d7ce1bf9-25b8-4b3e-b9dd-43f9a26f2d96

Committed 17 Oct 2025 05:51PM UTC coverage: 91.054%. Remained the same

Build # d7ce1bf9-25b8-4b3e-b9dd-43f9a26f2d96

Build Type

Pull #2055

circleci

Committed by

jrgriffiniii

Commit Message

- Ensuring that `parallelism` is set to 4
- Separating `system` RSpec spec suites in the CI build
- Using an `inconsistent` RSpec tag to mark inconsistently failing tests
- Ensuring that CI does not run for `inconsistent` tests

Pull Request Pull Request #2055: Ensuring that `parallelism` is set to 4 for CircleCI and separates `system` and inconsistently-failing tests into separate CI jobs

Run Details

2738 of 3007 relevant lines covered (91.05%)

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95.33

/app/models/project.rb

# frozen_string_literal: true
class Project < ApplicationRecord

  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`
  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 activate(current_user:)
    raise StandardError.new("Only approved projects can be activated") if self.status != Project::APPROVED_STATUS
    metadata_request = Mediaflux::AssetMetadataRequest.new(session_token: current_user.mediaflux_session, id: self.mediaflux_id)
    metadata_request.resolve
    raise metadata_request.response_error if metadata_request.error?
    if self.title == metadata_request.metadata[:title]
      self.metadata_model.status = Project::ACTIVE_STATUS
      self.save!
    else
      raise StandardError.new("Title mismatch: #{self.title} != #{metadata_request.metadata[:title]}")
    end
  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_short
    project_directory
  end

