord	1✔
3
4	class ProjectCreateError < StandardError; end	1✔
5
6	validates_with ProjectValidator	1✔
7	has_many :provenance_events, dependent: :destroy	1✔
8	before_save do \|project\|	1✔
9	# Ensure that the metadata JSONB postgres field is persisted properly
10	project.metadata = project.metadata_model	331✔
11	end
12
13	# Valid project status described in ADR 7
14	# See `architecture-decisions/0007-valid-project-statuses.md`
15	PENDING_STATUS = "pending"	1✔
16	APPROVED_STATUS = "approved"	1✔
17	ACTIVE_STATUS = "active"	1✔
18
19	delegate :to_json, to: :metadata_json # field in the database	1✔
20
21	def create!(initial_metadata:, user:)	1✔
22	self.metadata_model = initial_metadata	4✔
23	if self.valid?	4✔
24	if initial_metadata.project_id == ProjectMetadata::DOI_NOT_MINTED	3✔
25	self.draft_doi(user: user)	2✔
26	self.save!	2✔
27	ProvenanceEvent.generate_submission_events(project: self, user: user)	2✔
28	else
29	self.save!	1✔
30	end
31	# return doi
32	self.metadata_model.project_id	3✔
33	else
34	nil
35	end
36	end
37
38	def approve!(current_user:)	1✔
UNCOV 39	request = Mediaflux::ProjectCreateServiceRequest.new(session_token: current_user.mediaflux_session, project: self)	×
UNCOV 40	request.resolve	×
41
UNCOV 42	if request.mediaflux_id.to_i == 0	×
UNCOV 43	raise ProjectCreateError.new("Error saving project #{self.id} to Mediaflux: #{request.response_error}. Debug output: #{request.debug_output}")	×
44	end
45
46	self.mediaflux_id = request.mediaflux_id	×
47	self.metadata_model.status = Project::APPROVED_STATUS	×
48	self.save!	×
49
NEW 50	debug_output = if request.mediaflux_id == 0	×
NEW 51	"Error saving project #{self.id} to Mediaflux: #{request.response_error}. Debug output: #{request.debug_output}"	×
52	else
NEW 53	"#{request.debug_output}"	×
54	end
NEW 55	Rails.logger.error debug_output	×
56
NEW 57	add_users_request = Mediaflux::ProjectUserAddRequest.new(session_token: current_user.mediaflux_session, project: self)	×
NEW 58	add_users_request.resolve	×
59
NEW 60	user_debug = "#{add_users_request.debug_output}"	×
NEW 61	Rails.logger.error "Project #{self.id} users have been added to MediaFlux: #{user_debug}"	×
62
63	# create provenance events:
64	# - one for approving the project and
65	# - another for changing the status of the project
66	# - another with debug information from the create project service
67	ProvenanceEvent.generate_approval_events(project: self, user: current_user, debug_output: debug_output)	×
68
69	self.mediaflux_id	×
70	end
71
72	def reload	1✔
73	super	7✔
74	@metadata_model = ProjectMetadata.new_from_hash(self.metadata)	7✔
75	self	7✔
76	end
77
78	def draft_doi(user: nil)	1✔
79	puldatacite = PULDatacite.new	3✔
80	self.metadata_model.project_id = puldatacite.draft_doi	3✔
81	end
82
83	# Ideally this method should return a ProjectMetadata object (like `metadata_model` does)
84	# but we'll keep them both while we are refactoring the code so that we don't break
85	# everything at once since `metadata` is used everywhere.
