34fcfd04-4a59-4c24-91de-15a8ef14d8a4

Committed 18 Mar 2024 03:56PM UTC coverage: 95.979% (-0.3%) from 96.233%

Build # 34fcfd04-4a59-4c24-91de-15a8ef14d8a4

Build Type

push

circleci

Committed by

jrgriffiniii

Commit Message

wip

Run Details

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94.44

/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, :new_submission]

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

  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
    group = Group.find_by(code: params[:group_code]) || current_user.default_group
    @work = Work.new(created_by_user_id: current_user.id, group:)
    @form_resource_decorator = FormResourceDecorator.new(@work, current_user)
    if wizard_mode?
      render "new_submission"
    end
  end

  def create
    @work = Work.new(created_by_user_id: current_user.id, group_id: params_group_id, user_entered_doi: params["doi"].present?)
    @work.resource = FormToResourceService.convert(params, @work)
    @work.resource.migrated = migrated?
    if @work.valid?
      @work.draft!(current_user)
      upload_service = WorkUploadsEditService.new(@work, current_user)
      upload_service.update_precurated_file_list(added_files_param, deleted_files_param)
      redirect_to work_url(@work), notice: "Work was successfully created."
    else
      @form_resource_decorator = FormResourceDecorator.new(@work, current_user)
      render :new, status: :unprocessable_entity
    end
  end

  # Creates the new dataset
  def new_submission
    default_group_id = current_user.default_group.id
    @work = Work.new(created_by_user_id: current_user.id, group_id: default_group_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])
    UpdateSnapshotJob.perform_later(work_id: @work.id, last_snapshot_id: work.upload_snapshots.first&.id)
    @work_decorator = WorkDecorator.new(@work, current_user)

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

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

  def file_list
    if params[:id] == "NONE"
      # This is a special case when we render the file list for a work being created
      # (i.e. it does not have an id just yet)
      render json: []
    else
      @work = Work.find(params[:id])
      render json: @work.file_list
    end
  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.uid} is not admin")
        redirect_to root_path, notice: I18n.t("works.uneditable.approved")
      else
        @uploads = @work.uploads
        @wizard_mode = wizard_mode?
        @form_resource_decorator = FormResourceDecorator.new(@work, current_user)
        render "edit"
      end
    else
      Honeybadger.notify("Can not edit work: #{@work.id} is not editable by #{current_user.uid}")
      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.uid}")
      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.uid}")
      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])
    files = pre_curation_uploads_param || []
    if files.count > 0
      upload_service = WorkUploadsEditService.new(@work, current_user)
      @work = upload_service.update_precurated_file_list(files, [])
      @work.save!
      @work.reload_snapshots
    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)
    flash[:notice] = "Your files are being moved to the post-curation bucket in the background. Depending on the file sizes this may take some time."
    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_label = params["change_label"]
      new_note = html_escape(params["new-provenance-note"])

      work.add_provenance_note(new_date, new_note, current_user.id, new_label)
    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])
    validator = WorkValidator.new(@work)
    unless validator.valid_datacite?
      @errors = @work.errors.full_messages
    end
  end

  def readme_select
    @work = Work.find(params[:id])
    readme = Readme.new(@work, current_user)
    @readme = readme.file_name
    @wizard = true
  end

  def readme_uploaded
    @work = Work.find(params[:id])
    @wizard = true
    readme = Readme.new(@work, current_user)
    readme_error = readme.attach(readme_file_param)
    if readme_error.nil?
      redirect_to work_attachment_select_url(@work)
    else
      flash[:notice] = readme_error
      redirect_to work_readme_select_url(@work)
    end
  end

  def migrating?
    return @work.resource.migrated if @work&.resource && !params.key?(:migrate)

    params[:migrate]
  end
  helper_method :migrating?

  def doi_mutable?
    return true unless !@work.nil? && @work.persisted?

    !@work.approved?
  end
  helper_method :doi_mutable?

