Class: BulkSubmission
- Inherits:
-
Object
- Object
- BulkSubmission
- Extended by:
- ActiveModel::Naming
- Includes:
- ActiveModel::AttributeMethods, ActiveModel::Conversion, ActiveModel::Validations, ManifestUtil, Submission::AssetSubmissionFinder
- Defined in:
- app/models/bulk_submission.rb
Overview
A bulk submission is created through the upload of a spreadsheet (csv) It contains the information for setting up one or more submissions, allowing for the quick request of multiple pieces of work simultaneously. Bulk Submissions are not currently persisted.
Constant Summary collapse
- DEFAULT_ENCODING =
This is the default output from excel
'Windows-1252'.freeze
- COMMON_FIELDS =
[ # Needed to construct the submission ... 'template name', 'study id', 'study name', 'project id', 'project name', 'submission name', 'user login', # Needed to identify the assets and what happens to them ... 'asset group id', 'asset group name', 'fragment size from', 'fragment size to', 'pcr cycles', 'primer panel', 'read length', 'library type', 'bait library', 'bait library name', 'comments', 'number of lanes', 'pre-capture plex level', 'pre-capture group', 'gigabases expected', 'priority' ].freeze
- ALIAS_FIELDS =
{ 'plate barcode' => 'barcode', 'tube barcode' => 'barcode' }.freeze
Instance Attribute Summary collapse
-
#encoding ⇒ Object
Returns the value of attribute encoding.
-
#spreadsheet ⇒ Object
Returns the value of attribute spreadsheet.
Instance Method Summary collapse
- #add_study_to_assets(assets, study) ⇒ Object
-
#completed_submissions ⇒ Object
This is used to present a list of successes.
- #extract_request_options(details) ⇒ Object
-
#find_template(template_name) ⇒ Object
Returns the SubmissionTemplate and checks that it is valid.
- #id ⇒ Object
-
#initialize(attrs = {}) ⇒ BulkSubmission
constructor
A new instance of BulkSubmission.
- #persisted? ⇒ Boolean
-
#prepare_order(details) ⇒ Object
Returns an order for the given details.
- #process ⇒ Object
- #process_file ⇒ Object
- #shared_options!(rows) ⇒ Object
-
#submission_structure ⇒ Object
Process CSV into a structure this creates an array containing a hash for each distinct “submission name” “submission name” => array of orders where each order is a hash of headers to values (grouped by “asset group name”).
- #translate(header) ⇒ Object
- #valid_header? ⇒ Boolean
Methods included from ManifestUtil
#filter_end_of_header, #is_end_of_header?
Methods included from Submission::AssetSubmissionFinder
#find_all_assets_by_name_including_samples!, #find_tubes_including_samples_for!, #find_wells_including_samples_for!, #is_plate?, #is_tube?
Constructor Details
#initialize(attrs = {}) ⇒ BulkSubmission
Returns a new instance of BulkSubmission.
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# File 'app/models/bulk_submission.rb', line 45 def initialize(attrs = {}) self.spreadsheet = attrs[:spreadsheet] self.encoding = attrs.fetch(:encoding, DEFAULT_ENCODING) end |
Instance Attribute Details
#encoding ⇒ Object
Returns the value of attribute encoding
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# File 'app/models/bulk_submission.rb', line 34 def encoding @encoding end |
#spreadsheet ⇒ Object
Returns the value of attribute spreadsheet
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# File 'app/models/bulk_submission.rb', line 34 def spreadsheet @spreadsheet end |
Instance Method Details
#add_study_to_assets(assets, study) ⇒ Object
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# File 'app/models/bulk_submission.rb', line 255 def add_study_to_assets(assets, study) assets.map(&:samples).flatten.uniq.each do |sample| sample.studies << study unless sample.studies.include?(study) end end |
#completed_submissions ⇒ Object
This is used to present a list of successes
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# File 'app/models/bulk_submission.rb', line 392 def completed_submissions [@submission_ids, @completed_submissions] end |
#extract_request_options(details) ⇒ Object
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# File 'app/models/bulk_submission.rb', line 261 def (details) { read_length: details['read length'], multiplier: {} }.tap do || ['library_type'] = details['library type'] if details['library type'].present? if details['fragment size from'].present? ['fragment_size_required_from'] = details['fragment size from'] end if details['fragment size to'].present? ['fragment_size_required_to'] = details['fragment size to'] end ['pcr_cycles'] = details['pcr cycles'] if details['pcr cycles'].present? if details['bait library name'].present? [:bait_library_name] = details['bait library name'] end [:bait_library_name] ||= details['bait library'] if details['bait library'].present? if details['pre-capture plex level'].present? ['pre_capture_plex_level'] = details['pre-capture plex level'] end if details['gigabases expected'].present? ['gigabases_expected'] = details['gigabases expected'] end ['primer_panel_name'] = details['primer panel'] if details['primer panel'].present? end end |
