fa5427d1-c616-4db4-8869-6c67d0eea350

Committed 23 Jun 2025 06:40PM UTC coverage: 71.937% (-0.2%) from 72.107%

Build # fa5427d1-c616-4db4-8869-6c67d0eea350

Build Type

Pull #1533

circleci

Committed by

jrgriffiniii

Commit Message

Introducing some additional refactoring steps for the ProjectXmlPresenter; Implements a route for retrieving the Mediaflux XML document for project metadata

Pull Request Pull Request #1533: Implements a route for retrieving the Mediaflux XML document for project metadata

Run Details

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18 existing lines in 2 files now uncovered.

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81.28

/app/controllers/projects_controller.rb

# frozen_string_literal: true
class ProjectsController < ApplicationController

  before_action :set_breadcrumbs

  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?("mediaflux_id")
      @project.metadata_model.update_with_params(params, current_user)
      @project.approve!(mediaflux_id: params["mediaflux_id"],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?("mediaflux_id")
      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
6	def new	1✔
7	add_breadcrumb("New Project Request")	16✔
8	return build_new_project if current_user.eligible_sponsor?	16✔
9
10	redirect_to dashboard_path	2✔
11	end
12
13	def project_params	1✔
UNCOV 14	params.dup	×
15	end
16
17	def create	1✔
18	metadata_params = params.dup	12✔
19	metadata_params[:status] = Project::PENDING_STATUS	12✔
20	metadata_params[:created_by] = current_user.uid	12✔
21	metadata_params[:created_on] = Time.current.in_time_zone("America/New_York").iso8601	12✔
22	project_metadata = ProjectMetadata.new_from_params(metadata_params)	12✔
23
24	build_new_project # calling private method to build a new project and set a class variable @project	12✔
25	project.create!(initial_metadata: project_metadata, user: current_user)	12✔
26	if project.metadata_model.project_id != nil	12✔
27	begin
28	mailer = TigerdataMailer.with(project_id: project.id)	12✔
29	message_delivery = mailer.project_creation	12✔
30	message_delivery.deliver_later	12✔
31
32	redirect_to project_confirmation_path(project)	11✔
33	rescue StandardError => mailer_error
34	raise(TigerData::MailerError, mailer_error)	2✔
35	end
36	else
UNCOV 37	render :new	×
38	end
39	rescue TigerData::MailerError => mailer_error
40	logger_message = "Error encountered creating the project #{project.id} as user #{current_user.email}"	2✔
41	Rails.logger.error(logger_message)	2✔
42	honeybadger_context = {
43	current_user_email: current_user.email,	2✔
44	project_id: project.id,
45	project_metadata: project.metadata
46	}
47	Honeybadger.notify(mailer_error, context: honeybadger_context)	2✔
48
49	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✔
50	flash[:notice] = error_message	2✔
51
52	render :new	2✔
53	rescue StandardError => error
UNCOV 54	logger_message = if project.persisted?	×
55	"Error encountered creating the project #{project.id} as user #{current_user.email}"	×
56	else
UNCOV 57	"Error encountered creating the project #{metadata_params[:title]} as user #{current_user.email}"	×
58	end
UNCOV 59	Rails.logger.error(logger_message)	×
60	honeybadger_context = {
UNCOV 61	current_user_email: current_user.email,	×
62	project_id: project.id,
63	project_metadata: project.metadata
64	}
UNCOV 65	Honeybadger.notify(error, context: honeybadger_context)	×
66
UNCOV 67	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."	×
68
UNCOV 69	flash[:notice] = error_message	×
70	render :new	×
71	end
72
73	def details	1✔
74	return if project.blank?	33✔
75
76	add_breadcrumb(project.title, project_path)	32✔
77	add_breadcrumb("Details")	32✔
78
79	@departments = project.departments.join(", ")	32✔
80	@project_metadata = project.metadata_model	32✔
81
82	@data_sponsor = User.find_by(uid: @project_metadata.data_sponsor)	32✔
83	@data_manager = User.find_by(uid: @project_metadata.data_manager)	32✔
84
85	read_only_uids = @project_metadata.ro_users	32✔