  # Returns the raw BibTex citation information
  def bibtex
    work = Work.find(params[:id])
    creators = work.resource.creators.map { |creator| "#{creator.family_name}, #{creator.given_name}" }
    citation = DatasetCitation.new(creators, [work.resource.publication_year], work.resource.titles.first.title, work.resource.resource_type, work.resource.publisher, work.resource.doi)
    bibtex = citation.bibtex
    send_data bibtex, filename: "#{citation.bibtex_id}.bibtex", type: "text/plain", disposition: "attachment"
  end

  private

    # Extract the Work ID parameter
    # @return [String]
    def work_id_param
      params[:id]
    end

    # Find the Work requested by ID
    # @return [Work]
    def work
      Work.find(work_id_param)
    end

    # Determine whether or not the request is for the :index action in the RSS
    # response format
    # This is to enable PDC Discovery to index approved content via the RSS feed
    def rss_index_request?
      action_name == "index" && request.format.symbol == :rss
    end

    # Determine whether or not the request is for the :show action in the JSON
    # response format
    # @return [Boolean]
    def json_show_request?
      action_name == "show" && request.format.symbol == :json
    end

    # Determine whether or not the requested Work has been approved
    # @return [Boolean]
    def work_approved?
      work&.state == "approved"
    end

    ##
    # 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 rss_index_request?
      return true if json_show_request? && work_approved?
      false
    end

    def work_params
      params[:work] || {}
    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 readme_file_param
      return if patch_params.nil?

      patch_params[:readme_file]
    end

    # rubocop:disable Metrics/AbcSize
    # rubocop:disable Metrics/BlockNesting
    # rubocop:disable Metrics/CyclomaticComplexity
    # rubocop:disable Metrics/MethodLength
    # rubocop:disable Metrics/PerceivedComplexity
    def rescue_aasm_error
      yield
    rescue AASM::InvalidTransition => error
      message = error.message
      if @work.errors.count > 0
        message = @work.errors.to_a.join(", ")
      end
      message.chop! if message.last == "."
      Honeybadger.notify("Invalid #{@work.current_transition}: #{error.message} errors: #{message}")
      transition_error_message = "We apologize, the following errors were encountered: #{message}. Please contact the PDC Describe administrators for any assistance."
      @errors = [transition_error_message]

      if @work.persisted?
        redirect_to edit_work_url(id: @work.id), notice: transition_error_message, params:
      else
        new_params = {}
        new_params[:wizard] = wizard_mode? if wizard_mode?
        new_params[:migrate] = migrating? if migrating?
        @form_resource_decorator = FormResourceDecorator.new(@work, current_user)
        redirect_to new_work_url(params: new_params), notice: transition_error_message, params: new_params
      end
    rescue StandardError => generic_error
      if action_name == "create"
        if @work.persisted?
          Honeybadger.notify("Failed to create the new Dataset #{@work.id}: #{generic_error.message}")
          @form_resource_decorator = FormResourceDecorator.new(@work, current_user)
          redirect_to edit_work_url(id: @work.id), notice: "Failed to create the new Dataset #{@work.id}: #{generic_error.message}", params:
        else
          Honeybadger.notify("Failed to create a new Dataset #{@work.id}: #{generic_error.message}")
          new_params = {}
          new_params[:wizard] = wizard_mode? if wizard_mode?
          new_params[:migrate] = migrating? if migrating?
          @form_resource_decorator = FormResourceDecorator.new(@work, current_user)
          redirect_to new_work_url(params: new_params), notice: "Failed to create a new Dataset: #{generic_error.message}", params: new_params
        end
      else
        redirect_to root_url, notice: "We apologize, an error was encountered: #{generic_error.message}. Please contact the PDC Describe administrators."
      end
    end
    # rubocop:enable Metrics/PerceivedComplexity
    # rubocop:enable Metrics/MethodLength
    # rubocop:enable Metrics/CyclomaticComplexity
    # rubocop:enable Metrics/BlockNesting
    # rubocop:enable Metrics/AbcSize

    def error_action
      @form_resource_decorator = FormResourceDecorator.new(@work, current_user)
      if action_name == "create"
        :new
      elsif action_name == "validate"
        :edit
      elsif action_name == "new_submission"
        :new_submission
      else
        @work_decorator = WorkDecorator.new(@work, current_user)
        :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 = deleted_files_param || []
        deleted_uploads = upload_service.find_post_curation_uploads(upload_keys:)

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

      process_updates
    end

    def embargo_date_param
      params["embargo-date"]
    end

    def embargo_date
      return nil if embargo_date_param.blank?

