Class: SamplesController

Inherits:
ApplicationController show all
Includes:
AccessionHelper
Defined in:
app/controllers/samples_controller.rb

Overview

rubocop:todo Metrics/ClassLength

Constant Summary

Constants included from FlashTruncation

FlashTruncation::STRING_OVERHEAD

Instance Method Summary collapse

Methods included from AccessionHelper

#accessioning_enabled?, #permitted_to_accession?

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

Instance Method Details

#accession ⇒ Object

rubocop:disable Metrics/AbcSize,Metrics/MethodLength



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# File 'app/controllers/samples_controller.rb', line 152

def accession # rubocop:disable Metrics/AbcSize,Metrics/MethodLength
  # @sample needs to be set before initially for use in the ensure block
  @sample = Sample.find(params[:id])

  unless accessioning_enabled?
    flash[:error] = 'Accessioning is not enabled in this environment'
    redirect_to sample_path(@sample)
    return
  end
  # TODO: Y26-026 - Enforce accessioning permissions
  # unless permitted_to_accession?(@sample)
  #   flash[:error] = 'Permission required to accession this sample'
  #   redirect_to sample_path(@sample)
  #   return
  # end

  # Must check if an accession number is assigned _before_ performing the accession
  accession_action = @sample.accession_number? ? :update : :create

  # Synchronously perform accessioning job
  Accession.accession_sample(@sample, current_user, perform_now: true)

  if accession_action == :create
    flash[:notice] = "Accession number generated: #{@sample.sample_metadata.sample_ebi_accession_number}"
  elsif accession_action == :update
    flash[:notice] = 'Accessioned metadata updated'
  end

  # Handle errors for both synchronous and asynchronous accessioning
rescue Accession::InternalValidationError
  flash[:error] = "Please fill in the required fields: #{@sample.errors.full_messages.join(', ')}"
  redirect_to(edit_sample_path(@sample)) # send the user to edit the sample
rescue Accession::ExternalValidationError => e
  flash[:warning] = "No accession number was generated: #{e.message}"
rescue Accession::Error => e
  flash[:error] = "Accessioning Service Failed: #{e.message}"
rescue Faraday::Error => e
  flash[:error] = "Accessioning failed with a network error: #{e.message}"
ensure
  # Redirect back to where we came from if not already redirected
  redirect_back_with_anchor_or_to(sample_path(@sample)) unless performed?
end

#add_to_study ⇒ Object

rubocop:todo Metrics/AbcSize



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# File 'app/controllers/samples_controller.rb', line 125

def add_to_study # rubocop:todo Metrics/AbcSize
  sample = Sample.find(params[:id])
  study = Study.find(params[:study][:id])
  study.samples << sample
  redirect_to sample_path(sample)
rescue ActiveRecord::RecordInvalid => e
  flash[:error] = e.record.errors.full_messages
  redirect_to sample_path(sample)
end

#create ⇒ Object

rubocop:todo Metrics/AbcSize, Metrics/MethodLength



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# File 'app/controllers/samples_controller.rb', line 55

def create # rubocop:todo Metrics/AbcSize, Metrics/MethodLength
  @sample = Sample.new(params[:sample])

  study_id = params[:study_id]
  if study_id
    study = Study.find(study_id)
    study.samples << @sample
  end

  respond_to do |format|
    @sample.current_user = current_user
    if @sample.save
      flash[:notice] = 'Sample successfully created'
      format.html { redirect_to sample_path(@sample) }
      format.xml { render xml: @sample, status: :created, location: @sample }
      format.json { render json: @sample, status: :created, location: @sample }
    else
      flash[:error] = 'Problems creating your new sample'
      format.html { render action: :new }
      format.xml { render xml: @sample.errors, status: :unprocessable_entity }
      format.json { render json: @sample.errors, status: :unprocessable_entity }
    end
  end
end

