Class: SampleManifestUploadWithTagSequencesController

Inherits:
ApplicationController show all
Defined in:
app/controllers/sample_manifest_upload_with_tag_sequences_controller.rb

Constant Summary

Constants included from FlashTruncation

FlashTruncation::STRING_OVERHEAD

Instance Method Summary collapse

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

#apply_warning_flash(rows) ⇒ Object

rubocop:disable Metrics/AbcSize



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

def apply_warning_flash(rows) # rubocop:disable Metrics/AbcSize
  # There are more than 10 messages, truncate the list and add a note about it.
  # This is to prevent the flash from becoming too large and causing issues with cookies.
  row_messages = rows.flat_map { |row| row.warnings.full_messages }.uniq
  if row_messages.size > 10
    # IfUnlessModifier doesn't improve readability
    row_messages = row_messages.first(10) + ["and #{row_messages.size - 10} more..."]
  end

  flash[:warning] = { 'Sample manifest uploaded with warnings!': row_messages }

  redirect_target = (@uploader.study.present? ? sample_manifests_study_path(@uploader.study) : sample_manifests_path)
  redirect_to redirect_target
end

#create ⇒ Object 



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# File 'app/controllers/sample_manifest_upload_with_tag_sequences_controller.rb', line 9

def create
  return error('No file attached') if params[:upload].blank?

  if upload_manifest
    set_upload_flash_message
  else
    error('Your sample manifest couldn\'t be uploaded.')
  end
rescue AccessionService::AccessionValidationFailed => e
  error("Your sample manifest contained invalid data and could not be uploaded: #{e.message}")
end

#create_uploader ⇒ Object 



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# File 'app/controllers/sample_manifest_upload_with_tag_sequences_controller.rb', line 21

def create_uploader
  SampleManifest::Uploader.new(params[:upload], SampleManifestExcel.configuration, current_user, params[:override])
end

#error(message) ⇒ Object 



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# File 'app/controllers/sample_manifest_upload_with_tag_sequences_controller.rb', line 65

def error(message)
  flash.now[:error] = message
  prepare_manifest_pagination
  render :new
end

#new ⇒ Object 



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# File 'app/controllers/sample_manifest_upload_with_tag_sequences_controller.rb', line 5

def new
  prepare_manifest_pagination
end

#prepare_manifest_pagination ⇒ Object

rubocop:todo Metrics/MethodLength



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# File 'app/controllers/sample_manifest_upload_with_tag_sequences_controller.rb', line 71

def prepare_manifest_pagination # rubocop:todo Metrics/MethodLength
  pending_sample_manifests =
    SampleManifest
      .pending_manifests
      .includes(:study, :supplier, :user, :uploaded_document)
      .paginate(page: params[:page])
  completed_sample_manifests =
    SampleManifest
      .completed_manifests
      .includes(:study, :supplier, :user, :uploaded_document)
      .paginate(page: params[:page])
  @display_manifests = pending_sample_manifests | completed_sample_manifests
  @sample_manifests = SampleManifest.paginate(page: params[:page])
end

#rows_with_warnings ⇒ Object 



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# File 'app/controllers/sample_manifest_upload_with_tag_sequences_controller.rb', line 37

def rows_with_warnings
  @uploader.upload.rows.select do |row|
    row.respond_to?(:warnings) && row.warnings.any?
  end
end

#set_upload_flash_message ⇒ Object 



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# File 'app/controllers/sample_manifest_upload_with_tag_sequences_controller.rb', line 30

def set_upload_flash_message
  warning_rows = rows_with_warnings
  return success('Sample manifest successfully uploaded.') if warning_rows.empty?

  apply_warning_flash(warning_rows)
end

#success(message) ⇒ Object 



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# File 'app/controllers/sample_manifest_upload_with_tag_sequences_controller.rb', line 58

def success(message)
  flash[:notice] = message
  redirect_target = (@uploader.study.present? ? sample_manifests_study_path(@uploader.study) : sample_manifests_path)

  redirect_to redirect_target
end

#upload_manifest ⇒ Object 



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# File 'app/controllers/sample_manifest_upload_with_tag_sequences_controller.rb', line 25

def upload_manifest
  @uploader = create_uploader
  @uploader.run!
end