Class: SequenceServer::Routes

Inherits:
Sinatra::Base
  • Object
show all
Defined in:
lib/sequenceserver/routes.rb

Overview

Controller.

Instance Method Summary collapse

Instance Method Details

#display_large_result_warning?(xml_file_size) ⇒ Boolean 



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# File 'lib/sequenceserver/routes.rb', line 336

def display_large_result_warning?(xml_file_size)
  threshold = SequenceServer.config[:large_result_warning_threshold].to_i
  return false unless threshold.positive?

  return false if params[:bypass_file_size_warning] == 'true'

  xml_file_size > threshold
end

#large_result_warning_payload(jid) ⇒ Object 



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# File 'lib/sequenceserver/routes.rb', line 345

def large_result_warning_payload(jid)
  {
    user_warning: 'LARGE_RESULT',
    download_links: [
      { name: 'Standard Tabular Report', url: "download/#{jid}.std_tsv" },
      { name: 'Full Tabular Report', url: "/download/#{jid}.full_tsv" },
      { name: 'Results in XML', url: "/download/#{jid}.xml" },
      { name: 'Pairwise', url: "/download/#{jid}.pairwise" },
    ]
  }
end

#update_searchdata_from_job(searchdata) ⇒ Object

Get the query sequences, selected databases, and advanced params used.



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# File 'lib/sequenceserver/routes.rb', line 311

def update_searchdata_from_job(searchdata)
  job = fetch_job(params[:job_id])
  return { error: 'Job not found' }.to_json if job.nil?
  return if job.imported_xml_file

  # Only read job.qfile if we are not going to use Database.retrieve.
  searchdata[:query] = File.read(job.qfile) unless params[:query]

  # Which databases to pre-select.
  searchdata[:preSelectedDbs] = job.databases

  # job.advanced may be nil in case of old jobs. In this case, we do not
  # override searchdata so that default advanced parameters can be applied.
  # Note that, job.advanced will be an empty string if a user deletes the
  # default advanced parameters from the advanced params input field. In
  # this case, we do want the advanced params input field to be empty when
  # the user hits the back button. Thus we do not test for empty string.
  method = job.method.to_sym
  if job.advanced && job.advanced !=
                     searchdata.dig(:options, method, :default, :attributes).to_a.join(' ')
    searchdata[:options] = searchdata[:options].deep_copy
    searchdata[:options][method]['last search'] = { attributes: [job.advanced] }
  end
end