#edit ⇒ Object

rubocop:todo Metrics/AbcSize, Metrics/MethodLength



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# File 'app/controllers/samples_controller.rb', line 38

def edit # rubocop:todo Metrics/AbcSize, Metrics/MethodLength
  @sample = Sample.find(params[:id])
  authorize! :update, @sample

  if @sample.released? && cannot?(:update_released, @sample)
    flash[:error] = 'Cannot edit publicly released sample'
    redirect_to sample_path(@sample)
    return
  end

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

#history ⇒ Object

rubocop:enable Metrics/MethodLength



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# File 'app/controllers/samples_controller.rb', line 120

def history
  @sample = Sample.find(params[:id])
  respond_to { |format| format.html }
end

#index ⇒ Object 



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# File 'app/controllers/samples_controller.rb', line 11

def index
  @samples = Sample.order(created_at: :desc).page(params[:page])
  respond_to do |format|
    format.html
    format.xml
    format.json { render json: Sample.all.to_json }
  end
end

#new ⇒ Object 



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# File 'app/controllers/samples_controller.rb', line 33

def new
  @sample = Sample.new
  @studies = Study.alphabetical
end

#release ⇒ Object 



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# File 'app/controllers/samples_controller.rb', line 80

def release
  @sample = Sample.find(params[:id])
  authorize! :release, @sample

  if @sample.released?
    flash[:notice] = "Sample '#{@sample.name}' already publically released"
  else
    @sample.release
    flash[:notice] = "Sample '#{@sample.name}' publically released"
  end
  redirect_to sample_path(@sample)
end

#remove_from_study ⇒ Object

rubocop:todo Metrics/AbcSize



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# File 'app/controllers/samples_controller.rb', line 135

def remove_from_study # rubocop:todo Metrics/AbcSize
  study = Study.find(params[:study_id])
  sample = Sample.find(params[:id])
  StudySample.find_by(study_id: params[:study_id], sample_id: params[:id]).destroy
  flash[:notice] = "Sample was removed from study #{study.name.humanize}"
  redirect_to sample_path(sample)
end

#show ⇒ Object

rubocop:disable Metrics/AbcSize



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# File 'app/controllers/samples_controller.rb', line 20

def show # rubocop:disable Metrics/AbcSize
  @sample = Sample.includes(:assets, :studies).find(params[:id])
  @studies = Study.where(state: %w[pending active]).alphabetical
  @page_name = @sample.name
  @component_samples = @sample.component_samples.paginate({ page: params[:page], per_page: 25 })

  respond_to do |format|
    format.html
    format.xml { render layout: false }
    format.json { render json: @sample.to_json }
  end
end

#show_accession ⇒ Object 



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# File 'app/controllers/samples_controller.rb', line 143

def show_accession
  @sample = Sample.find(params[:id])
  respond_to do |format|
    accession_service = AccessionService.select_for_sample(@sample)
    xml_text = accession_service.accession_sample_xml(@sample)
    format.xml { render(xml: xml_text) }
  end
end

#update ⇒ Object

rubocop:todo Metrics/MethodLength



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# File 'app/controllers/samples_controller.rb', line 94

def update # rubocop:todo Metrics/AbcSize
  @sample = Sample.find(params[:id])
  @sample.current_user = current_user
  authorize! :update, @sample

  cleaned_params = params[:sample].permit(default_permitted_metadata_fields)

  # if consent is being withdrawn and wasn't previously, set a couple of fields
  if (cleaned_params[:sample_metadata_attributes][:consent_withdrawn] == 'true') && !@sample.consent_withdrawn
    cleaned_params[:date_of_consent_withdrawn] = DateTime.now
    cleaned_params[:user_id_of_consent_withdrawn] = current_user.id
  end

  if @sample.update(cleaned_params)
    flash[:notice] = 'Sample details have been updated'
    flash[:warning] = @sample.errors.full_messages if @sample.errors.present? # also shows warnings from accessioning
    redirect_to sample_path(@sample)
  else
    flash[:error] = 'Failed to update attributes for sample'
    flash[:warning] = @sample.errors.full_messages if @sample.errors.present?
    redirect_to edit_sample_path(@sample)
  end
end