  def status
    metadata_model.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) OR (metadata_json->>'data_sponsor' = ?) OR (metadata_json->>'data_manager' = ?)"
    args = [query_ro, query_rw, uid, uid]
    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.all_projects
    Project.all
  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	5✔
3
4	validates_with ProjectValidator	5✔
5	has_many :provenance_events, dependent: :destroy	5✔
6	before_save do \|project\|	5✔
7	# Ensure that the metadata JSONB postgres field is persisted properly
8	project.metadata = project.metadata_model	789✔
9	end
10
11	# Valid project status described in ADR 7
12	# See `architecture-decisions/0007-valid-project-statuses.md`
13	APPROVED_STATUS = "approved"	5✔
14	ACTIVE_STATUS = "active"	5✔
15
16	delegate :to_json, to: :metadata_json # field in the database	5✔
17
18	def create!(initial_metadata:, user:)	5✔
19	self.metadata_model = initial_metadata	5✔
20	if self.valid?	5✔
21	if initial_metadata.project_id == ProjectMetadata::DOI_NOT_MINTED	3✔
22	self.draft_doi(user: user)	2✔
23	self.save!	2✔
24	ProvenanceEvent.generate_submission_events(project: self, user: user)	2✔
25	else
26	self.save!	1✔
27	end
28	# return doi
29	self.metadata_model.project_id	3✔
30	else
31	nil
32	end
33	end
34
35	def activate(current_user:)	5✔
36	raise StandardError.new("Only approved projects can be activated") if self.status != Project::APPROVED_STATUS	115✔
37	metadata_request = Mediaflux::AssetMetadataRequest.new(session_token: current_user.mediaflux_session, id: self.mediaflux_id)	115✔
38	metadata_request.resolve	115✔
39	raise metadata_request.response_error if metadata_request.error?	115✔
40	if self.title == metadata_request.metadata[:title]	115✔
41	self.metadata_model.status = Project::ACTIVE_STATUS	115✔
42	self.save!	115✔
43	else
44	raise StandardError.new("Title mismatch: #{self.title} != #{metadata_request.metadata[:title]}")	×
45	end
46	end
47
48	def draft_doi(user: nil)	5✔
49	puldatacite = PULDatacite.new	123✔
50	self.metadata_model.project_id = puldatacite.draft_doi	123✔
51	end
52
53	# Ideally this method should return a ProjectMetadata object (like `metadata_model` does)
54	# but we'll keep them both while we are refactoring the code so that we don't break
55	# everything at once since `metadata` is used everywhere.
56	def metadata	5✔
57	@metadata_hash = (metadata_json \|\| {}).with_indifferent_access	476✔
58	end
59
60	def metadata_model	5✔
61	@metadata_model \|\|= ProjectMetadata.new_from_hash(self.metadata)	9,123✔
62	end
63
64	def metadata_model=(new_metadata_model)	5✔
65	@metadata_model = new_metadata_model	314✔
66	end
67
68	def metadata=(metadata_model)	5✔
69	# Convert our metadata to a hash so it can be saved on our JSONB field
70	metadata_hash = JSON.parse(metadata_model.to_json)	1,644✔
71	self.metadata_json = metadata_hash	1,644✔
72	end
73
74	def title	5✔
75	self.metadata_model.title	542✔
76	end
77
78	def departments	5✔
79	unsorted = metadata_model.departments \|\| []	15✔
80	unsorted.sort	15✔
81	end
82
83	def project_directory	5✔
84	metadata_model.project_directory \|\| ""	179✔
85	end
86
87	def project_directory_short	5✔
88	project_directory	10✔
89	end
90
91	def status	5✔
92	metadata_model.status	520✔
93	end
94
95	def in_mediaflux?	5✔
96	mediaflux_id.present?	26✔
97	end
98
99	def self.users_projects(user)	5✔
100	# See https://scalegrid.io/blog/using-jsonb-in-postgresql-how-to-effectively-store-index-json-data-in-postgresql/
101	# for information on the @> operator
102	uid = user.uid	84✔
103	query_ro = '{"data_user_read_only":["' + uid + '"]}'	84✔
104	query_rw = '{"data_user_read_write":["' + uid + '"]}'	84✔
105	query = "(metadata_json @> ? :: jsonb) OR (metadata_json @> ? :: jsonb) OR (metadata_json->>'data_sponsor' = ?) OR (metadata_json->>'data_manager' = ?)"	84✔
106	args = [query_ro, query_rw, uid, uid]	84✔
107	Project.where( query, *args)	84✔
108	end
109
110	def self.sponsored_projects(sponsor)	5✔
111	Project.where("metadata_json->>'data_sponsor' = ?", sponsor)	1✔
112	end
113
114	def self.managed_projects(manager)	5✔
115	Project.where("metadata_json->>'data_manager' = ?", manager)	1✔
116	end
117
118	def self.all_projects	5✔
119	Project.all	4✔
120	end
121
122	def user_has_access?(user:)	5✔
123	return true if user.eligible_sysadmin?	56✔
124	metadata_model.data_sponsor == user.uid \|\| metadata_model.data_manager == user.uid \|\|	48✔
125	metadata_model.data_user_read_only.include?(user.uid) \|\| metadata_model.data_user_read_write.include?(user.uid)
126	end
127
128	def created_by_user	5✔
129	User.find_by(uid: metadata_model.created_by)	×
130	end
131
132	def to_xml	5✔
133	ProjectShowPresenter.new(self).to_xml	1✔
134	end
135
136	# @return [String] XML representation of the <meta> element
137	def mediaflux_meta_xml(user:)	5✔
138	doc = ProjectMediaflux.document(project: self, user: user)	3✔
139	doc.xpath("/response/reply/result/asset/meta").to_s	3✔
140	end
141
142	def mediaflux_metadata(session_id:)	5✔
143	@mediaflux_metadata \|\|= begin	762✔
144	accum_req = Mediaflux::AssetMetadataRequest.new(session_token: session_id, id: mediaflux_id)	138✔
