54385a8c-ec76-421e-81fd-41bf4c9d5b76

Committed 21 Jul 2025 08:55PM UTC coverage: 66.374% (-5.3%) from 71.631%

Build # 54385a8c-ec76-421e-81fd-41bf4c9d5b76

Build Type

push

circleci

Committed by

web-flow

Commit Message

Upgrade mediaflux build to v0.7.0 (#1617)

* Upgrade mediaflux build to v0.7.0

* prettier

* Upgrade mflux version used by the test suite

* tagging integration tests

* tagging integration tests

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81.91

/app/controllers/projects_controller.rb

# frozen_string_literal: true
class ProjectsController < ApplicationController

  before_action :set_breadcrumbs
  before_action :authenticate_user!

  def new
    add_breadcrumb("New Project Request")
    return build_new_project if current_user.eligible_sponsor?

    redirect_to dashboard_path
  end

  def project_params
    params.dup
  end

  def create
    metadata_params = params.dup
    metadata_params[:status] = Project::PENDING_STATUS
    metadata_params[:created_by] = current_user.uid
    metadata_params[:created_on] = Time.current.in_time_zone("America/New_York").iso8601
    project_metadata = ProjectMetadata.new_from_params(metadata_params)

    build_new_project # calling private method to build a new project and set a class variable @project
    project.create!(initial_metadata: project_metadata, user: current_user)
    if project.metadata_model.project_id != nil
      begin
        mailer = TigerdataMailer.with(project_id: project.id)
        message_delivery = mailer.project_creation
        message_delivery.deliver_later

        redirect_to project_confirmation_path(project)
      rescue StandardError => mailer_error
        raise(TigerData::MailerError, mailer_error)
      end
    else
      render :new
    end
  rescue TigerData::MailerError => mailer_error
    logger_message = "Error encountered creating the project #{project.id} as user #{current_user.email}"
    Rails.logger.error(logger_message)
    honeybadger_context = {
      current_user_email: current_user.email,
      project_id: project.id,
      project_metadata: project.metadata
    }
    Honeybadger.notify(mailer_error, context: honeybadger_context)

    error_message = "We are sorry, while the project was successfully created, an error was encountered which prevents the delivery of an e-mail message confirming this. Please know that this error has been logged, and shall be reviewed by members of RDSS."
    flash[:notice] = error_message

    render :new
  rescue StandardError => error
    logger_message = if project.persisted?
                      "Error encountered creating the project #{project.id} as user #{current_user.email}"
                     else
                      "Error encountered creating the project #{metadata_params[:title]} as user #{current_user.email}"
                     end
    Rails.logger.error(logger_message)
    honeybadger_context = {
      current_user_email: current_user.email,
      project_id: project.id,
      project_metadata: project.metadata
    }
    Honeybadger.notify(error, context: honeybadger_context)

    error_message = "We are sorry, the project was not successfully created, and an error was encountered which prevents the delivery of an e-mail message confirming this. Please know that this error has been logged, and shall be reviewed by members of RDSS promptly."

    flash[:notice] = error_message
    render :new
  end

  def details
    return if project.blank?

    add_breadcrumb(project.title, project_path)
    add_breadcrumb("Details")

    @departments = project.departments.join(", ")
    @project_metadata = project.metadata_model

    @data_sponsor = User.find_by(uid: @project_metadata.data_sponsor)
    @data_manager = User.find_by(uid: @project_metadata.data_manager)

    read_only_uids = @project_metadata.ro_users
    data_read_only_users = read_only_uids.map { |uid| ReadOnlyUser.find_by(uid:) }.reject(&:blank?)

    read_write_uids = @project_metadata.rw_users
    data_read_write_users = read_write_uids.map { |uid| User.find_by(uid:) }.reject(&:blank?)

    unsorted_data_users = data_read_only_users + data_read_write_users
    sorted_data_users = unsorted_data_users.sort_by { |u| u.family_name || u.uid }
    @data_users = sorted_data_users.uniq { |u| u.uid }
    user_model_names = @data_users.map(&:display_name_safe)
    @data_user_names = user_model_names.join(", ")

    @provenance_events = project.provenance_events.where.not(event_type: ProvenanceEvent::STATUS_UPDATE_EVENT_TYPE)

    @project_eligible_to_edit = true if project.status == Project::APPROVED_STATUS && eligible_editor?