#find_template(template_name) ⇒ Object
Returns the SubmissionTemplate and checks that it is valid
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# File 'app/models/bulk_submission.rb', line 384 def find_template(template_name) template = SubmissionTemplate.find_by(name: template_name) or raise StandardError, "Cannot find template #{template_name}" raise(StandardError, "Template: '#{template_name}' is deprecated and no longer in use.") unless template.visible template end |
#id ⇒ Object
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# File 'app/models/bulk_submission.rb', line 43 def id; nil; end |
#persisted? ⇒ Boolean
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# File 'app/models/bulk_submission.rb', line 41 def persisted?; false; end |
#prepare_order(details) ⇒ Object
Returns an order for the given details
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# File 'app/models/bulk_submission.rb', line 289 def prepare_order(details) # rubocop:todo Metrics/CyclomaticComplexity # Retrieve common attributes study = Study.find_by_id_or_name!(details['study id'], details['study name']) project = Project.find_by_id_or_name!(details['project id'], details['project name']) user = User.find_by(login: details['user login']) or raise StandardError, "Cannot find user #{details['user login'].inspect}" # Extract the request options from the row details = (details) # Check the library type matches a value from the table if ['library_type'].present? # find is case insensitive but we want the correct case sensitive name for requests or we get issues downstream in NPG lt = LibraryType.find_by(name: ['library_type'])&.name or raise StandardError, "Cannot find library type #{['library_type'].inspect}" ['library_type'] = lt end # Set up the order attributes attributes = { study: study, project: project, user: user, comments: details['comments'], request_options: , pre_cap_group: details['pre-capture group'] } # Deal with the asset group: either it's one we should be loading, or one we should be creating. attributes[:asset_group] = study.asset_groups.find_by_id_or_name(details['asset group id'], details['asset group name']) attributes[:asset_group_name] = details['asset group name'] if attributes[:asset_group].nil? ## # We go ahead and find our assets regardless of whether we have an asset group. # While this takes longer, it helps to detect cases where an asset group name has been # reused. This is a common cause of submission problems. # Locate either the assets by name or ID, or find the plate and it's well if is_plate?(details) found_assets = find_wells_including_samples_for!(details) # We've probably got a tube elsif is_tube?(details) found_assets = find_tubes_including_samples_for!(details) else asset_ids, asset_names = details.fetch('asset ids', ''), details.fetch('asset names', '') found_assets = if attributes[:asset_group] && asset_ids.blank? && asset_names.blank? [] elsif asset_names.present? Array(find_all_assets_by_name_including_samples!(asset_names)).uniq elsif asset_ids.present? raise StandardError, 'Specifying assets by id is no longer possible. Please provide a name or barcode.' else raise StandardError, 'Please specify a barcode or name for each asset.' end assets_found, expecting = found_assets.map do |asset| "#{asset.name}(#{asset.id})" end, asset_ids.size + asset_names.size if assets_found.size < expecting raise StandardError, "Too few assets found for #{details['rows']}: #{assets_found.inspect}" end if assets_found.size > expecting raise StandardError, "Too many assets found for #{details['rows']}: #{assets_found.inspect}" end end if attributes[:asset_group].nil? attributes[:assets] = found_assets elsif found_assets.present? && found_assets != attributes[:asset_group].assets raise StandardError, "Asset Group '#{attributes[:asset_group].name}' contains different assets to those you specified. You may be reusing an asset group name" end add_study_to_assets(found_assets, study) # Create the order. Ensure that the number of lanes is correctly set. sub_template = find_template(details['template name']) number_of_lanes = details.fetch('number of lanes', 1).to_i sub_template.new_order(attributes).tap do |new_order| new_order.request_type_multiplier do |multiplexed_request_type_id| new_order.[:multiplier][multiplexed_request_type_id] = number_of_lanes end end rescue => e errors.add :spreadsheet, "There was a problem on row(s) #{details['rows']}: #{e.}" nil end |
#process ⇒ Object