      Date.parse(embargo_date_param)
    rescue Date::Error
      Rails.logger.error("Failed to parse the embargo date #{embargo_date_param} for Work #{@work.id}")
      nil
    end

    def update_params
      {
        group_id: params_group_id,
        embargo_date:,
        resource: FormToResourceService.convert(params, @work)
      }
    end

    def added_files_param
      Array(work_params[:pre_curation_uploads_added])
    end

    def deleted_files_param
      deleted_count = (work_params["deleted_files_count"] || "0").to_i
      (1..deleted_count).map { |i| work_params["deleted_file_#{i}"] }.select(&:present?)
    end

    def process_updates
      resource_before = @work.resource
      if @work.update(update_params)
        resource_compare = WorkCompareService.new(resource_before, update_params[:resource])
        @work.log_changes(resource_compare, current_user.id)

        if @wizard_mode
          redirect_to work_readme_select_url(@work)
        else
          redirect_to work_url(@work), notice: "Work was successfully updated."
        end
      else
        # This is needed for rendering HTML views with validation errors
        @uploads = @work.uploads
        @wizard_mode = wizard_mode?
        @form_resource_decorator = FormResourceDecorator.new(@work, current_user)

        render :edit, status: :unprocessable_entity
      end
    end

    def params_group_id
      # Do not allow a nil for the group id
      @params_group_id ||= begin
        group_id = params[:group_id]
        if group_id.blank?
          group_id = current_user.default_group.id
          Honeybadger.notify("We got a nil group as part of the parameters #{params} #{request}")
        end
        group_id
      end
    end

    def migrated?
      return false unless params.key?(:submit)