    @project_metadata = @project.metadata
    @project_id = @project_metadata[:project_id] || {}
    @storage_capacity = @project_metadata[:storage_capacity]
    @size = @storage_capacity[:size]
    @unit = @storage_capacity[:unit]

    @requested_size = @size[:requested]
    @requested_unit = @unit[:requested]

    @approved_size = @size[:approved]
    @approved_unit = @unit[:approved]

    @storage_expectations = @project_metadata[:storage_performance_expectations]
    @requested_storage_expectations = @storage_expectations[:requested]
    @approved_storage_expectations = @storage_expectations[:approved]

    @project_purpose = @project_metadata[:project_purpose]


    @project_session = "details"


    respond_to do |format|
      format.html do
        @project = ProjectShowPresenter.new(project)
      end
      format.json do
        render json: project.to_json
      end
      format.xml do
        render xml: project.to_xml
      end
    end
  end

  def edit
    add_breadcrumb(project.title, project_path)
    add_breadcrumb("Edit")
    project
    if project.metadata_model.status != Project::APPROVED_STATUS
      flash[:notice] = "Pending projects can not be edited."
      redirect_to project
    elsif project.metadata_model.status == Project::APPROVED_STATUS && !eligible_editor? #check if the current user is a sponsor or a manager
      flash[:notice] = "Only data sponsors and data managers can revise this project."
      redirect_to project
    end
  end

  def update
    @project = Project.find(params[:id])
    #Approve action
    if params.key?("approved")
      @project.metadata_model.update_with_params(params, current_user)
      @project.approve!(current_user:)
    end

    #Edit action
    if params.key?("title")
      @project.metadata_model.status = @project.metadata_model.status || Project::PENDING_STATUS
      @project.metadata_model.update_with_params(params, current_user)
    end

    # @todo ProjectMetadata should be refactored to implement ProjectMetadata.valid?(updated_metadata)
    if project.save and params.key?("approved")
      redirect_to project_approval_received_path(@project)
    elsif project.save and params.key?("title")
      redirect_to project_revision_confirmation_path(@project)
    else
      render :edit
    end
  end

  def index
    if current_user.eligible_sysadmin?
      @projects = Project.all
    else
      flash[:alert] = I18n.t(:access_denied)
      redirect_to dashboard_path
    end
  end

  def confirmation; end
  def revision_confirmation; end

  def show

    return if project.blank?
    add_breadcrumb(project.title, project_path)
    add_breadcrumb("Contents")

    @latest_completed_download = current_user.user_requests.where(project_id: @project.id, state: "completed").order(:completion_time).last
    @storage_usage = project.storage_usage(session_id: current_user.mediaflux_session)
    @storage_capacity = project.storage_capacity(session_id: current_user.mediaflux_session)

    @num_files = project.asset_count(session_id: current_user.mediaflux_session)

    @file_list = project.file_list(session_id: current_user.mediaflux_session, size: 100)
    @files = @file_list[:files]
    @files.sort_by!(&:path)
    @project = ProjectShowPresenter.new(project)

    @project_session = "content"
    respond_to do |format|
      format.html { render }
      format.xml { render xml: @project.to_xml }
    end
  end

  # GET "projects/:id/:id-mf"
  #
  # This action is used to render the mediaflux metadata for a project.
  def show_mediaflux
    project_id = params[:id]
    project = Project.find(project_id)

    respond_to do |format|
      format.xml do
        render xml: project.mediaflux_meta_xml
      end
    end
  end

  def project_job_service
    @project_job_service ||= ProjectJobService.new(project:)
  end

  def list_contents
    return if project.blank?