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# File 'app/models/bulk_submission.rb', line 126 def process # Store the details of the successful submissions so the user can be presented with a summary @submission_ids = [] @completed_submissions = {} csv_content = spreadsheet.read @csv_rows = CSV.parse(csv_content.encode!('utf-8', encoding)) if spreadsheet_valid? submission_details = submission_structure raise ActiveRecord::RecordInvalid, self if errors.count > 0 # Within a single transaction process each of the rows of the CSV file as a separate submission. Any name # fields need to be mapped to IDs, and the 'assets' field needs to be split up and processed if present. ActiveRecord::Base.transaction do submission_details.each do |submissions| submissions.each do |submission_name, orders| user = User.find_by(login: orders.first['user login']) if user.nil? errors.add :spreadsheet, orders.first['user login'].nil? ? "No user specified for #{submission_name}" : "Cannot find user #{orders.first["user login"].inspect}" next end begin orders_processed = orders.map(&method(:prepare_order)).compact submission = Submission.create!(name: submission_name, user: user, orders: orders_processed, priority: max_priority(orders)) submission.built! # Collect successful submissions @submission_ids << submission.id @completed_submissions[submission.id] = "Submission #{submission.id} built (#{submission.orders.count} orders)" rescue Submission::ProjectValidation::Error => e errors.add :spreadsheet, "There was an issue with a project: #{e.}" end end end # If there are any errors then the transaction needs to be rolled back. raise ActiveRecord::Rollback if errors.present? end end end |
#process_file ⇒ Object
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# File 'app/models/bulk_submission.rb', line 52 def process_file # Slightly inelegant file-type checking # TODO (jr) Find a better way of verifying the CSV file? if spreadsheet.present? if spreadsheet.size == 0 errors.add(:spreadsheet, 'The supplied file was empty') else if spreadsheet.original_filename.end_with?('.csv') process else errors.add(:spreadsheet, 'The supplied file was not a CSV file') end end end rescue CSV::MalformedCSVError errors.add(:spreadsheet, 'The supplied file was not a valid CSV file (try opening it with MS Excel)') rescue Encoding::InvalidByteSequenceError errors.add(:encoding, "didn't match for the provided file.") end |
#shared_options!(rows) ⇒ Object
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# File 'app/models/bulk_submission.rb', line 242 def (rows) # Builds an array of the common fields. Raises and exception if the fields are inconsistent COMMON_FIELDS.map do |field| option = rows.map { |r| r[field] }.uniq if option.count > 1 provided_values = option.map { |o| "'#{o}'" }.to_sentence errors.add(:spreadsheet, "#{field} should be identical for all requests in asset group '#{rows.first['asset group name']}'. Given values were: #{provided_values}.") end [field, option.first] end end |
#submission_structure ⇒ Object
Process CSV into a structure
this creates an array containing a hash for each distinct "submission name"
"submission name" => array of orders
where each order is a hash of headers to values (grouped by "asset group name")
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# File 'app/models/bulk_submission.rb', line 216 def submission_structure Hash.new { |h, i| h[i] = Array.new }.tap do |submission| csv_data_rows.each_with_index do |row, index| next if row.all?(&:nil?) details = headers.each_with_index.filter_map do |header, pos| validate_entry(header, pos, row, index + start_row) end.to_h.merge('row' => index + start_row) submission[details['submission name']] << details end end.map do |submission_name, rows| order = rows.group_by do |details| details['asset group name'] end.map do |_group_name, rows| (rows).to_h.tap do |details| details['rows'] = rows.comma_separate_field_list_for_display('row') details['asset ids'] = rows.field_list('asset id', 'asset ids') details['asset names'] = rows.field_list('asset name', 'asset names') details['plate well'] = rows.field_list('plate well') details['barcode'] = rows.field_list('barcode') end.delete_if { |_, v| v.blank? } end { submission_name => order } end end |
#translate(header) ⇒ Object
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# File 'app/models/bulk_submission.rb', line 200 def translate(header) ALIAS_FIELDS[header] || header end |
#valid_header? ⇒ Boolean
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# File 'app/models/bulk_submission.rb', line 104 def valid_header? return false if headers.nil? return true if headers.include? 'submission name' errors.add :spreadsheet, "You submitted an incompatible spreadsheet. Please ensure your spreadsheet contains the 'submission name' column" false end |