5db21940-59bd-4742-a25d-02e5e58d6646

Build # 5db21940-59bd-4742-a25d-02e5e58d6646

Build Type

circleci

Committed by Carolyn Cole

Commit Message

Creating a folder in Amazon so the curators do not need to do it by hand fixes #1001

Pull Request Pull Request #1014: Creating a folder in Amazon so the curators do not need to do it by hand

Run Details

3 of 3 new or added lines in 2 files covered. (100.0%)

1703 of 1872 relevant lines covered (90.97%)

80.56 hits per line

Source File
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79.34

/app/controllers/works_controller.rb

# frozen_string_literal: true

require "nokogiri"
require "open-uri"

# rubocop:disable Metrics/ClassLength
class WorksController < ApplicationController
  include ERB::Util
  around_action :rescue_aasm_error, only: [:approve, :withdraw, :resubmit, :validate, :create]

  skip_before_action :authenticate_user!
  before_action :authenticate_user!, unless: :public_request?

  ##
  # Public requests are requests that do not require authentication.
  # This is to enable PDC Discovery to index approved content via the RSS feed and
  # .json calls to individual works without needing to log in as a user.
  # Note that only approved works can be fetched for indexing.
  def public_request?
    return true if action_name == "index" && request.format.symbol == :rss
    return true if action_name == "show" && request.format.symbol == :json && Work.find(params[:id]).state == "approved"
    false
  end

  def index
    @works = Work.all
    respond_to do |format|
      format.html
      format.rss { render layout: false }
    end
  end

  # Renders the "step 0" information page before creating a new dataset
  def new
    if wizard_mode?
      render "new_submission"
    else
      @work = Work.new(created_by_user_id: current_user.id, collection: current_user.default_collection)
    end
  end

  def create
    @work = Work.new(created_by_user_id: current_user.id, collection_id: params_collection_id, user_entered_doi: params["doi"].present?)
    @work.resource = FormToResourceService.convert(params, @work)
    if @work.valid?
      @work.draft!(current_user)
      redirect_to work_url(@work), notice: "Work was successfully created."
    else
      render :new, status: :unprocessable_entity
    end
  end

  # Creates the new dataset
  def new_submission
    default_collection_id = current_user.default_collection.id
    work = Work.new(created_by_user_id: current_user.id, collection_id: default_collection_id)
    work.resource = FormToResourceService.convert(params, work)
    work.draft!(current_user)
    redirect_to edit_work_path(work, wizard: true)
  end

  ##
  # Show the information for the dataset with the given id
  # When requested as .json, return the internal json resource
  def show
    @work = Work.find(params[:id])
    @changes =  WorkActivity.changes_for_work(@work.id)
    @messages = WorkActivity.messages_for_work(@work.id)

    respond_to do |format|
      format.html do
        # Ensure that the Work belongs to a Collection
        @collection = @work.collection
        raise(Work::InvalidCollectionError, "The Work #{@work.id} does not belong to any Collection") unless @collection

        @can_curate = current_user.can_admin?(@collection)
        @work.mark_new_notifications_as_read(current_user.id)
      end
      format.json { render json: @work.to_json }
    end
  end

  def file_list
    @work = Work.find(params[:id])
    render json: @work.pre_curation_uploads_fast
  end

  def resolve_doi
    @work = Work.find_by_doi(params[:doi])
    redirect_to @work
  end

  def resolve_ark
    @work = Work.find_by_ark(params[:ark])
    redirect_to @work
  end

  # GET /works/1/edit
  def edit
    @work = Work.find(params[:id])
    if current_user && @work.editable_by?(current_user)
      if @work.approved? && !@work.administered_by?(current_user)
        Honeybadger.notify("Can not edit work: #{@work.id} is approved but #{current_user} is not admin")
        redirect_to root_path, notice: I18n.t("works.uneditable.approved")
      else
        @uploads = @work.uploads
        @wizard_mode = wizard_mode?
        render "edit"
      end
    else
      Honeybadger.notify("Can not edit work: #{@work.id} is not editable by #{current_user}")
      redirect_to root_path, notice: I18n.t("works.uneditable.privs")
    end
  end

  def update
    @work = Work.find(params[:id])
    if current_user.blank? || !@work.editable_by?(current_user)
      Honeybadger.notify("Can not update work: #{@work.id} is not editable by #{current_user}")
      redirect_to root_path, notice: I18n.t("works.uneditable.privs")
    elsif !@work.editable_in_current_state?(current_user)
      Honeybadger.notify("Can not update work: #{@work.id} is not editable in current state by #{current_user}")
      redirect_to root_path, notice: I18n.t("works.uneditable.approved")
    else
      update_work
    end
  end