    project_job_service.list_contents_job(user: current_user)

    json_response = {
      message: "File list for \"#{project.title}\" is being generated in the background. A link to the downloadable file list will be available in the \"Recent Activity\" section of your dashboard when it is available. You may safely navigate away from this page or close this tab."
    }
    render json: json_response
  rescue => ex
    message = "Error producing document list (project id: #{project&.id}): #{ex.message}"
    Rails.logger.error(message)
    Honeybadger.notify(message)
    render json: { message: "Document list could not be generated." }
  end

  def file_list_download
    job_id = params[:job_id]
    user_request = FileInventoryRequest.where(job_id:job_id).first
    if user_request.nil?
      # TODO: handle error
      redirect_to "/"
    else
      filename = user_request.output_file
      send_data File.read(filename), type: "text/plain", filename: "filelist.csv", disposition: "attachment"
    end
  end

  def approve
    if current_user.eligible_sysadmin?
      add_breadcrumb(project.title, project_path)
      add_breadcrumb("Approval Settings", project_approve_path)
      add_breadcrumb("Edit")
      project
      @departments = project.departments.join(", ")
      @project_metadata = project.metadata
      sponsor_uid = @project_metadata[:data_sponsor]
      @data_sponsor = User.find_by(uid: sponsor_uid)
      @provenance_events = project.provenance_events.where.not(event_type: ProvenanceEvent::STATUS_UPDATE_EVENT_TYPE)

      @title = @project_metadata["title"]
    else redirect_to dashboard_path
    end
  end

  def create_script
    project_id = params[:id]
    project = Project.find(project_id)
    service = MediafluxScriptFactory.new(project: project)
    respond_to do |format|
      format.json { render json: {script: service.aterm_script} }
    end
  end

  private

    def build_new_project
      @project ||= Project.new
    end

    def project
      @project ||= begin
        project = Project.find(params[:id])
        if project.user_has_access?(user: current_user)
          project
        else
          flash[:alert] = I18n.t(:access_denied)
          redirect_to dashboard_path
          nil
        end
      end
    end

    def eligible_editor?
      return true if current_user.eligible_sponsor? or current_user.eligible_manager?
    end

    def shared_file_location(filename)
      raise "Shared location is not configured" if Rails.configuration.mediaflux["shared_files_location"].blank?
      location = Pathname.new(Rails.configuration.mediaflux["shared_files_location"])
      location.join(filename).to_s
    end

