Class: StudiesController

Inherits:
ApplicationController show all
Includes:
AccessionHelper, Informatics::Globals, REXML
Defined in:
app/controllers/studies_controller.rb

Overview

rubocop:todo Metrics/ClassLength

Constant Summary

Constants included from FlashTruncation

FlashTruncation::STRING_OVERHEAD

Class Method Summary collapse

Instance Method Summary collapse

Methods included from AccessionHelper

#accessioning_enabled?, #permitted_to_accession?

Methods included from Informatics::Globals

#application, #application=, #defaults, #defaults=, #global_searchable_classes, #search_options

Methods inherited from ApplicationController

#block_api_access, #evil_parameter_hack!, #extract_header_info, #set_cache_disabled!

Methods included from AuthenticatedSystem

included

Methods included from FlashTruncation

#max_flash_size, #truncate_flash, #truncate_flash_array

Class Method Details

.role_helper(name, success_action, error_action) ⇒ Object

rubocop:todo Metrics/MethodLength



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# File 'app/controllers/studies_controller.rb', line 340

def self.role_helper(name, success_action, error_action) # rubocop:todo Metrics/AbcSize
  define_method(:"#{name}_role") do
    ActiveRecord::Base.transaction do
      @study = Study.find(params[:id])
      @user = User.find(params.require(:role).fetch(:user))

      if request.xhr?
        yield(@user, @study, params[:role][:authorizable_type].to_s)
        status, flash.now[:notice] = 200, "Role #{success_action}"
      else
        status, flash.now[:error] = 401, "A problem occurred while #{error_action} the role"
      end

      @roles = @study.roles.reload
      render partial: 'roles', status: status
    end
  end
end

Instance Method Details

#accession ⇒ Object 



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# File 'app/controllers/studies_controller.rb', line 240

def accession
  @study = Study.find(params[:id])
  return accessioning_not_enabled_redirect unless accessioning_enabled?

  # TODO: Y26-026 - Enforce accessioning permissions
  # return accession_permission_denied_redirect unless permitted_to_accession?(@study)

  handle_accession_action(
    notice: -> { "Accession number generated: #{@study.ebi_accession_number}" }
  ) do
    @study.validate_study_for_accessioning!
    accession_service = AccessionService.select_for_study(@study)
    accession_service.submit_study_for_user(@study, current_user)
  end
end

#accession_all_samples ⇒ void

This method returns an undefined value.

Accession all samples in the study.

If the study does not have an accession number, adds an error to the study and returns. Otherwise, iterates through each sample in the study and attempts to accession it, unless the sample already has an accession number. If an Accession::Error occurs for a sample, adds the error message to the study's errors.

NOTE: this does not check if the current user has permission to accession samples in this study



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# File 'app/controllers/studies_controller.rb', line 266

def accession_all_samples # rubocop:disable Metrics/AbcSize,Metrics/MethodLength
  @study = Study.find(params[:id])
  return accessioning_not_enabled_redirect unless accessioning_enabled?

  # TODO: Y26-026 - Enforce accessioning permissions
  # return accession_permission_denied_redirect unless permitted_to_accession?(@study)

  unless @study.accession_number?
    flash[:error] = 'Please accession the study before accessioning samples'
    return redirect_to(study_path(@study))
  end
  unless @study.samples_accessionable?
    flash[:error] = 'Study cannot accession samples, see Study Accessioning tab for details'
    return redirect_to(study_path(@study))
  end

  @study.samples.find_each do |sample|
    next if sample.accession_number?

    begin
      Accession.accession_sample(sample, current_user)
    rescue Accession::Error => e
      @study.errors.add(:base, e.message)
    end
  end

  if @study.errors.any?
    flash[:error] = compile_accession_errors(@study.errors)
  else
    flash[:notice] = 'All of the samples in this study have been sent for accessioning. ' \
                     'Please check back in 5 minutes to confirm that accessioning was successful.'
  end
  redirect_to(study_path(@study))
end

#close ⇒ Object 



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# File 'app/controllers/studies_controller.rb', line 175

def close
  @study = Study.find(params[:id])
  authorize! :activate, @study
  comment = params[:comment]
  @study.comments.create(description: comment, user_id: current_user.id)
  @study.deactivate!
  @study.save
  flash[:notice] = "This study has been deactivated: #{comment}"
  redirect_to study_path(@study)
end

#collaborators ⇒ Object 



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# File 'app/controllers/studies_controller.rb', line 156

def collaborators
  @study = Study.find(params[:id])
  @all_roles = Role.distinct.pluck(:name)
  @roles = Role.where(authorizable_id: @study.id, authorizable_type: 'Study')
  @users = User.order(:first_name)
end

#create ⇒ Object

Create the Study from new with the details from its form. Redirect to the index page with a notice.