  # Prompt to select how to submit their files
  def attachment_select
    @work = Work.find(params[:id])
    @wizard_mode = true
  end

  # User selected a specific way to submit their files
  def attachment_selected
    @work = Work.find(params[:id])
    @wizard_mode = true
    @work.files_location = params["attachment_type"]
    @work.save!

    # create a directory for the work if the curator will need to move files by hand
    @work.s3_query_service.create_directory if @work.files_location != "file_upload"

    next_url = case @work.files_location
               when "file_upload"
                 work_file_upload_url(@work)
               when "file_cluster"
                 work_file_cluster_url(@work)
               else
                 work_file_other_url(@work)
               end
    redirect_to next_url
  end

  # Allow user to upload files directly
  def file_upload
    @work = Work.find(params[:id])
  end

  def file_uploaded
    @work = Work.find(params[:id])
    if pre_curation_uploads_param
      @work.pre_curation_uploads.attach(pre_curation_uploads_param)
      @work.save!
    end

    redirect_to(work_review_path)
  rescue StandardError => active_storage_error
    Rails.logger.error("Failed to attach the file uploads for the work #{@work.doi}: #{active_storage_error}")
    flash[:notice] = "Failed to attach the file uploads for the work #{@work.doi}: #{active_storage_error}. Please contact rdss@princeton.edu for assistance."

    redirect_to work_file_upload_path(@work)
  end

  # Allow user to indicate where their files are located in the PUL Research Cluster
  def file_cluster
    @work = Work.find(params[:id])
  end

  # Allow user to indicate where their files are located in the WWW
  def file_other
    @work = Work.find(params[:id])
  end

  def review
    @work = Work.find(params[:id])
    if request.method == "POST"
      @work.location_notes = params["location_notes"]
      @work.save!
    end
  end

  def validate
    @work = Work.find(params[:id])
    @work.submission_notes = params["submission_notes"]
    @uploads = @work.uploads
    @wizard_mode = true
    @work.complete_submission!(current_user)
    redirect_to user_url(current_user)
  end

  def approve
    @work = Work.find(params[:id])
    @work.approve!(current_user)
    redirect_to work_path(@work)
  end

  def withdraw
    @work = Work.find(params[:id])
    @work.withdraw!(current_user)
    redirect_to work_path(@work)
  end

  def resubmit
    @work = Work.find(params[:id])
    @work.resubmit!(current_user)
    redirect_to work_path(@work)
  end

  def assign_curator
    work = Work.find(params[:id])
    work.change_curator(params[:uid], current_user)
    if work.errors.count > 0
      render json: { errors: work.errors.map(&:type) }, status: :bad_request
    else
      render json: {}
    end
  rescue => ex
    Rails.logger.error("Error changing curator for work: #{work.id}. Exception: #{ex.message}")
    render json: { errors: ["Cannot save dataset"] }, status: :bad_request
  end

  def add_message
    work = Work.find(params[:id])
    if params["new-message"].present?
      new_message_param = params["new-message"]
      sanitized_new_message = html_escape(new_message_param)

      work.add_message(sanitized_new_message, current_user.id)
    end
    redirect_to work_path(id: params[:id])
  end

  def add_provenance_note
    work = Work.find(params[:id])
    if params["new-provenance-note"].present?
      new_date = params["new-provenance-date"]
      new_note = html_escape(params["new-provenance-note"])

      work.add_provenance_note(new_date, new_note, current_user.id)
    end
    redirect_to work_path(id: params[:id])
  end