86	def metadata	1✔
87	@metadata_hash = (metadata_json \|\| {}).with_indifferent_access	430✔
88	end
89
90	def metadata_model	1✔
91	@metadata_model \|\|= ProjectMetadata.new_from_hash(self.metadata)	3,855✔
92	end
93
94	def metadata_model=(new_metadata_model)	1✔
95	@metadata_model = new_metadata_model	311✔
96	end
97
98	def metadata=(metadata_model)	1✔
99	# Convert our metadata to a hash so it can be saved on our JSONB field
100	metadata_hash = JSON.parse(metadata_model.to_json)	706✔
101	self.metadata_json = metadata_hash	706✔
102	end
103
104	def title	1✔
105	self.metadata_model.title	263✔
106	end
107
108	def departments	1✔
109	unsorted = metadata_model.departments \|\| []	77✔
110	unsorted.sort	77✔
111	end
112
113	def project_directory	1✔
114	metadata_model.project_directory \|\| ""	173✔
115	end
116
117	def project_directory_parent_path	1✔
118	# The tigerdata.project.create expectes every project to be under "tigerdata"
119	Mediaflux::Connection.root	11✔
120	end
121
122	def project_directory_short	1✔
123	project_directory	15✔
124	end
125
126	def status	1✔
127	metadata_model.status	555✔
128	end
129
130	def pending?	1✔
131	status == PENDING_STATUS	269✔
132	end
133
134	def in_mediaflux?	1✔
135	mediaflux_id.present?	61✔
136	end
137
138	def self.users_projects(user)	1✔
139	# See https://scalegrid.io/blog/using-jsonb-in-postgresql-how-to-effectively-store-index-json-data-in-postgresql/
140	# for information on the @> operator
141	uid = user.uid	61✔
142	query_ro = '{"data_user_read_only":["' + uid + '"]}'	61✔
143	query_rw = '{"data_user_read_write":["' + uid + '"]}'	61✔
144	query = "(metadata_json @> ? :: jsonb) OR (metadata_json @> ? :: jsonb)"	61✔
145	args = [query_ro, query_rw]	61✔
146	if user.eligible_sponsor?	61✔
147	query += "OR (metadata_json->>'data_sponsor' = ?)"	16✔
148	args << uid	16✔
149	end
150	if user.eligible_manager?	61✔
151	query += "OR (metadata_json->>'data_manager' = ?)"	12✔
152	args << uid	12✔
153	end
154	Project.where( query, *args)	61✔
155	end
156
157	def self.sponsored_projects(sponsor)	1✔
158	Project.where("metadata_json->>'data_sponsor' = ?", sponsor)	1✔
159	end
160
161	def self.managed_projects(manager)	1✔
162	Project.where("metadata_json->>'data_manager' = ?", manager)	1✔
163	end
164
165	def self.pending_projects	1✔
166	Project.where("mediaflux_id IS NULL")	57✔
167	end
168
169	def self.approved_projects	1✔
170	Project.where("mediaflux_id IS NOT NULL")	57✔
171	end
172
173	def self.data_user_projects(user)	1✔
174	# See https://scalegrid.io/blog/using-jsonb-in-postgresql-how-to-effectively-store-index-json-data-in-postgresql/
175	# for information on the @> operator
176	query_ro = '{"data_user_read_only":["' + user + '"]}'	1✔
177	query_rw = '{"data_user_read_write":["' + user + '"]}'	1✔
178	Project.where("(metadata_json @> ? :: jsonb) OR (metadata_json @> ? :: jsonb)", query_ro, query_rw)	1✔
179	end
180
181	def user_has_access?(user:)	1✔
182	return true if user.eligible_sysadmin?	46✔
183	metadata_model.data_sponsor == user.uid \|\| metadata_model.data_manager == user.uid \|\|	36✔
184	metadata_model.data_user_read_only.include?(user.uid) \|\| metadata_model.data_user_read_write.include?(user.uid)
185	end
186
187	def created_by_user	1✔
188	User.find_by(uid: metadata_model.created_by)	12✔
189	end
190
191	def to_xml	1✔
192	ProjectShowPresenter.new(self).to_xml	4✔
193	end
194
195	# @return [String] XML representation of the <meta> element
196	def mediaflux_meta_xml(user:)	1✔
197	doc = ProjectMediaflux.document(project: self, user: user)	1✔
198	doc.xpath("/response/reply/result/asset/meta").to_s	1✔
199	end
200
201	def mediaflux_metadata(session_id:)	1✔
202	@mediaflux_metadata \|\|= begin	109✔
203	accum_req = Mediaflux::AssetMetadataRequest.new(session_token: session_id, id: mediaflux_id)	29✔
204	accum_req.metadata	29✔
205	end
206	@mediaflux_metadata	109✔
207	end
208
209	def asset_count(session_id:)	1✔
210	values = mediaflux_metadata(session_id:)	11✔
211	values.fetch(:total_file_count, 0)	11✔
212	end
213
214	def self.default_storage_unit	1✔
215	"KB"	26✔
216	end
217
218	def self.default_storage_usage	1✔
219	"0 #{default_storage_unit}"	25✔
220	end
221
222	def storage_usage(session_id:)	1✔
223	values = mediaflux_metadata(session_id:)	24✔
224	values.fetch(:quota_used, self.class.default_storage_usage) # if the storage is empty use the default	24✔
225	end
226
227	def storage_usage_raw(session_id:)	1✔
228	values = mediaflux_metadata(session_id:)	×
229	values.fetch(:quota_used_raw, 0) # if the storage raw is empty use zero	×
230	end
231
232	def self.default_storage_capacity	1✔
233	"0 GB"	24✔
234	end
235
236	def storage_capacity(session_id:)	1✔
237	values = mediaflux_metadata(session_id:)	24✔
238	quota_value = values.fetch(:quota_allocation, '') #if quota does not exist, set value to an empty string	24✔
239	if quota_value.blank?	24✔
240	return self.class.default_storage_capacity	24✔
241	else
242	return quota_value	×
243	end
244	end
245
246	def storage_capacity_raw(session_id:)	1✔
247	values = mediaflux_metadata(session_id:)	48✔
248	quota_value = values.fetch(:quota_allocation_raw, 0) #if quota does not exist, set value to 0	48✔
249	quota_value	48✔
250	end
251
252	# Fetches the first n files
253	def file_list(session_id:, size: 10)	1✔
254	return { files: [] } if mediaflux_id.nil?	11✔
255
256	query_req = Mediaflux::QueryRequest.new(session_token: session_id, collection: mediaflux_id, deep_search: true, aql_query: "type!='application/arc-asset-collection'")	4✔
257	iterator_id = query_req.result	4✔
258
259	iterator_req = Mediaflux::IteratorRequest.new(session_token: session_id, iterator: iterator_id, size: size)	4✔
260	results = iterator_req.result	4✔
261
262	# Destroy _after_ fetching the first set of results from iterator_req.