      params[:submit] == "Migrate"
    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, :new_submission]	1✔
10
11	skip_before_action :authenticate_user!	1✔
12	before_action :authenticate_user!, unless: :public_request?	1✔
13
14	def index	1✔
15	@works = Work.all	4✔
16	respond_to do \|format\|	4✔
17	format.html	4✔
18	format.rss { render layout: false }	6✔
19	end
20	end
21
22	# Renders the "step 0" information page before creating a new dataset
23	def new	1✔
24	group = Group.find_by(code: params[:group_code]) \|\| current_user.default_group	49✔
25	@work = Work.new(created_by_user_id: current_user.id, group:)	49✔
26	@form_resource_decorator = FormResourceDecorator.new(@work, current_user)	49✔
27	if wizard_mode?	49✔
28	render "new_submission"	23✔
29	end
30	end
31
32	def create	1✔
33	@work = Work.new(created_by_user_id: current_user.id, group_id: params_group_id, user_entered_doi: params["doi"].present?)	32✔
34	@work.resource = FormToResourceService.convert(params, @work)	32✔
35	@work.resource.migrated = migrated?	32✔
36	if @work.valid?	32✔
37	@work.draft!(current_user)	28✔
38	upload_service = WorkUploadsEditService.new(@work, current_user)	27✔
39	upload_service.update_precurated_file_list(added_files_param, deleted_files_param)	27✔
40	redirect_to work_url(@work), notice: "Work was successfully created."	27✔
41	else
42	@form_resource_decorator = FormResourceDecorator.new(@work, current_user)	4✔
43	render :new, status: :unprocessable_entity	4✔
44	end
45	end
46
47	# Creates the new dataset
48	def new_submission	1✔
49	default_group_id = current_user.default_group.id	19✔
50	@work = Work.new(created_by_user_id: current_user.id, group_id: default_group_id)	19✔
51	@work.resource = FormToResourceService.convert(params, @work)	19✔
52	@work.draft!(current_user)	19✔
53	redirect_to edit_work_path(@work, wizard: true)	18✔
54	end
55
56	##
57	# Show the information for the dataset with the given id
58	# When requested as .json, return the internal json resource
59	def show	1✔
60	@work = Work.find(params[:id])	88✔
61	UpdateSnapshotJob.perform_later(work_id: @work.id, last_snapshot_id: work.upload_snapshots.first&.id)	88✔
62	@work_decorator = WorkDecorator.new(@work, current_user)	88✔
63
64	respond_to do \|format\|	88✔
65	format.html do	88✔
66	# Ensure that the Work belongs to a Group
67	group = @work_decorator.group	85✔
68	raise(Work::InvalidGroupError, "The Work #{@work.id} does not belong to any Group") unless group	85✔
69
70	@can_curate = current_user.can_admin?(group)	84✔
71	@work.mark_new_notifications_as_read(current_user.id)	84✔
72	end
73	format.json { render json: @work.to_json }	91✔
74	end
75	end
76
77	def file_list	1✔
78	if params[:id] == "NONE"	178✔
79	# This is a special case when we render the file list for a work being created
80	# (i.e. it does not have an id just yet)
81	render json: []	29✔
82	else
83	@work = Work.find(params[:id])	149✔
84	render json: @work.file_list	149✔
85	end
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])	106✔
101	if current_user && @work.editable_by?(current_user)	106✔
102	if @work.approved? && !@work.administered_by?(current_user)	104✔
103	Honeybadger.notify("Can not edit work: #{@work.id} is approved but #{current_user.uid} is not admin")	2✔
104	redirect_to root_path, notice: I18n.t("works.uneditable.approved")	2✔
105	else
106	@uploads = @work.uploads	102✔
107	@wizard_mode = wizard_mode?	102✔
108	@form_resource_decorator = FormResourceDecorator.new(@work, current_user)	102✔
109	render "edit"	102✔
110	end
111	else
112	Honeybadger.notify("Can not edit work: #{@work.id} is not editable by #{current_user.uid}")	2✔
113	redirect_to root_path, notice: I18n.t("works.uneditable.privs")	2✔
114	end
115	end
116
117	def update	1✔
118	@work = Work.find(params[:id])	102✔
119	if current_user.blank? \|\| !@work.editable_by?(current_user)	102✔
120	Honeybadger.notify("Can not update work: #{@work.id} is not editable by #{current_user.uid}")	1✔
121	redirect_to root_path, notice: I18n.t("works.uneditable.privs")	1✔
122	elsif !@work.editable_in_current_state?(current_user)	101✔
123	Honeybadger.notify("Can not update work: #{@work.id} is not editable in current state by #{current_user.uid}")	1✔
124	redirect_to root_path, notice: I18n.t("works.uneditable.approved")	1✔
125	else
126	update_work	100✔
127	end
128	end
129
130	# Prompt to select how to submit their files
131	def attachment_select	1✔
132	@work = Work.find(params[:id])	2✔
133	@wizard_mode = true	2✔
134	end
135
136	# User selected a specific way to submit their files