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# File 'app/controllers/studies_controller.rb', line 83

def create # rubocop:todo Metrics/AbcSize, Metrics/MethodLength
  ActiveRecord::Base.transaction do
    @study = Study.new(params['study'].merge(user: current_user))
    @study.save!
    current_user.grant_manager(@study)
    User.find(params[:study_owner_id]).grant_owner(@study) if params[:study_owner_id].present?
  end

  flash[:notice] = 'Your study has been created'
  respond_to do |format|
    format.html { redirect_to study_path(@study) }
    format.xml { render xml: @study, status: :created, location: @study }
    format.json { render json: @study, status: :created, location: @study }
  end
rescue ActiveRecord::RecordInvalid => e
  flash.now[:error] = 'Problems creating your new study'
  respond_to do |format|
    format.html { render action: 'new' }
    format.xml { render xml: @study.errors, status: :unprocessable_entity }
    format.json { render json: @study.errors, status: :unprocessable_entity }
  end
end

#dac_accession ⇒ Object 



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# File 'app/controllers/studies_controller.rb', line 301

def dac_accession
  @study = Study.find(params[:id])
  return accessioning_not_enabled_redirect unless accessioning_enabled?

  # TODO: Y26-026 - Enforce accessioning permissions
  # return accession_permission_denied_redirect unless permitted_to_accession?(@study)

  handle_accession_action(
    notice: -> { "Accession number generated: #{@study.dac_accession_number}" }
  ) do
    accession_service = AccessionService.select_for_study(@study)
    accession_service.submit_dac_for_user(@study, current_user)
  end
end

#edit ⇒ Object 



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# File 'app/controllers/studies_controller.rb', line 75

def edit
  @study = Study.find(params[:id])
  flash.now[:warning] = @study.warnings if @study.warnings.present?
  @users = User.all
end

#follow ⇒ Object

rubocop:todo Metrics/AbcSize



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# File 'app/controllers/studies_controller.rb', line 163

def follow # rubocop:todo Metrics/AbcSize
  @study = Study.find(params[:id])
  if current_user.follower_of?(@study)
    current_user.remove_role 'follower', @study
    flash[:notice] = "You have stopped following the '#{@study.name}' study."
  else
    current_user.grant_follower(@study)
    flash[:notice] = "You are now following the '#{@study.name}' study."
  end
  redirect_to study_information_path(@study)
end

#handle_accession_action(notice:) ⇒ Object

rubocop:todo Metrics/AbcSize, Metrics/MethodLength



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# File 'app/controllers/studies_controller.rb', line 222

def handle_accession_action(notice:) # rubocop:todo Metrics/AbcSize, Metrics/MethodLength
  yield
  flash[:notice] = notice.call
  redirect_to(study_path(@study))
rescue ActiveRecord::RecordInvalid => e
  flash.now[:error] = 'Please fill in the required fields'
  render(action: :edit)
rescue AccessionService::NumberNotRequired => e
  flash[:warning] = e.message || 'An accession number is not required for this study'
  redirect_to(study_path(@study))
rescue AccessionService::NumberNotGenerated => e
  flash[:warning] = "No accession number was generated: #{e.message}"
  redirect_to(study_path(@study))
rescue AccessionService::AccessionServiceError => e
  flash[:error] = e.message
  redirect_to(edit_study_path(@study))
end

#index ⇒ Object 



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# File 'app/controllers/studies_controller.rb', line 43

def index
  # Please do not user current_user outside this block, you kill the API calls
  setup_studies_from_scope(@exclude_nested_resource)
  respond_to do |format|
    format.html
    format.xml { render(action: (@exclude_nested_resource ? 'index' : 'index_deprecated_xml')) }
    format.json { render json: Study.all.to_json }
  end
end

#new ⇒ Object 



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# File 'app/controllers/studies_controller.rb', line 70

def new
  @study = Study.new
  respond_to { |format| format.html }
end

#open ⇒ Object 



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# File 'app/controllers/studies_controller.rb', line 186

def open
  @study = Study.find(params[:id])
  authorize! :activate, @study
  @study.activate!
  @study.save
  flash[:notice] = 'This study has been activated'
  redirect_to study_path(@study)
end

#policy_accession ⇒ Object 



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# File 'app/controllers/studies_controller.rb', line 316

def policy_accession
  @study = Study.find(params[:id])
  return accessioning_not_enabled_redirect unless accessioning_enabled?

  # TODO: Y26-026 - Enforce accessioning permissions
  # return accession_permission_denied_redirect unless permitted_to_accession?(@study)

  handle_accession_action(
    notice: -> { "Accession number generated: #{@study.policy_accession_number}" }
  ) do
    accession_service = AccessionService.select_for_study(@study)
    accession_service.submit_policy_for_user(@study, current_user)
  end
end

#projects ⇒ Object 



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# File 'app/controllers/studies_controller.rb', line 364

def projects
  @study = Study.find(params[:id])
  @projects = @study.projects.page(params[:page])
end

#properties ⇒ Object 



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# File 'app/controllers/studies_controller.rb', line 146

def properties
  @study = Study.find(params[:id])

  respond_to do |format|
    format.html
    format.xml
    format.json { render json: @study.to_json }
  end
end