263	# This call is required since it possible that we have read less assets than
264	# what the collection has but we are done with the iterator.
265	Mediaflux::IteratorDestroyRequest.new(session_token: session_id, iterator: iterator_id).resolve	4✔
266
267	results	4✔
268	end
269
270	# Fetches the entire file list to a file
271	def file_list_to_file(session_id:, filename:)	1✔
272	return { files: [] } if mediaflux_id.nil?	1✔
273
274	query_req = Mediaflux::QueryRequest.new(session_token: session_id, collection: mediaflux_id, deep_search: true, aql_query: "type!='application/arc-asset-collection'")	×
275	iterator_id = query_req.result	×
276
277	start_time = Time.zone.now	×
278	prefix = "file_list_to_file #{session_id[0..7]} #{self.metadata_model.project_id}"	×
279	log_elapsed(start_time, prefix, "STARTED")	×
280
281	File.open(filename, "w") do \|file\|	×
282	page_number = 0	×
283	# file header
284	file.write("ID, PATH, NAME, COLLECTION?, LAST_MODIFIED, SIZE\r\n")	×
285	loop do	×
286	iterator_start_time = Time.zone.now	×
287	page_number += 1	×
288	iterator_req = Mediaflux::IteratorRequest.new(session_token: session_id, iterator: iterator_id, size: 1000)	×
289	iterator_resp = iterator_req.result	×
290	log_elapsed(iterator_start_time, prefix, "FETCHED page #{page_number} from iterator")	×
291	lines = files_from_iterator(iterator_resp)	×
292	file.write(lines.join("\r\n") + "\r\n")	×
293	break if iterator_resp[:complete] \|\| iterator_req.error?	×
294	end
295	log_elapsed(start_time, prefix, "ENDED")	×
296	end
297
298	# Destroy _after_ fetching the results from iterator_req
299	# This call is technically not necessary since Mediaflux automatically deletes the iterator
300	# once we have ran through it and by now we have. But it does not hurt either.
301	Mediaflux::IteratorDestroyRequest.new(session_token: session_id, iterator: iterator_id).resolve	×
302	end
303
304
305	private	1✔
306
307	def files_from_iterator(iterator_resp)	1✔
308	lines = []	×
309	iterator_resp[:files].each do \|asset\|	×
310	lines << "#{asset.id}, #{asset.path_only}, #{asset.name}, #{asset.collection}, #{asset.last_modified}, #{asset.size}"	×
311	end
312	lines	×
313	end
314
315	def project_directory_pathname	1✔
316	# allow the directory to be modified by changes in the metadata_json
317	@project_directory_pathname = nil if @original_directory.present? && @original_directory != metadata_model.project_directory	×
318
319	@project_directory_pathname \|\|= begin	×
320	@original_directory = metadata_model.project_directory	×
321	Pathname.new(@original_directory)	×
322	end
323	end
324
325	# Ensure that the project directory is a valid path
326	def safe_directory(directory)	1✔
327	Project.safe_directory(directory)	×
328	end
329
330	def log_elapsed(start_time, prefix, message)	1✔
331	elapsed_time = Time.zone.now - start_time	×
332	timing_info = "#{format('%.2f', elapsed_time)} s"	×
333	Rails.logger.info "#{prefix}: #{message}, #{timing_info}"	×
334	end
335	end

pulibrary / tigerdata-app / b489533f-9066-4a1f-b488-40e1f0465f4b

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