app/controllers/samples_controller.rb
# frozen_string_literal: true
# rubocop:todo Metrics/ClassLength
class SamplesController < ApplicationController
# WARNING! This filter bypasses security mechanisms in rails 4 and mimics rails 2 behviour.
# It should be removed wherever possible and the correct Strong Parameter options applied in its place.
before_action :evil_parameter_hack!
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
def show
@sample = Sample.includes(:assets, :studies).find(params[:id])
@studies = Study.where(state: %w[pending active]).alphabetical
respond_to do |format|
format.html
format.xml { render layout: false }
format.json { render json: @sample.to_json }
end
end
def new
@sample = Sample.new
@studies = Study.alphabetical
end
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
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|
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
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
# rubocop:todo Metrics/MethodLength
def update # rubocop:todo Metrics/AbcSize
@sample = Sample.find(params[:id])
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'
redirect_to sample_path(@sample)
else
flash[:error] = 'Failed to update attributes for sample'
render action: 'edit', id: @sample.id
end
end
# rubocop:enable Metrics/MethodLength
def history
@sample = Sample.find(params[:id])
respond_to { |format| format.html }
end
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
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
def show_accession
@sample = Sample.find(params[:id])
respond_to do |format|
xml_text = @sample.accession_service.accession_sample_xml(@sample)
format.xml { render(text: xml_text) }
end
end
# rubocop:todo Metrics/MethodLength
def accession # rubocop:todo Metrics/AbcSize
@sample = Sample.find(params[:id])
@sample.validate_ena_required_fields!
@sample.accession_service.submit_sample_for_user(@sample, current_user)
flash[:notice] = "Accession number generated: #{@sample.sample_metadata.sample_ebi_accession_number}"
redirect_to(sample_path(@sample))
rescue ActiveRecord::RecordInvalid => e
flash[:error] = "Please fill in the required fields: #{@sample.errors.full_messages.join(', ')}"
redirect_to(edit_sample_path(@sample))
rescue AccessionService::NumberNotRequired => e
flash[:warning] = e.message || 'An accession number is not required for this study'
redirect_to(sample_path(@sample))
rescue AccessionService::NumberNotGenerated => e
flash[:warning] = "No accession number was generated: #{e.message}"
redirect_to(sample_path(@sample))
rescue AccessionService::AccessionServiceError => e
flash[:error] = e.message
redirect_to(sample_path(@sample))
end
# rubocop:enable Metrics/MethodLength
# rubocop:todo Metrics/MethodLength
def taxon_lookup # rubocop:todo Metrics/AbcSize
if params[:term]
url = configatron.taxon_lookup_url + "/esearch.fcgi?db=taxonomy&term=#{params[:term].gsub(/\s/, '_')}"
elsif params[:id]
url = configatron.taxon_lookup_url + "/efetch.fcgi?db=taxonomy&mode=xml&id=#{params[:id]}"
else
return
end
rc = RestClient::Resource.new(URI.parse(url).to_s)
if configatron.disable_web_proxy == true
RestClient.proxy = nil
elsif configatron.fetch(:proxy).present?
RestClient.proxy = configatron.proxy
rc.headers['User-Agent'] = 'Internet Explorer 5.0'
elsif ENV['http_proxy'].present?
RestClient.proxy = ENV['http_proxy']
end
# rc.verbose = true
body = rc.get.body
respond_to do |format|
format.js { render plain: body }
format.xml { render plain: body }
# format.html {render :nothing}
end
end
# rubocop:enable Metrics/MethodLength
private
def default_permitted_metadata_fields
{
sample_metadata_attributes: %i[
consent_withdrawn
organism
gc_content
cohort
gender
country_of_origin
geographical_region
ethnicity
dna_source
volume
mother
father
replicate
sample_public_name
sample_common_name
sample_strain_att
sample_taxon_id
sample_ebi_accession_number
sample_sra_hold
sample_description
sibling
is_resubmitted
date_of_sample_collection
date_of_sample_extraction
sample_extraction_method
sample_purified
purification_method
concentration
concentration_determined_by
sample_type
sample_storage_conditions
supplier_name
reference_genome_id
genotype
phenotype
age
developmental_stage
cell_type
disease_state
compound
dose
immunoprecipitate
growth_condition
rnai
organism_part
time_point
disease
subject
treatment
donor_id
]
}
end
end
# rubocop:enable Metrics/ClassLength