137	def attachment_selected	1✔
138	@work = Work.find(params[:id])	3✔
139	@wizard_mode = true	3✔
140	@work.files_location = params["attachment_type"]	3✔
141	@work.save!	3✔
142
143	# create a directory for the work if the curator will need to move files by hand
144	@work.s3_query_service.create_directory if @work.files_location != "file_upload"	3✔
145
146	next_url = case @work.files_location	3✔
147	when "file_upload"
148	work_file_upload_url(@work)	1✔
149	when "file_cluster"
150	work_file_cluster_url(@work)	1✔
151	else
152	work_file_other_url(@work)	1✔
153	end
154	redirect_to next_url	3✔
155	end
156
157	# Allow user to upload files directly
158	def file_upload	1✔
159	@work = Work.find(params[:id])	3✔
160	end
161
162	def file_uploaded	1✔
163	@work = Work.find(params[:id])	4✔
164	files = pre_curation_uploads_param \|\| []	4✔
165	if files.count > 0	4✔
166	upload_service = WorkUploadsEditService.new(@work, current_user)	3✔
167	@work = upload_service.update_precurated_file_list(files, [])	3✔
168	@work.save!	2✔
169	@work.reload_snapshots	2✔
170	end
171	redirect_to(work_review_path)	3✔
172	rescue StandardError => active_storage_error
173	Rails.logger.error("Failed to attach the file uploads for the work #{@work.doi}: #{active_storage_error}")	1✔
174	flash[:notice] = "Failed to attach the file uploads for the work #{@work.doi}: #{active_storage_error}. Please contact rdss@princeton.edu for assistance."	1✔
175
176	redirect_to work_file_upload_path(@work)	1✔
177	end
178
179	# Allow user to indicate where their files are located in the PUL Research Cluster
180	def file_cluster	1✔
181	@work = Work.find(params[:id])	1✔
182	end
183
184	# Allow user to indicate where their files are located in the WWW
185	def file_other	1✔
186	@work = Work.find(params[:id])	1✔
187	end
188
189	def review	1✔
190	@work = Work.find(params[:id])	2✔
191	if request.method == "POST"	2✔
192	@work.location_notes = params["location_notes"]	1✔
193	@work.save!	1✔
194	end
195	end
196
197	def validate	1✔
198	@work = Work.find(params[:id])	26✔
199	@work.submission_notes = params["submission_notes"]	26✔
200	@uploads = @work.uploads	26✔
201	@wizard_mode = true	26✔
202	@work.complete_submission!(current_user)	26✔
203	redirect_to user_url(current_user)	25✔
204	end
205
206	def approve	1✔
207	@work = Work.find(params[:id])	14✔
208	@work.approve!(current_user)	14✔
209	flash[:notice] = "Your files are being moved to the post-curation bucket in the background. Depending on the file sizes this may take some time."	6✔
210	redirect_to work_path(@work)	6✔
211	end
212
213	def withdraw	1✔
214	@work = Work.find(params[:id])	2✔
215	@work.withdraw!(current_user)	2✔
216	redirect_to work_path(@work)	1✔
217	end
218
219	def resubmit	1✔
220	@work = Work.find(params[:id])	2✔
221	@work.resubmit!(current_user)	2✔
222	redirect_to work_path(@work)	1✔
223	end
224
225	def assign_curator	1✔
226	work = Work.find(params[:id])	5✔
227	work.change_curator(params[:uid], current_user)	5✔
228	if work.errors.count > 0	4✔
229	render json: { errors: work.errors.map(&:type) }, status: :bad_request	1✔
230	else
231	render json: {}	3✔
232	end
233	rescue => ex
234	Rails.logger.error("Error changing curator for work: #{work.id}. Exception: #{ex.message}")	1✔
235	render json: { errors: ["Cannot save dataset"] }, status: :bad_request	1✔
236	end
237
238	def add_message	1✔
239	work = Work.find(params[:id])	6✔
240	if params["new-message"].present?	6✔
241	new_message_param = params["new-message"]	6✔
242	sanitized_new_message = html_escape(new_message_param)	6✔
243
244	work.add_message(sanitized_new_message, current_user.id)	6✔
245	end
246	redirect_to work_path(id: params[:id])	6✔
247	end
248
249	def add_provenance_note	1✔
250	work = Work.find(params[:id])	2✔
251	if params["new-provenance-note"].present?	2✔
252	new_date = params["new-provenance-date"]	2✔
253	new_label = params["change_label"]	2✔
254	new_note = html_escape(params["new-provenance-note"])	2✔
255
256	work.add_provenance_note(new_date, new_note, current_user.id, new_label)	2✔
257	end
258	redirect_to work_path(id: params[:id])	2✔
259	end
260
261	# Outputs the Datacite XML representation of the work
262	def datacite	1✔
263	work = Work.find(params[:id])	2✔
264	render xml: work.to_xml	2✔
265	end
266
267	def datacite_validate	1✔
268	@errors = []	3✔
269	@work = Work.find(params[:id])	3✔
270	validator = WorkValidator.new(@work)	3✔
271	unless validator.valid_datacite?	3✔
272	@errors = @work.errors.full_messages	2✔
273	end
274	end
275