145	accum_req.metadata	138✔
146	end
147	@mediaflux_metadata	758✔
148	end
149
150	def asset_count(session_id:)	5✔
151	values = mediaflux_metadata(session_id:)	30✔
152	values.fetch(:total_file_count, 0)	30✔
153	end
154
155	def self.default_storage_unit	5✔
156	"KB"	248✔
157	end
158
159	def self.default_storage_usage	5✔
160	"0 #{default_storage_unit}"	247✔
161	end
162
163	def storage_usage(session_id:)	5✔
164	values = mediaflux_metadata(session_id:)	250✔
165	values.fetch(:quota_used, self.class.default_storage_usage) # if the storage is empty use the default	246✔
166	end
167
168	def storage_usage_raw(session_id:)	5✔
169	values = mediaflux_metadata(session_id:)	41✔
170	values.fetch(:quota_used_raw, 0) # if the storage raw is empty use zero	41✔
171	end
172
173	def self.default_storage_capacity	5✔
174	"0 GB"	204✔
175	end
176
177	def storage_capacity(session_id:)	5✔
178	values = mediaflux_metadata(session_id:)	246✔
179	quota_value = values.fetch(:quota_allocation, '') #if quota does not exist, set value to an empty string	246✔
180	if quota_value.blank?	246✔
181	return self.class.default_storage_capacity	204✔
182	else
183	return quota_value	42✔
184	end
185	end
186
187	def storage_capacity_raw(session_id:)	5✔
188	values = mediaflux_metadata(session_id:)	193✔
189	quota_value = values.fetch(:quota_allocation_raw, 0) #if quota does not exist, set value to 0	193✔
190	quota_value	193✔
191	end
192
193	# Fetches the first n files
194	def file_list(session_id:, size: 10)	5✔
195	return { files: [] } if mediaflux_id.nil?	33✔
196
197	query_req = Mediaflux::QueryRequest.new(session_token: session_id, collection: mediaflux_id, deep_search: true, aql_query: "type!='application/arc-asset-collection'")	26✔
198	iterator_id = query_req.result	26✔
199
200	iterator_req = Mediaflux::IteratorRequest.new(session_token: session_id, iterator: iterator_id, size: size)	26✔
201	results = iterator_req.result	26✔
202
203	# Destroy _after_ fetching the first set of results from iterator_req.
204	# This call is required since it possible that we have read less assets than
205	# what the collection has but we are done with the iterator.
206	Mediaflux::IteratorDestroyRequest.new(session_token: session_id, iterator: iterator_id).resolve	26✔
207
208	results	26✔
209	end
210
211	# Fetches the entire file list to a file
212	def file_list_to_file(session_id:, filename:)	5✔
213	return { files: [] } if mediaflux_id.nil?	12✔
214
215	query_req = Mediaflux::QueryRequest.new(session_token: session_id, collection: mediaflux_id, deep_search: true, aql_query: "type!='application/arc-asset-collection'")	11✔
216	iterator_id = query_req.result	11✔
217
218	start_time = Time.zone.now	11✔
219	prefix = "file_list_to_file #{session_id[0..7]} #{self.metadata_model.project_id}"	11✔
220	log_elapsed(start_time, prefix, "STARTED")	11✔
221
222	File.open(filename, "w") do \|file\|	11✔
223	page_number = 0	11✔
224	# file header
225	file.write("ID, PATH, NAME, COLLECTION?, LAST_MODIFIED, SIZE\r\n")	11✔
226	loop do	11✔
227	iterator_start_time = Time.zone.now	11✔
228	page_number += 1	11✔
229	iterator_req = Mediaflux::IteratorRequest.new(session_token: session_id, iterator: iterator_id, size: 1000)	11✔
230	iterator_resp = iterator_req.result	11✔
231	log_elapsed(iterator_start_time, prefix, "FETCHED page #{page_number} from iterator")	11✔
232	lines = files_from_iterator(iterator_resp)	11✔
233	file.write(lines.join("\r\n") + "\r\n")	11✔
234	break if iterator_resp[:complete] \|\| iterator_req.error?	11✔
235	end
236	log_elapsed(start_time, prefix, "ENDED")	11✔
237	end
238
239	# Destroy _after_ fetching the results from iterator_req
240	# This call is technically not necessary since Mediaflux automatically deletes the iterator
241	# once we have ran through it and by now we have. But it does not hurt either.
242	Mediaflux::IteratorDestroyRequest.new(session_token: session_id, iterator: iterator_id).resolve	11✔
243	end
244
245
246	private	5✔
247
248	def files_from_iterator(iterator_resp)	5✔
249	lines = []	11✔
250	iterator_resp[:files].each do \|asset\|	11✔
251	lines << "#{asset.id}, #{asset.path_only}, #{asset.name}, #{asset.collection}, #{asset.last_modified}, #{asset.size}"	16✔
252	end
253	lines	11✔
254	end
255
256	def project_directory_pathname	5✔
257	# allow the directory to be modified by changes in the metadata_json
258	@project_directory_pathname = nil if @original_directory.present? && @original_directory != metadata_model.project_directory	×
259
260	@project_directory_pathname \|\|= begin	×
261	@original_directory = metadata_model.project_directory	×
262	Pathname.new(@original_directory)	×
263	end
264	end
265
266	# Ensure that the project directory is a valid path
267	def safe_directory(directory)	5✔
268	Project.safe_directory(directory)	×
269	end
270
271	def log_elapsed(start_time, prefix, message)	5✔
272	elapsed_time = Time.zone.now - start_time	33✔
273	timing_info = "#{format('%.2f', elapsed_time)} s"	33✔
274	Rails.logger.info "#{prefix}: #{message}, #{timing_info}"	33✔
275	end
276	end

pulibrary / tigerdata-app / d7ce1bf9-25b8-4b3e-b9dd-43f9a26f2d96

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