    def set_breadcrumbs
      add_breadcrumb("Dashboard",dashboard_path)
    end
end

1	# frozen_string_literal: true
2	class ProjectsController < ApplicationController	1✔
3
4	before_action :set_breadcrumbs	1✔
5	before_action :authenticate_user!	1✔
6
7	def new	1✔
8	add_breadcrumb("New Project Request")	16✔
9	return build_new_project if current_user.eligible_sponsor?	16✔
10
11	redirect_to dashboard_path	2✔
12	end
13
14	def project_params	1✔
15	params.dup	×
16	end
17
18	def create	1✔
19	metadata_params = params.dup	12✔
20	metadata_params[:status] = Project::PENDING_STATUS	12✔
21	metadata_params[:created_by] = current_user.uid	12✔
22	metadata_params[:created_on] = Time.current.in_time_zone("America/New_York").iso8601	12✔
23	project_metadata = ProjectMetadata.new_from_params(metadata_params)	12✔
24
25	build_new_project # calling private method to build a new project and set a class variable @project	12✔
26	project.create!(initial_metadata: project_metadata, user: current_user)	12✔
27	if project.metadata_model.project_id != nil	12✔
28	begin
29	mailer = TigerdataMailer.with(project_id: project.id)	12✔
30	message_delivery = mailer.project_creation	12✔
31	message_delivery.deliver_later	12✔
32
33	redirect_to project_confirmation_path(project)	11✔
34	rescue StandardError => mailer_error
35	raise(TigerData::MailerError, mailer_error)	2✔
36	end
37	else
38	render :new	×
39	end
40	rescue TigerData::MailerError => mailer_error
41	logger_message = "Error encountered creating the project #{project.id} as user #{current_user.email}"	2✔
42	Rails.logger.error(logger_message)	2✔
43	honeybadger_context = {
44	current_user_email: current_user.email,	2✔
45	project_id: project.id,
46	project_metadata: project.metadata
47	}
48	Honeybadger.notify(mailer_error, context: honeybadger_context)	2✔
49
50	error_message = "We are sorry, while the project was successfully created, an error was encountered which prevents the delivery of an e-mail message confirming this. Please know that this error has been logged, and shall be reviewed by members of RDSS."	2✔
51	flash[:notice] = error_message	2✔
52
53	render :new	2✔
54	rescue StandardError => error
55	logger_message = if project.persisted?	×
56	"Error encountered creating the project #{project.id} as user #{current_user.email}"	×
57	else
58	"Error encountered creating the project #{metadata_params[:title]} as user #{current_user.email}"	×
59	end
60	Rails.logger.error(logger_message)	×
61	honeybadger_context = {
62	current_user_email: current_user.email,	×
63	project_id: project.id,
64	project_metadata: project.metadata
65	}
66	Honeybadger.notify(error, context: honeybadger_context)	×
67
68	error_message = "We are sorry, the project was not successfully created, and an error was encountered which prevents the delivery of an e-mail message confirming this. Please know that this error has been logged, and shall be reviewed by members of RDSS promptly."	×
69
70	flash[:notice] = error_message	×
71	render :new	×
72	end
73
74	def details	1✔
75	return if project.blank?	31✔
76
77	add_breadcrumb(project.title, project_path)	30✔
78	add_breadcrumb("Details")	30✔
79
80	@departments = project.departments.join(", ")	30✔
81	@project_metadata = project.metadata_model	30✔
82
83	@data_sponsor = User.find_by(uid: @project_metadata.data_sponsor)	30✔
84	@data_manager = User.find_by(uid: @project_metadata.data_manager)	30✔
85
86	read_only_uids = @project_metadata.ro_users	30✔
87	data_read_only_users = read_only_uids.map { \|uid\| ReadOnlyUser.find_by(uid:) }.reject(&:blank?)	46✔
88
89	read_write_uids = @project_metadata.rw_users	30✔
90	data_read_write_users = read_write_uids.map { \|uid\| User.find_by(uid:) }.reject(&:blank?)	42✔
91
92	unsorted_data_users = data_read_only_users + data_read_write_users	30✔
93	sorted_data_users = unsorted_data_users.sort_by { \|u\| u.family_name \|\| u.uid }	58✔