  # Outputs the Datacite XML representation of the work
  def datacite
    work = Work.find(params[:id])
    render xml: work.to_xml
  end

  def datacite_validate
    @errors = []
    @work = Work.find(params[:id])
    datacite_xml = Nokogiri::XML(@work.to_xml)
    schema_location = Rails.root.join("config", "schema")
    Dir.chdir(schema_location) do
      xsd = Nokogiri::XML::Schema(File.read("datacite_4_4.xsd"))
      xsd.validate(datacite_xml).each do |error|
        @errors << error
      end
    end
  end

  private

    def work_params
      params[:work] || params
    end

    def patch_params
      return {} unless params.key?(:patch)

      params[:patch]
    end

    def pre_curation_uploads_param
      return if patch_params.nil?

      patch_params[:pre_curation_uploads]
    end

    def rescue_aasm_error
      yield
    rescue AASM::InvalidTransition => error
      message = error.message
      if @work.errors.count > 0
        message = @work.errors.to_a.join(", ")
      end
      Honeybadger.notify("Invalid #{@work.current_transition}: #{error.message} errors: #{message}")
      @errors = ["Cannot #{@work.current_transition}: #{message}"]
      render error_action, status: :unprocessable_entity
    end

    def error_action
      if action_name == "create"
        :new
      elsif action_name == "validate"
        :edit
      else
        :show
      end
    end

    def wizard_mode?
      params[:wizard] == "true"
    end

    def update_work
      @wizard_mode = wizard_mode?
      upload_service = WorkUploadsEditService.new(@work, current_user)
      if @work.approved?
        upload_keys = work_params[:deleted_uploads] || []
        deleted_uploads = upload_service.find_post_curation_uploads(upload_keys: upload_keys)

        return head(:forbidden) unless deleted_uploads.empty?
      else
        @work = upload_service.update_precurated_file_list(work_params)
      end

      process_updates
    end

    def update_params
      {
        collection_id: params_collection_id,
        resource: FormToResourceService.convert(params, @work)
      }
    end

    def process_updates
      resource_before = @work.resource
      if @work.update(update_params)

        resource_compare = ResourceCompareService.new(resource_before, update_params[:resource])
        @work.log_changes(resource_compare, current_user.id)

        if @wizard_mode
          redirect_to work_attachment_select_url(@work)
        else
          redirect_to work_url(@work), notice: "Work was successfully updated."
        end
      else
        @uploads = @work.uploads
        render :edit, status: :unprocessable_entity
      end
    end

    def params_collection_id
      # Do not allow a nil for the collection id
      @params_collection_id ||= begin
        collection_id = params[:collection_id]
        if collection_id.blank?
          collection_id = current_user.default_collection.id
          Honeybadger.notify("We got a nil collection as part of the parameters #{params} #{request}")
        end
        collection_id
      end
    end
end
# rubocop:enable Metrics/ClassLength