276	def readme_select	1✔
277	@work = Work.find(params[:id])	3✔
278	readme = Readme.new(@work, current_user)	3✔
279	@readme = readme.file_name	3✔
280	@wizard = true	3✔
281	end
282
283	def readme_uploaded	1✔
284	@work = Work.find(params[:id])	3✔
285	@wizard = true	3✔
286	readme = Readme.new(@work, current_user)	3✔
287	readme_error = readme.attach(readme_file_param)	3✔
288	if readme_error.nil?	3✔
289	redirect_to work_attachment_select_url(@work)	2✔
290	else
291	flash[:notice] = readme_error	1✔
292	redirect_to work_readme_select_url(@work)	1✔
293	end
294	end
295
296	def migrating?	1✔
297	return @work.resource.migrated if @work&.resource && !params.key?(:migrate)	61✔
298
299	params[:migrate]	44✔
300	end
301	helper_method :migrating?	1✔
302
303	def doi_mutable?	1✔
304	return true unless !@work.nil? && @work.persisted?	149✔
305
306	!@work.approved?	93✔
307	end
308	helper_method :doi_mutable?	1✔
309
310	# Returns the raw BibTex citation information
311	def bibtex	1✔
312	work = Work.find(params[:id])	1✔
313	creators = work.resource.creators.map { \|creator\| "#{creator.family_name}, #{creator.given_name}" }	15✔
314	citation = DatasetCitation.new(creators, [work.resource.publication_year], work.resource.titles.first.title, work.resource.resource_type, work.resource.publisher, work.resource.doi)	1✔
315	bibtex = citation.bibtex	1✔
316	send_data bibtex, filename: "#{citation.bibtex_id}.bibtex", type: "text/plain", disposition: "attachment"	1✔
317	end
318
319	private	1✔
320
321	# Extract the Work ID parameter
322	# @return [String]
323	def work_id_param	1✔
324	params[:id]	92✔
325	end
326
327	# Find the Work requested by ID
328	# @return [Work]
329	def work	1✔
330	Work.find(work_id_param)	92✔
331	end
332
333	# Determine whether or not the request is for the :index action in the RSS
334	# response format
335	# This is to enable PDC Discovery to index approved content via the RSS feed
336	def rss_index_request?	1✔
337	action_name == "index" && request.format.symbol == :rss	675✔
338	end
339
340	# Determine whether or not the request is for the :show action in the JSON
341	# response format
342	# @return [Boolean]
343	def json_show_request?	1✔
344	action_name == "show" && request.format.symbol == :json	673✔
345	end
346
347	# Determine whether or not the requested Work has been approved
348	# @return [Boolean]
349	def work_approved?	1✔
350	work&.state == "approved"	4✔
351	end
352
353	##
354	# Public requests are requests that do not require authentication.
355	# This is to enable PDC Discovery to index approved content via the RSS feed
356	# and .json calls to individual works without needing to log in as a user.
357	# Note that only approved works can be fetched for indexing.
358	def public_request?	1✔
359	return true if rss_index_request?	675✔
360	return true if json_show_request? && work_approved?	673✔
361	false	671✔
362	end
363
364	def work_params	1✔
365	params[:work] \|\| {}	261✔
366	end
367
368	def patch_params	1✔
369	return {} unless params.key?(:patch)	14✔
370
371	params[:patch]	12✔
372	end
373
374	def pre_curation_uploads_param	1✔
375	return if patch_params.nil?	4✔
376
377	patch_params[:pre_curation_uploads]	4✔
378	end
379
380	def readme_file_param	1✔
381	return if patch_params.nil?	3✔
382
383	patch_params[:readme_file]	3✔
384	end
385
386	# rubocop:disable Metrics/AbcSize
387	# rubocop:disable Metrics/BlockNesting
388	# rubocop:disable Metrics/CyclomaticComplexity
389	# rubocop:disable Metrics/MethodLength
390	# rubocop:disable Metrics/PerceivedComplexity
391	def rescue_aasm_error	1✔
392	yield	95✔
393	rescue AASM::InvalidTransition => error
394	message = error.message	12✔
395	if @work.errors.count > 0	12✔
396	message = @work.errors.to_a.join(", ")	7✔
397	end
398	message.chop! if message.last == "."	12✔
399	Honeybadger.notify("Invalid #{@work.current_transition}: #{error.message} errors: #{message}")	12✔
400	transition_error_message = "We apologize, the following errors were encountered: #{message}. Please contact the PDC Describe administrators for any assistance."	12✔
401	@errors = [transition_error_message]	12✔
402
403	if @work.persisted?	12✔
404	redirect_to edit_work_url(id: @work.id), notice: transition_error_message, params:	11✔
405	else
406	new_params = {}	1✔
407	new_params[:wizard] = wizard_mode? if wizard_mode?	1✔
408	new_params[:migrate] = migrating? if migrating?	1✔
409	@form_resource_decorator = FormResourceDecorator.new(@work, current_user)	1✔
410	redirect_to new_work_url(params: new_params), notice: transition_error_message, params: new_params	1✔