94	@data_users = sorted_data_users.uniq { \|u\| u.uid }	50✔
95	user_model_names = @data_users.map(&:display_name_safe)	30✔
96	@data_user_names = user_model_names.join(", ")	30✔
97
98	@provenance_events = project.provenance_events.where.not(event_type: ProvenanceEvent::STATUS_UPDATE_EVENT_TYPE)	30✔
99
100	@project_eligible_to_edit = true if project.status == Project::APPROVED_STATUS && eligible_editor?	30✔
101
102	@project_metadata = @project.metadata	30✔
103	@project_id = @project_metadata[:project_id] \|\| {}	30✔
104	@storage_capacity = @project_metadata[:storage_capacity]	30✔
105	@size = @storage_capacity[:size]	30✔
106	@unit = @storage_capacity[:unit]	30✔
107
108	@requested_size = @size[:requested]	30✔
109	@requested_unit = @unit[:requested]	30✔
110
111	@approved_size = @size[:approved]	30✔
112	@approved_unit = @unit[:approved]	30✔
113
114	@storage_expectations = @project_metadata[:storage_performance_expectations]	30✔
115	@requested_storage_expectations = @storage_expectations[:requested]	30✔
116	@approved_storage_expectations = @storage_expectations[:approved]	30✔
117
118	@project_purpose = @project_metadata[:project_purpose]	30✔
119
120
121	@project_session = "details"	30✔
122
123
124	respond_to do \|format\|	30✔
125	format.html do	30✔
126	@project = ProjectShowPresenter.new(project)	27✔
127	end
128	format.json do	30✔
129	render json: project.to_json	2✔
130	end
131	format.xml do	30✔
132	render xml: project.to_xml	1✔
133	end
134	end
135	end
136
137	def edit	1✔
138	add_breadcrumb(project.title, project_path)	14✔
139	add_breadcrumb("Edit")	14✔
140	project	14✔
141	if project.metadata_model.status != Project::APPROVED_STATUS	14✔
142	flash[:notice] = "Pending projects can not be edited."	1✔
143	redirect_to project	1✔
144	elsif project.metadata_model.status == Project::APPROVED_STATUS && !eligible_editor? #check if the current user is a sponsor or a manager	13✔
145	flash[:notice] = "Only data sponsors and data managers can revise this project."	2✔
146	redirect_to project	2✔
147	end
148	end
149
150	def update	1✔
151	@project = Project.find(params[:id])	7✔
152	#Approve action
153	if params.key?("approved")	7✔
154	@project.metadata_model.update_with_params(params, current_user)	3✔
155	@project.approve!(current_user:)	3✔
156	end
157
158	#Edit action
159	if params.key?("title")	7✔
160	@project.metadata_model.status = @project.metadata_model.status \|\| Project::PENDING_STATUS	4✔
161	@project.metadata_model.update_with_params(params, current_user)	4✔
162	end
163
164	# @todo ProjectMetadata should be refactored to implement ProjectMetadata.valid?(updated_metadata)
165	if project.save and params.key?("approved")	7✔
166	redirect_to project_approval_received_path(@project)	3✔
167	elsif project.save and params.key?("title")	4✔
168	redirect_to project_revision_confirmation_path(@project)	4✔
169	else
170	render :edit	×
171	end
172	end
173
174	def index	1✔
175	if current_user.eligible_sysadmin?	5✔
176	@projects = Project.all	1✔
177	else
178	flash[:alert] = I18n.t(:access_denied)	4✔
179	redirect_to dashboard_path	4✔
180	end
181	end
182
183	def confirmation; end	1✔
184	def revision_confirmation; end	1✔
185
186	def show	1✔
187
188	return if project.blank?	29✔
189	add_breadcrumb(project.title, project_path)	28✔
190	add_breadcrumb("Contents")	28✔
191
192	@latest_completed_download = current_user.user_requests.where(project_id: @project.id, state: "completed").order(:completion_time).last	28✔
193	@storage_usage = project.storage_usage(session_id: current_user.mediaflux_session)	28✔
194	@storage_capacity = project.storage_capacity(session_id: current_user.mediaflux_session)	24✔
195
196	@num_files = project.asset_count(session_id: current_user.mediaflux_session)	24✔
197
198	@file_list = project.file_list(session_id: current_user.mediaflux_session, size: 100)	24✔