1	# frozen_string_literal: true
2
3	require "nokogiri"	1✔
4	require "open-uri"	1✔
5
6	# rubocop:disable Metrics/ClassLength
7	class WorksController < ApplicationController	1✔
8	include ERB::Util	1✔
9	around_action :rescue_aasm_error, only: [:approve, :withdraw, :resubmit, :validate, :create]	1✔
10
11	skip_before_action :authenticate_user!	1✔
12	before_action :authenticate_user!, unless: :public_request?	1✔
13
14	##
15	# Public requests are requests that do not require authentication.
16	# This is to enable PDC Discovery to index approved content via the RSS feed and
17	# .json calls to individual works without needing to log in as a user.
18	# Note that only approved works can be fetched for indexing.
19	def public_request?	1✔
20	return true if action_name == "index" && request.format.symbol == :rss	51✔
21	return true if action_name == "show" && request.format.symbol == :json && Work.find(params[:id]).state == "approved"	50✔
22	false	50✔
23	end
24
25	def index	1✔
26	@works = Work.all	3✔
27	respond_to do \|format\|	3✔
28	format.html	3✔
29	format.rss { render layout: false }	4✔
30	end
31	end
32
33	# Renders the "step 0" information page before creating a new dataset
34	def new	1✔
35	if wizard_mode?	2✔
36	render "new_submission"	1✔
37	else
38	@work = Work.new(created_by_user_id: current_user.id, collection: current_user.default_collection)	1✔
39	end
40	end
41
42	def create	1✔
43	@work = Work.new(created_by_user_id: current_user.id, collection_id: params_collection_id, user_entered_doi: params["doi"].present?)	2✔
44	@work.resource = FormToResourceService.convert(params, @work)	2✔
45	if @work.valid?	2✔
46	@work.draft!(current_user)	2✔
47	redirect_to work_url(@work), notice: "Work was successfully created."	2✔
48	else
49	render :new, status: :unprocessable_entity	×
50	end
51	end
52
53	# Creates the new dataset
54	def new_submission	1✔
55	default_collection_id = current_user.default_collection.id	1✔
56	work = Work.new(created_by_user_id: current_user.id, collection_id: default_collection_id)	1✔
57	work.resource = FormToResourceService.convert(params, work)	1✔
58	work.draft!(current_user)	1✔
59	redirect_to edit_work_path(work, wizard: true)	1✔
60	end
61
62	##
63	# Show the information for the dataset with the given id
64	# When requested as .json, return the internal json resource
65	def show	1✔
66	@work = Work.find(params[:id])	4✔
67	@changes = WorkActivity.changes_for_work(@work.id)	4✔
68	@messages = WorkActivity.messages_for_work(@work.id)	4✔
69
70	respond_to do \|format\|	4✔
71	format.html do	4✔
72	# Ensure that the Work belongs to a Collection
73	@collection = @work.collection	4✔
74	raise(Work::InvalidCollectionError, "The Work #{@work.id} does not belong to any Collection") unless @collection	4✔
75
76	@can_curate = current_user.can_admin?(@collection)	4✔
77	@work.mark_new_notifications_as_read(current_user.id)	4✔
78	end
79	format.json { render json: @work.to_json }	4✔
80	end
81	end
82
83	def file_list	1✔
84	@work = Work.find(params[:id])	3✔
85	render json: @work.pre_curation_uploads_fast	3✔
86	end
87
88	def resolve_doi	1✔
89	@work = Work.find_by_doi(params[:doi])	3✔
90	redirect_to @work	2✔
91	end
92
93	def resolve_ark	1✔
94	@work = Work.find_by_ark(params[:ark])	3✔
95	redirect_to @work	2✔
96	end
97
98	# GET /works/1/edit
99	def edit	1✔
100	@work = Work.find(params[:id])	3✔
101	if current_user && @work.editable_by?(current_user)	3✔
102	if @work.approved? && !@work.administered_by?(current_user)	2✔
103	Honeybadger.notify("Can not edit work: #{@work.id} is approved but #{current_user} is not admin")	1✔
104	redirect_to root_path, notice: I18n.t("works.uneditable.approved")	1✔
105	else
106	@uploads = @work.uploads	1✔
107	@wizard_mode = wizard_mode?	1✔
108	render "edit"	1✔
109	end
110	else
111	Honeybadger.notify("Can not edit work: #{@work.id} is not editable by #{current_user}")	1✔
112	redirect_to root_path, notice: I18n.t("works.uneditable.privs")	1✔