86	data_read_only_users = read_only_uids.map { \|uid\| ReadOnlyUser.find_by(uid:) }.reject(&:blank?)	48✔
87
88	read_write_uids = @project_metadata.rw_users	32✔
89	data_read_write_users = read_write_uids.map { \|uid\| User.find_by(uid:) }.reject(&:blank?)	44✔
90
91	unsorted_data_users = data_read_only_users + data_read_write_users	32✔
92	sorted_data_users = unsorted_data_users.sort_by { \|u\| u.family_name \|\| u.uid }	60✔
93	@data_users = sorted_data_users.uniq { \|u\| u.uid }	52✔
94	user_model_names = @data_users.map(&:display_name_safe)	32✔
95	@data_user_names = user_model_names.join(", ")	32✔
96
97	@provenance_events = project.provenance_events.where.not(event_type: ProvenanceEvent::STATUS_UPDATE_EVENT_TYPE)	32✔
98
99	@project_eligible_to_edit = true if project.status == Project::APPROVED_STATUS && eligible_editor?	32✔
100
101	@project_metadata = @project.metadata	32✔
102	@project_id = @project_metadata[:project_id] \|\| {}	32✔
103	@storage_capacity = @project_metadata[:storage_capacity]	32✔
104	@size = @storage_capacity[:size]	32✔
105	@unit = @storage_capacity[:unit]	32✔
106
107	@requested_size = @size[:requested]	32✔
108	@requested_unit = @unit[:requested]	32✔
109
110	@approved_size = @size[:approved]	32✔
111	@approved_unit = @unit[:approved]	32✔
112
113	@storage_expectations = @project_metadata[:storage_performance_expectations]	32✔
114	@requested_storage_expectations = @storage_expectations[:requested]	32✔
115	@approved_storage_expectations = @storage_expectations[:approved]	32✔
116
117	@project_purpose = @project_metadata[:project_purpose]	32✔
118
119
120	@project_session = "details"	32✔
121
122
123	respond_to do \|format\|	32✔
124	format.html do	32✔
125	@project = ProjectShowPresenter.new(project)	29✔
126	end
127	format.json do	32✔
128	render json: project.to_json	2✔
129	end
130	format.xml do	32✔
131	render xml: project.to_xml	1✔
132	end
133	end
134	end
135
136	def edit	1✔
137	add_breadcrumb(project.title, project_path)	16✔
138	add_breadcrumb("Edit")	16✔
139	project	16✔
140	if project.metadata_model.status != Project::APPROVED_STATUS	16✔
141	flash[:notice] = "Pending projects can not be edited."	1✔
142	redirect_to project	1✔
143	elsif project.metadata_model.status == Project::APPROVED_STATUS && !eligible_editor? #check if the current user is a sponsor or a manager	15✔
144	flash[:notice] = "Only data sponsors and data managers can revise this project."	2✔
145	redirect_to project	2✔
146	end
147	end
148
149	def update	1✔
150	@project = Project.find(params[:id])	8✔
151	#Approve action
152	if params.key?("mediaflux_id")	8✔
153	@project.metadata_model.update_with_params(params, current_user)	2✔
154	@project.approve!(mediaflux_id: params["mediaflux_id"],current_user:)	2✔
155	end
156
157	#Edit action
158	if params.key?("title")	8✔
159	@project.metadata_model.status = @project.metadata_model.status \|\| Project::PENDING_STATUS	6✔
160	@project.metadata_model.update_with_params(params, current_user)	6✔
161	end
162
163	# @todo ProjectMetadata should be refactored to implement ProjectMetadata.valid?(updated_metadata)
164	if project.save and params.key?("mediaflux_id")	8✔
165	redirect_to project_approval_received_path(@project)	2✔
166	elsif project.save and params.key?("title")	6✔
167	redirect_to project_revision_confirmation_path(@project)	6✔
168	else
UNCOV 169	render :edit	×
170	end
171	end
172
173	def index	1✔
174	if current_user.eligible_sysadmin?	5✔
175	@projects = Project.all	1✔
176	else
177	flash[:alert] = I18n.t(:access_denied)	4✔
178	redirect_to dashboard_path	4✔
179	end
180	end
181
182	def confirmation; end	1✔
183	def revision_confirmation; end	1✔
184
185	def show	1✔
186
187	return if project.blank?	37✔
188	add_breadcrumb(project.title, project_path)	36✔
189	add_breadcrumb("Contents")	36✔
190
191	@latest_completed_download = current_user.user_requests.where(project_id: @project.id, state: "completed").order(:completion_time).last	36✔
192	@storage_usage = project.storage_usage(session_id: current_user.mediaflux_session)	36✔