199	@files = @file_list[:files]	24✔
200	@files.sort_by!(&:path)	24✔
201	@project = ProjectShowPresenter.new(project)	24✔
202
203	@project_session = "content"	24✔
204	respond_to do \|format\|	24✔
205	format.html { render }	47✔
206	format.xml { render xml: @project.to_xml }	25✔
207	end
208	end
209
210	# GET "projects/:id/:id-mf"
211	#
212	# This action is used to render the mediaflux metadata for a project.
213	def show_mediaflux	1✔
214	project_id = params[:id]	1✔
215	project = Project.find(project_id)	1✔
216
217	respond_to do \|format\|	1✔
218	format.xml do	1✔
219	render xml: project.mediaflux_meta_xml	1✔
220	end
221	end
222	end
223
224	def project_job_service	1✔
UNCOV 225	@project_job_service \|\|= ProjectJobService.new(project:)	×
226	end
227
228	def list_contents	1✔
229	return if project.blank?	1✔
230
UNCOV 231	project_job_service.list_contents_job(user: current_user)	×
232
233	json_response = {
UNCOV 234	message: "File list for \"#{project.title}\" is being generated in the background. A link to the downloadable file list will be available in the \"Recent Activity\" section of your dashboard when it is available. You may safely navigate away from this page or close this tab."	×
235	}
UNCOV 236	render json: json_response	×
237	rescue => ex
238	message = "Error producing document list (project id: #{project&.id}): #{ex.message}"	×
239	Rails.logger.error(message)	×
240	Honeybadger.notify(message)	×
241	render json: { message: "Document list could not be generated." }	×
242	end
243
244	def file_list_download	1✔
245	job_id = params[:job_id]	×
246	user_request = FileInventoryRequest.where(job_id:job_id).first	×
247	if user_request.nil?	×
248	# TODO: handle error
249	redirect_to "/"	×
250	else
251	filename = user_request.output_file	×
252	send_data File.read(filename), type: "text/plain", filename: "filelist.csv", disposition: "attachment"	×
253	end
254	end
255
256	def approve	1✔
257	if current_user.eligible_sysadmin?	6✔
258	add_breadcrumb(project.title, project_path)	3✔
259	add_breadcrumb("Approval Settings", project_approve_path)	3✔
260	add_breadcrumb("Edit")	3✔
261	project	3✔
262	@departments = project.departments.join(", ")	3✔
263	@project_metadata = project.metadata	3✔
264	sponsor_uid = @project_metadata[:data_sponsor]	3✔
265	@data_sponsor = User.find_by(uid: sponsor_uid)	3✔
266	@provenance_events = project.provenance_events.where.not(event_type: ProvenanceEvent::STATUS_UPDATE_EVENT_TYPE)	3✔
267
268	@title = @project_metadata["title"]	3✔
269	else redirect_to dashboard_path	3✔
270	end
271	end
272
273	def create_script	1✔
274	project_id = params[:id]	×
275	project = Project.find(project_id)	×
276	service = MediafluxScriptFactory.new(project: project)	×
277	respond_to do \|format\|	×
278	format.json { render json: {script: service.aterm_script} }	×
279	end
280	end
281
282	private	1✔
283
284	def build_new_project	1✔
285	@project \|\|= Project.new	26✔
286	end
287
288	def project	1✔
289	@project \|\|= begin	530✔
290	project = Project.find(params[:id])	76✔
291	if project.user_has_access?(user: current_user)	76✔
292	project	73✔
293	else
294	flash[:alert] = I18n.t(:access_denied)	3✔
295	redirect_to dashboard_path	3✔
296	nil	3✔
297	end
298	end
299	end
300
301	def eligible_editor?	1✔
302	return true if current_user.eligible_sponsor? or current_user.eligible_manager?	20✔
303	end
304
305	def shared_file_location(filename)	1✔
306	raise "Shared location is not configured" if Rails.configuration.mediaflux["shared_files_location"].blank?	×
307	location = Pathname.new(Rails.configuration.mediaflux["shared_files_location"])	×
308	location.join(filename).to_s	×
309	end
310
311	def set_breadcrumbs	1✔
312	add_breadcrumb("Dashboard",dashboard_path)	141✔
313	end
314	end

pulibrary / tigerdata-app / 54385a8c-ec76-421e-81fd-41bf4c9d5b76

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