113	end
114	end
115
116	def update	1✔
117	@work = Work.find(params[:id])	6✔
118	if current_user.blank? \|\| !@work.editable_by?(current_user)	6✔
119	Honeybadger.notify("Can not update work: #{@work.id} is not editable by #{current_user}")	×
120	redirect_to root_path, notice: I18n.t("works.uneditable.privs")	×
121	elsif !@work.editable_in_current_state?(current_user)	6✔
122	Honeybadger.notify("Can not update work: #{@work.id} is not editable in current state by #{current_user}")	×
123	redirect_to root_path, notice: I18n.t("works.uneditable.approved")	×
124	else
125	update_work	6✔
126	end
127	end
128
129	# Prompt to select how to submit their files
130	def attachment_select	1✔
131	@work = Work.find(params[:id])	1✔
132	@wizard_mode = true	1✔
133	end
134
135	# User selected a specific way to submit their files
136	def attachment_selected	1✔
137	@work = Work.find(params[:id])	×
138	@wizard_mode = true	×
139	@work.files_location = params["attachment_type"]	×
140	@work.save!	×
141
142	# create a directory for the work if the curator will need to move files by hand
143	@work.s3_query_service.create_directory if @work.files_location != "file_upload"	×
144
145	next_url = case @work.files_location	×
146	when "file_upload"
147	work_file_upload_url(@work)	×
148	when "file_cluster"
149	work_file_cluster_url(@work)	×
150	else
151	work_file_other_url(@work)	×
152	end
153	redirect_to next_url	×
154	end
155
156	# Allow user to upload files directly
157	def file_upload	1✔
158	@work = Work.find(params[:id])	1✔
159	end
160
161	def file_uploaded	1✔
162	@work = Work.find(params[:id])	3✔
163	if pre_curation_uploads_param	3✔
164	@work.pre_curation_uploads.attach(pre_curation_uploads_param)	2✔
165	@work.save!	1✔
166	end
167
168	redirect_to(work_review_path)	2✔
169	rescue StandardError => active_storage_error
170	Rails.logger.error("Failed to attach the file uploads for the work #{@work.doi}: #{active_storage_error}")	1✔
171	flash[:notice] = "Failed to attach the file uploads for the work #{@work.doi}: #{active_storage_error}. Please contact rdss@princeton.edu for assistance."	1✔
172
173	redirect_to work_file_upload_path(@work)	1✔
174	end
175
176	# Allow user to indicate where their files are located in the PUL Research Cluster
177	def file_cluster	1✔
178	@work = Work.find(params[:id])	1✔
179	end
180
181	# Allow user to indicate where their files are located in the WWW
182	def file_other	1✔
183	@work = Work.find(params[:id])	1✔
184	end
185
186	def review	1✔
187	@work = Work.find(params[:id])	1✔
188	if request.method == "POST"	1✔
189	@work.location_notes = params["location_notes"]	1✔
190	@work.save!	1✔
191	end
192	end
193
194	def validate	1✔
195	@work = Work.find(params[:id])	×
196	@work.submission_notes = params["submission_notes"]	×
197	@uploads = @work.uploads	×
198	@wizard_mode = true	×
199	@work.complete_submission!(current_user)	×
200	redirect_to user_url(current_user)	×
201	end
202
203	def approve	1✔
204	@work = Work.find(params[:id])	×
205	@work.approve!(current_user)	×
206	redirect_to work_path(@work)	×
207	end
208
209	def withdraw	1✔
210	@work = Work.find(params[:id])	2✔
211	@work.withdraw!(current_user)	2✔
212	redirect_to work_path(@work)	1✔
213	end
214
215	def resubmit	1✔
216	@work = Work.find(params[:id])	2✔
217	@work.resubmit!(current_user)	2✔
218	redirect_to work_path(@work)	1✔
219	end
220
221	def assign_curator	1✔
222	work = Work.find(params[:id])	3✔
223	work.change_curator(params[:uid], current_user)	3✔
224	if work.errors.count > 0	2✔
225	render json: { errors: work.errors.map(&:type) }, status: :bad_request	×
226	else
227	render json: {}	2✔
228	end
229	rescue => ex
230	Rails.logger.error("Error changing curator for work: #{work.id}. Exception: #{ex.message}")	1✔
231	render json: { errors: ["Cannot save dataset"] }, status: :bad_request	1✔
232	end
233
234	def add_message	1✔
235	work = Work.find(params[:id])	2✔
236	if params["new-message"].present?	2✔