193	@storage_capacity = project.storage_capacity(session_id: current_user.mediaflux_session)	32✔
194
195	@num_files = project.asset_count(session_id: current_user.mediaflux_session)	32✔
196
197	@file_list = project.file_list(session_id: current_user.mediaflux_session, size: 100)	32✔
198	@files = @file_list[:files]	32✔
199	@files.sort_by!(&:path)	32✔
200	@project = ProjectShowPresenter.new(project)	32✔
201
202	@project_session = "content"	32✔
203	respond_to do \|format\|	32✔
204	format.html { render }	62✔
205	format.xml { render xml: @project.to_xml }	34✔
206	end
207	end
208
209	# GET "projects/:id/:id-mf"
210	#
211	# This action is used to render the mediaflux metadata for a project.
212	def show_mediaflux	1✔
NEW 213	project_id = params[:id]	×
NEW 214	project = Project.find(project_id)	×
215
NEW 216	respond_to do \|format\|	×
NEW 217	format.xml do	×
NEW 218	render xml: project.mediaflux_meta_xml	×
219	end
220	end
221	end
222
223	def project_job_service	1✔
224	@project_job_service \|\|= ProjectJobService.new(project:)	1✔
225	end
226
227	def list_contents	1✔
228	return if project.blank?	2✔
229
230	project_job_service.list_contents_job(user: current_user)	1✔
231
232	json_response = {
233	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."	1✔
234	}
235	render json: json_response	1✔
236	rescue => ex
UNCOV 237	message = "Error producing document list (project id: #{project&.id}): #{ex.message}"	×
238	Rails.logger.error(message)	×
239	Honeybadger.notify(message)	×
240	render json: { message: "Document list could not be generated." }	×
241	end
242
243	def file_list_download	1✔
UNCOV 244	job_id = params[:job_id]	×
245	user_request = FileInventoryRequest.where(job_id:job_id).first	×
246	if user_request.nil?	×
247	# TODO: handle error
UNCOV 248	redirect_to "/"	×
249	else
UNCOV 250	filename = user_request.output_file	×
251	send_data File.read(filename), type: "text/plain", filename: "filelist.csv", disposition: "attachment"	×
252	end
253	end
254
255	def approve	1✔
256	if current_user.eligible_sysadmin?	7✔
257	add_breadcrumb(project.title, project_path)	4✔
258	add_breadcrumb("Approval Settings", project_approve_path)	4✔
259	add_breadcrumb("Edit")	4✔
260	project	4✔
261	@departments = project.departments.join(", ")	4✔
262	@project_metadata = project.metadata	4✔
263	sponsor_uid = @project_metadata[:data_sponsor]	4✔
264	@data_sponsor = User.find_by(uid: sponsor_uid)	4✔
265	@provenance_events = project.provenance_events.where.not(event_type: ProvenanceEvent::STATUS_UPDATE_EVENT_TYPE)	4✔
266
267	@title = @project_metadata["title"]	4✔
268	else redirect_to dashboard_path	3✔
269	end
270	end
271
272	def create_script	1✔
UNCOV 273	project_id = params[:id]	×
274	project = Project.find(project_id)	×
275	service = MediafluxScriptFactory.new(project: project)	×
276	respond_to do \|format\|	×
277	format.json { render json: {script: service.aterm_script} }	×
278	end
279	end
280
281	private	1✔
282
283	def build_new_project	1✔
284	@project \|\|= Project.new	26✔
285	end
286
287	def project	1✔
288	@project \|\|= begin	619✔
289	project = Project.find(params[:id])	90✔
290	if project.user_has_access?(user: current_user)	90✔
291	project	87✔
292	else
293	flash[:alert] = I18n.t(:access_denied)	3✔
294	redirect_to dashboard_path	3✔
295	nil	3✔
296	end
297	end
298	end
299
300	def eligible_editor?	1✔
301	return true if current_user.eligible_sponsor? or current_user.eligible_manager?	22✔
302	end
303
304	def shared_file_location(filename)	1✔
UNCOV 305	raise "Shared location is not configured" if Rails.configuration.mediaflux["shared_files_location"].blank?	×
306	location = Pathname.new(Rails.configuration.mediaflux["shared_files_location"])	×
307	location.join(filename).to_s	×
308	end
309
310	def set_breadcrumbs	1✔
311	add_breadcrumb("Dashboard",dashboard_path)	149✔
312	end
313	end

pulibrary / tigerdata-app / fa5427d1-c616-4db4-8869-6c67d0eea350

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