411	end
412	rescue StandardError => generic_error
413	if action_name == "create"	1✔
414	if @work.persisted?	1✔
415	Honeybadger.notify("Failed to create the new Dataset #{@work.id}: #{generic_error.message}")	×
416	@form_resource_decorator = FormResourceDecorator.new(@work, current_user)	×
417	redirect_to edit_work_url(id: @work.id), notice: "Failed to create the new Dataset #{@work.id}: #{generic_error.message}", params:	×
418	else
419	Honeybadger.notify("Failed to create a new Dataset #{@work.id}: #{generic_error.message}")	1✔
420	new_params = {}	1✔
421	new_params[:wizard] = wizard_mode? if wizard_mode?	1✔
422	new_params[:migrate] = migrating? if migrating?	1✔
423	@form_resource_decorator = FormResourceDecorator.new(@work, current_user)	1✔
424	redirect_to new_work_url(params: new_params), notice: "Failed to create a new Dataset: #{generic_error.message}", params: new_params	1✔
425	end
426	else
427	redirect_to root_url, notice: "We apologize, an error was encountered: #{generic_error.message}. Please contact the PDC Describe administrators."	×
428	end
429	end
430	# rubocop:enable Metrics/PerceivedComplexity
431	# rubocop:enable Metrics/MethodLength
432	# rubocop:enable Metrics/CyclomaticComplexity
433	# rubocop:enable Metrics/BlockNesting
434	# rubocop:enable Metrics/AbcSize
435
436	def error_action	1✔
437	@form_resource_decorator = FormResourceDecorator.new(@work, current_user)	×
438	if action_name == "create"	×
439	:new	×
440	elsif action_name == "validate"	×
441	:edit	×
442	elsif action_name == "new_submission"	×
443	:new_submission	×
444	else
445	@work_decorator = WorkDecorator.new(@work, current_user)	×
446	:show	×
447	end
448	end
449
450	def wizard_mode?	1✔
451	params[:wizard] == "true"	256✔
452	end
453
454	def update_work	1✔
455	@wizard_mode = wizard_mode?	100✔
456	upload_service = WorkUploadsEditService.new(@work, current_user)	100✔
457	if @work.approved?	100✔
458	upload_keys = deleted_files_param \|\| []	5✔
459	deleted_uploads = upload_service.find_post_curation_uploads(upload_keys:)	5✔
460
461	return head(:forbidden) unless deleted_uploads.empty?	5✔
462	else
463	@work = upload_service.update_precurated_file_list(added_files_param, deleted_files_param)	95✔
464	end
465
466	process_updates	99✔
467	end
468
469	def embargo_date_param	1✔
470	params["embargo-date"]	201✔
471	end
472
473	def embargo_date	1✔
474	return nil if embargo_date_param.blank?	195✔
475
476	Date.parse(embargo_date_param)	4✔
477	rescue Date::Error
478	Rails.logger.error("Failed to parse the embargo date #{embargo_date_param} for Work #{@work.id}")	2✔
479	nil	2✔
480	end
481
482	def update_params	1✔
483	{
484	group_id: params_group_id,	195✔
485	embargo_date:,
486	resource: FormToResourceService.convert(params, @work)
487	}
488	end
489
490	def added_files_param	1✔
491	Array(work_params[:pre_curation_uploads_added])	122✔
492	end
493
494	def deleted_files_param	1✔
495	deleted_count = (work_params["deleted_files_count"] \|\| "0").to_i	127✔
496	(1..deleted_count).map { \|i\| work_params["deleted_file_#{i}"] }.select(&:present?)	139✔
497	end
498
499	def process_updates	1✔
500	resource_before = @work.resource	99✔
501	if @work.update(update_params)	99✔
502	resource_compare = WorkCompareService.new(resource_before, update_params[:resource])	96✔
UNCOV 503	@work.log_changes(resource_compare, current_user.id)	×
504
UNCOV 505	if @wizard_mode	×
UNCOV 506	redirect_to work_readme_select_url(@work)	×
507	else
UNCOV 508	redirect_to work_url(@work), notice: "Work was successfully updated."	×
509	end
510	else
511	# This is needed for rendering HTML views with validation errors
512	@uploads = @work.uploads	3✔
513	@wizard_mode = wizard_mode?	3✔
514	@form_resource_decorator = FormResourceDecorator.new(@work, current_user)	3✔
515
516	render :edit, status: :unprocessable_entity	3✔
517	end
518	end
519
520	def params_group_id	1✔
521	# Do not allow a nil for the group id
522	@params_group_id \|\|= begin	227✔
523	group_id = params[:group_id]	131✔
524	if group_id.blank?	131✔
525	group_id = current_user.default_group.id	9✔
526	Honeybadger.notify("We got a nil group as part of the parameters #{params} #{request}")	9✔
527	end
528	group_id	131✔
529	end
530	end
531
532	def migrated?	1✔
533	return false unless params.key?(:submit)	32✔
534
535	params[:submit] == "Migrate"	28✔
536	end
537	end
538	# rubocop:enable Metrics/ClassLength

pulibrary / pdc_describe / 34fcfd04-4a59-4c24-91de-15a8ef14d8a4

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