class Team < ApplicationRecord include SearchableModel # Not really MVC-compliant, but we just use it for logger # output in space_taken related functions include ActionView::Helpers::NumberHelper auto_strip_attributes :name, :description, nullify: false validates :name, length: { minimum: Constants::NAME_MIN_LENGTH, maximum: Constants::NAME_MAX_LENGTH } validates :description, length: { maximum: Constants::TEXT_MAX_LENGTH } validates :space_taken, presence: true belongs_to :created_by, foreign_key: 'created_by_id', class_name: 'User', optional: true belongs_to :last_modified_by, foreign_key: 'last_modified_by_id', class_name: 'User', optional: true has_many :user_teams, inverse_of: :team, dependent: :destroy has_many :users, through: :user_teams has_many :samples, inverse_of: :team has_many :samples_tables, inverse_of: :team, dependent: :destroy has_many :sample_groups, inverse_of: :team has_many :sample_types, inverse_of: :team has_many :projects, inverse_of: :team has_many :custom_fields, inverse_of: :team has_many :protocols, inverse_of: :team, dependent: :destroy has_many :protocol_keywords, inverse_of: :team, dependent: :destroy has_many :tiny_mce_assets, inverse_of: :team, dependent: :destroy has_many :repositories, dependent: :destroy def search_users(query = nil) a_query = "%#{query}%" users.where.not(confirmed_at: nil) .where('full_name ILIKE ? OR email ILIKE ?', a_query, a_query) end # Imports samples into db # -1 == sample_name, # -2 == sample_type, # -3 == sample_group # TODO: use constants def import_samples(sheet, mappings, user) errors = false nr_of_added = 0 total_nr = 0 header_skipped = false # First let's query for all custom_fields we're refering to custom_fields = [] sname_index = -1 stype_index = -1 sgroup_index = -1 mappings.each.with_index do |(_, v), i| if v == '-1' # Fill blank space, so our indices stay the same custom_fields << nil sname_index = i elsif v == '-2' custom_fields << nil stype_index = i elsif v == '-3' custom_fields << nil sgroup_index = i else cf = CustomField.find_by_id(v) # Even if doesn't exist we add nil value in order not to destroy our # indices custom_fields << cf end end rows = SpreadsheetParser.spreadsheet_enumerator(sheet) # Now we can iterate through sample data and save stuff into db rows.each do |row| # Skip empty rows next if row.empty? unless header_skipped header_skipped = true next end total_nr += 1 row = SpreadsheetParser.parse_row(row, sheet) sample = Sample.new(name: row[sname_index], team: self, user: user) sample.transaction do unless sample.valid? errors = true raise ActiveRecord::Rollback end row.each.with_index do |value, index| next unless value.present? if index == stype_index stype = SampleType.where(team: self) .where('name ILIKE ?', value.strip) .take unless stype stype = SampleType.new(name: value.strip, team: self) unless stype.save errors = true raise ActiveRecord::Rollback end end sample.sample_type = stype elsif index == sgroup_index sgroup = SampleGroup.where(team: self) .where('name ILIKE ?', value.strip) .take unless sgroup sgroup = SampleGroup.new(name: value.strip, team: self) unless sgroup.save errors = true raise ActiveRecord::Rollback end end sample.sample_group = sgroup elsif value && custom_fields[index] # we're working with CustomField scf = SampleCustomField.new( sample: sample, custom_field: custom_fields[index], value: value ) unless scf.valid? errors = true raise ActiveRecord::Rollback end sample.sample_custom_fields << scf end end if Sample.import([sample], recursive: true, validate: false).failed_instances.any? errors = true raise ActiveRecord::Rollback end nr_of_added += 1 end end if errors return { status: :error, nr_of_added: nr_of_added, total_nr: total_nr } else return { status: :ok, nr_of_added: nr_of_added, total_nr: total_nr } end end def to_csv(samples, headers) require "csv" # Parse headers (magic numbers should be refactored - see # sample-datatable.js) header_names = [] headers.each do |header| if header == "-1" header_names << I18n.t("samples.table.sample_name") elsif header == "-2" header_names << I18n.t("samples.table.sample_type") elsif header == "-3" header_names << I18n.t("samples.table.sample_group") elsif header == "-4" header_names << I18n.t("samples.table.added_by") elsif header == "-5" header_names << I18n.t("samples.table.added_on") else cf = CustomField.find_by_id(header) if cf header_names << cf.name else header_names << nil end end end CSV.generate do |csv| csv << header_names samples.each do |sample| sample_row = [] headers.each do |header| if header == "-1" sample_row << sample.name elsif header == "-2" sample_row << (sample.sample_type.nil? ? I18n.t("samples.table.no_type") : sample.sample_type.name) elsif header == "-3" sample_row << (sample.sample_group.nil? ? I18n.t("samples.table.no_group") : sample.sample_group.name) elsif header == "-4" sample_row << sample.user.full_name elsif header == "-5" sample_row << I18n.l(sample.created_at, format: :full) else scf = SampleCustomField.where( custom_field_id: header, sample_id: sample.id ).take if scf sample_row << scf.value else sample_row << nil end end end csv << sample_row end end end # Get all header fields for samples (used in importing for mappings - dropdowns) def get_available_sample_fields fields = {}; # First and foremost add sample name fields["-1"] = I18n.t("samples.table.sample_name") fields["-2"] = I18n.t("samples.table.sample_type") fields["-3"] = I18n.t("samples.table.sample_group") # Add all other custom fields CustomField.where(team_id: id).order(:created_at).each do |cf| fields[cf.id] = cf.name end fields end # (re)calculate the space taken by this team def calculate_space_taken st = 0 projects.includes( experiments: { my_modules: { protocols: { steps: :assets }, results: { result_asset: :asset } } } ).find_each do |project| project.project_my_modules.find_each do |my_module| my_module.protocol.steps.find_each do |step| step.assets.find_each { |asset| st += asset.estimated_size } step.tiny_mce_assets.find_each { |tiny| st += tiny.estimated_size } end my_module.results.find_each do |result| st += result.asset.estimated_size if result.is_asset if result.is_text tiny_assets = TinyMceAsset.where(result_text: result.result_text) tiny_assets.find_each { |tiny| st += tiny.estimated_size } end end end end # project.experiments.each |experiment| self.space_taken = [st, Constants::MINIMAL_TEAM_SPACE_TAKEN].max Rails::logger.info "Team #{self.id}: " + "space (re)calculated to: " + "#{self.space_taken}B (#{number_to_human_size(self.space_taken)})" end # Take specified amount of bytes def take_space(space) orig_space = self.space_taken self.space_taken += space Rails::logger.info "Team #{self.id}: " + "space taken: " + "#{orig_space}B + #{space}B = " + "#{self.space_taken}B (#{number_to_human_size(self.space_taken)})" end # Release specified amount of bytes def release_space(space) orig_space = self.space_taken self.space_taken = [space_taken - space, Constants::MINIMAL_TEAM_SPACE_TAKEN].max Rails::logger.info "Team #{self.id}: " + "space released: " + "#{orig_space}B - #{space}B = " + "#{self.space_taken}B (#{number_to_human_size(self.space_taken)})" end def protocol_keywords_list ProtocolKeyword.where(team: self).pluck(:name) end end