237	new_message_param = params["new-message"]	2✔
238	sanitized_new_message = html_escape(new_message_param)	2✔
239
240	work.add_message(sanitized_new_message, current_user.id)	2✔
241	end
242	redirect_to work_path(id: params[:id])	2✔
243	end
244
245	def add_provenance_note	1✔
246	work = Work.find(params[:id])	×
247	if params["new-provenance-note"].present?	×
248	new_date = params["new-provenance-date"]	×
249	new_note = html_escape(params["new-provenance-note"])	×
250
251	work.add_provenance_note(new_date, new_note, current_user.id)	×
252	end
253	redirect_to work_path(id: params[:id])	×
254	end
255
256	# Outputs the Datacite XML representation of the work
257	def datacite	1✔
258	work = Work.find(params[:id])	1✔
259	render xml: work.to_xml	1✔
260	end
261
262	def datacite_validate	1✔
263	@errors = []	×
264	@work = Work.find(params[:id])	×
265	datacite_xml = Nokogiri::XML(@work.to_xml)	×
266	schema_location = Rails.root.join("config", "schema")	×
267	Dir.chdir(schema_location) do	×
268	xsd = Nokogiri::XML::Schema(File.read("datacite_4_4.xsd"))	×
269	xsd.validate(datacite_xml).each do \|error\|	×
270	@errors << error	×
271	end
272	end
273	end
274
275	private	1✔
276
277	def work_params	1✔
278	params[:work] \|\| params	6✔
279	end
280
281	def patch_params	1✔
282	return {} unless params.key?(:patch)	8✔
283
284	params[:patch]	6✔
285	end
286
287	def pre_curation_uploads_param	1✔
288	return if patch_params.nil?	4✔
289
290	patch_params[:pre_curation_uploads]	4✔
291	end
292
293	def rescue_aasm_error	1✔
294	yield	6✔
295	rescue AASM::InvalidTransition => error
296	message = error.message	2✔
297	if @work.errors.count > 0	2✔
298	message = @work.errors.to_a.join(", ")	×
299	end
300	Honeybadger.notify("Invalid #{@work.current_transition}: #{error.message} errors: #{message}")	2✔
301	@errors = ["Cannot #{@work.current_transition}: #{message}"]	2✔
302	render error_action, status: :unprocessable_entity	2✔
303	end
304
305	def error_action	1✔
306	if action_name == "create"	2✔
307	:new	×
308	elsif action_name == "validate"	2✔
309	:edit	×
310	else
311	:show	2✔
312	end
313	end
314
315	def wizard_mode?	1✔
316	params[:wizard] == "true"	9✔
317	end
318
319	def update_work	1✔
320	@wizard_mode = wizard_mode?	6✔
321	upload_service = WorkUploadsEditService.new(@work, current_user)	6✔
322	if @work.approved?	6✔
323	upload_keys = work_params[:deleted_uploads] \|\| []	2✔
324	deleted_uploads = upload_service.find_post_curation_uploads(upload_keys: upload_keys)	2✔
325
326	return head(:forbidden) unless deleted_uploads.empty?	2✔
327	else
328	@work = upload_service.update_precurated_file_list(work_params)	4✔
329	end
330
331	process_updates	5✔
332	end
333
334	def update_params	1✔
335	{
336	collection_id: params_collection_id,	10✔
337	resource: FormToResourceService.convert(params, @work)
338	}
339	end
340
341	def process_updates	1✔
342	resource_before = @work.resource	5✔
343	if @work.update(update_params)	5✔
344
345	resource_compare = ResourceCompareService.new(resource_before, update_params[:resource])	5✔
346	@work.log_changes(resource_compare, current_user.id)	5✔
347
348	if @wizard_mode	5✔
349	redirect_to work_attachment_select_url(@work)	1✔
350	else
351	redirect_to work_url(@work), notice: "Work was successfully updated."	4✔
352	end
353	else
354	@uploads = @work.uploads	×
355	render :edit, status: :unprocessable_entity	×
356	end
357	end
358
359	def params_collection_id	1✔
360	# Do not allow a nil for the collection id
361	@params_collection_id \|\|= begin	12✔
362	collection_id = params[:collection_id]	6✔
363	if collection_id.blank?	6✔
364	collection_id = current_user.default_collection.id	1✔
365	Honeybadger.notify("We got a nil collection as part of the parameters #{params} #{request}")	1✔
366	end
367	collection_id	6✔
368	end
369	end
370	end
371	# rubocop:enable Metrics/ClassLength

pulibrary / pdc_describe / 5db21940-59bd-4742-a25d-02e5e58d6646

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