#sample_manifests ⇒ Object 



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# File 'app/controllers/studies_controller.rb', line 369

def sample_manifests
  @study = Study.find(params[:id])
  @sample_manifests = @study.sample_manifests.page(params[:page]).order(id: :desc)
end

#setup_studies_from_scope(exclude_nested_resource = false) ⇒ Object

rubocop:todo Metrics/AbcSize



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# File 'app/controllers/studies_controller.rb', line 19

def setup_studies_from_scope(exclude_nested_resource = false) # rubocop:todo Metrics/AbcSize
  if logged_in? && (not exclude_nested_resource)
    @alternatives = [
      'interesting',
      'followed',
      'managed & active',
      'managed & inactive',
      'pending',
      'pending ethical approval',
      'contaminated with human dna',
      'remove x and autosomes',
      'active',
      'inactive',
      'collaborations',
      'all'
    ]
    @studies = studies_from_scope(@alternatives[params[:scope].to_i])
  elsif params[:project_id] && !(project = Project.find(params[:project_id])).nil?
    @studies = project.studies.newest_first.includes(:user, :roles)
  else
    @studies = Study.newest_first.with_user_included.with_related_users_included
  end
end

#show ⇒ Object 



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# File 'app/controllers/studies_controller.rb', line 60

def show
  @study = Study.find(params[:id])
  flash.keep
  respond_to do |format|
    format.html { redirect_to study_information_path(@study) }
    format.xml { render layout: false }
    format.json { render json: @study.to_json }
  end
end

#show_accession ⇒ Object 



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# File 'app/controllers/studies_controller.rb', line 195

def show_accession
  @study = Study.find(params[:id])
  respond_to do |format|
    accession_service = AccessionService.select_for_study(@study)
    xml_text = accession_service.accession_study_xml(@study)
    format.xml { render(xml: xml_text) }
  end
end

#show_dac_accession ⇒ Object 



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# File 'app/controllers/studies_controller.rb', line 213

def show_dac_accession
  @study = Study.find(params[:id])
  respond_to do |format|
    accession_service = AccessionService.select_for_study(@study)
    xml_text = accession_service.accession_dac_xml(@study)
    format.xml { render(xml: xml_text) }
  end
end

#show_policy_accession ⇒ Object 



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# File 'app/controllers/studies_controller.rb', line 204

def show_policy_accession
  @study = Study.find(params[:id])
  respond_to do |format|
    accession_service = AccessionService.select_for_study(@study)
    xml_text = accession_service.accession_policy_xml(@study)
    format.xml { render(xml: xml_text) }
  end
end

#sra ⇒ Object 



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# File 'app/controllers/studies_controller.rb', line 331

def sra
  @study = Study.find(params[:id])
end

#state ⇒ Object 



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# File 'app/controllers/studies_controller.rb', line 335

def state
  @study = Study.find(params[:id])
end

#study_list ⇒ Object 



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# File 'app/controllers/studies_controller.rb', line 53

def study_list
  return redirect_to(studies_path) unless request.xhr?

  setup_studies_from_scope
  render partial: 'study_list', locals: { studies: @studies.with_related_owners_included }
end

#study_reports ⇒ Object 



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# File 'app/controllers/studies_controller.rb', line 379

def study_reports
  @study = Study.find(params[:id])
  @study_reports = StudyReport.for_study(@study).page(params[:page]).order(id: :desc)
end

#study_status ⇒ Object

rubocop:enable Metrics/MethodLength



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# File 'app/controllers/studies_controller.rb', line 133

def study_status
  @study = Study.find(params[:id])
  authorize! :activate, @study

  if @study.inactive? || @study.pending?
    @study.activate!
  elsif @study.active?
    @study.deactivate!
  end
  flash[:notice] = 'Study status was updated successfully'
  redirect_to study_path(@study)
end

#suppliers ⇒ Object 



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# File 'app/controllers/studies_controller.rb', line 374

def suppliers
  @study = Study.find(params[:id])
  @suppliers = @study.suppliers.page(params[:page])
end

#update ⇒ Object

rubocop:todo Metrics/MethodLength



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# File 'app/controllers/studies_controller.rb', line 107

def update # rubocop:todo Metrics/AbcSize
  @study = Study.find(params[:id])

  ActiveRecord::Base.transaction do
    @study.update!(params[:study])
    if params[:study_owner_id].present?
      owner = User.find(params[:study_owner_id])
      unless owner.owner_of?(@study)
        @study.owners.first.remove_role('owner', @study) if @study.owners.size == 1
        owner.grant_owner(@study)
      end
    end

    flash[:notice] = 'Your study has been updated'

    redirect_to study_path(@study)
  end
rescue ActiveRecord::RecordInvalid => e
  # don't use @study.errors.map(&:to_s) because it throws an exception when within a rescue block
  Rails.logger.warn "Failed to update attributes: #{@study.errors.map { |error| error.to_s }}" # rubocop:disable Style/SymbolProc
  flash.now[:error] = 'Failed to update attributes for study!'
  render action: 'edit', id: @study.id
end