class MyModule < ApplicationRecord include ArchivableModel, SearchableModel enum state: Extends::TASKS_STATES before_create :create_blank_protocol 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 :x, :y, :workflow_order, presence: true validates :experiment, presence: true validates :my_module_group, presence: true, if: "!my_module_group_id.nil?" 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 belongs_to :archived_by, foreign_key: 'archived_by_id', class_name: 'User', optional: true belongs_to :restored_by, foreign_key: 'restored_by_id', class_name: 'User', optional: true belongs_to :experiment, inverse_of: :my_modules, optional: true belongs_to :my_module_group, inverse_of: :my_modules, optional: true has_many :results, inverse_of: :my_module, dependent: :destroy has_many :my_module_tags, inverse_of: :my_module, dependent: :destroy has_many :tags, through: :my_module_tags has_many :task_comments, foreign_key: :associated_id, dependent: :destroy has_many :inputs, class_name: 'Connection', foreign_key: 'input_id', inverse_of: :to, dependent: :destroy has_many :outputs, class_name: 'Connection', foreign_key: 'output_id', inverse_of: :from, dependent: :destroy has_many :my_modules, through: :outputs, source: :to has_many :my_module_antecessors, through: :inputs, source: :from, class_name: 'MyModule' has_many :sample_my_modules, inverse_of: :my_module, dependent: :destroy has_many :samples, through: :sample_my_modules has_many :my_module_repository_rows, inverse_of: :my_module, dependent: :destroy has_many :repository_rows, through: :my_module_repository_rows has_many :user_my_modules, inverse_of: :my_module, dependent: :destroy has_many :users, through: :user_my_modules has_many :activities, inverse_of: :my_module has_many :report_elements, inverse_of: :my_module, dependent: :destroy has_many :protocols, inverse_of: :my_module, dependent: :destroy scope :is_archived, ->(is_archived) { where('archived = ?', is_archived) } # A module takes this much space in canvas (x, y) in database WIDTH = 30 HEIGHT = 14 def self.search( user, include_archived, query = nil, page = 1, current_team = nil, options = {} ) exp_ids = Experiment .search(user, include_archived, nil, Constants::SEARCH_NO_LIMIT) .pluck(:id) if current_team experiments_ids = Experiment .search(user, include_archived, nil, 1, current_team) .select('id') new_query = MyModule .distinct .where('my_modules.experiment_id IN (?)', experiments_ids) .where_attributes_like([:name, :description], query, options) if include_archived return new_query else return new_query.where('my_modules.archived = ?', false) end elsif include_archived new_query = MyModule .distinct .where('my_modules.experiment_id IN (?)', exp_ids) .where_attributes_like([:name, :description], query, options) else new_query = MyModule .distinct .where('my_modules.experiment_id IN (?)', exp_ids) .where('my_modules.archived = ?', false) .where_attributes_like([:name, :description], query, options) end # Show all results if needed if page == Constants::SEARCH_NO_LIMIT new_query else new_query .limit(Constants::SEARCH_LIMIT) .offset((page - 1) * Constants::SEARCH_LIMIT) end end # Removes assigned samples from module and connections with other # modules. def archive (current_user) self.x = 0 self.y = 0 # Remove association with module group. self.my_module_group = nil MyModule.transaction do archived = super # Unassociate all samples from module. archived = SampleMyModule.destroy_all(:my_module => self) if archived # Remove all connection between modules. archived = Connection.delete_all(:input_id => id) if archived archived = Connection.delete_all(:output_id => id) if archived unless archived raise ActiveRecord::Rollback end end archived end # Similar as super restore, but also calculate new module position def restore(current_user) restored = false # Calculate new module position new_pos = get_new_position self.x = new_pos[:x] self.y = new_pos[:y] MyModule.transaction do restored = super unless restored raise ActiveRecord::Rollback end end experiment.delay.generate_workflow_img restored end def unassigned_users User.find_by_sql( "SELECT DISTINCT users.id, users.full_name FROM users " + "INNER JOIN user_projects ON users.id = user_projects.user_id " + "INNER JOIN experiments ON experiments.project_id = user_projects.project_id " + "WHERE experiments.id = #{experiment_id.to_s}" + " AND users.id NOT IN " + "(SELECT DISTINCT user_id FROM user_my_modules WHERE user_my_modules.my_module_id = #{id.to_s})" ) end def unassigned_samples Sample.where(team_id: experiment.project.team).where.not(id: samples) end def unassigned_tags Tag.find_by_sql( "SELECT DISTINCT tags.id, tags.name, tags.color FROM tags " + "INNER JOIN experiments ON experiments.project_id = tags.project_id " + "WHERE experiments.id = #{experiment_id.to_s} AND tags.id NOT IN " + "(SELECT DISTINCT tag_id FROM my_module_tags WHERE my_module_tags.my_module_id = #{id.to_s})" ) end def last_activities(count = Constants::ACTIVITY_AND_NOTIF_SEARCH_LIMIT) Activity.where(my_module_id: id).order(:created_at).last(count) end # Get module comments ordered by created_at time. Results are paginated # using last comment id and per_page parameters. def last_comments(last_id = 1, per_page = Constants::COMMENTS_SEARCH_LIMIT) last_id = Constants::INFINITY if last_id <= 1 comments = TaskComment.joins(:my_module) .where(my_modules: { id: id }) .where('comments.id < ?', last_id) .order(created_at: :desc) .limit(per_page) comments.reverse end def last_activities(last_id = 1, count = Constants::ACTIVITY_AND_NOTIF_SEARCH_LIMIT) last_id = Constants::INFINITY if last_id <= 1 Activity.joins(:my_module) .where(my_module_id: id) .where('activities.id < ?', last_id) .order(created_at: :desc) .limit(count) .uniq end def protocol # Temporary function (until we fully support # multiple protocols per module) protocols.count > 0 ? protocols.first : nil end def first_n_samples(count = Constants::SEARCH_LIMIT) samples.order(name: :asc).limit(count) end def number_of_samples samples.count end def is_overdue?(datetime = DateTime.current) due_date.present? and datetime.utc > due_date.utc end def overdue_for_days(datetime = DateTime.current) if due_date.blank? or due_date.utc > datetime.utc return 0 else return ((datetime.utc.to_i - due_date.utc.to_i) / (60*60*24).to_f).ceil end end def is_one_day_prior?(datetime = DateTime.current) is_due_in?(datetime, 1.day) end def is_due_in?(datetime, diff) due_date.present? and datetime.utc < due_date.utc and datetime.utc > (due_date.utc - diff) end def space_taken st = 0 protocol.steps.find_each do |step| st += step.space_taken end results .includes(:result_asset) .find_each do |result| st += result.space_taken end st end def archived_results results .select('results.*') .select('ra.id AS result_asset_id') .select('rt.id AS result_table_id') .select('rx.id AS result_text_id') .joins('LEFT JOIN result_assets AS ra ON ra.result_id = results.id') .joins('LEFT JOIN result_tables AS rt ON rt.result_id = results.id') .joins('LEFT JOIN result_texts AS rx ON rx.result_id = results.id') .where(:archived => true) end # Treat this module as root, get all modules of that subtree def get_downstream_modules final = [] modules = [self] while !modules.empty? my_module = modules.shift if !final.include?(my_module) final << my_module end modules.push(*my_module.my_modules.flatten) end final end # Treat this module as inversed root, get all modules of that inversed subtree def get_upstream_modules final = [] modules = [self] while !modules.empty? my_module = modules.shift if !final.include?(my_module) final << my_module end modules.push(*my_module.my_module_antecessors.flatten) end final end # Generate the samples belonging to this module # in JSON form, suitable for display in handsontable.js def samples_json_hot(order) data = [] samples.order(created_at: order).each do |sample| sample_json = [] sample_json << sample.name if sample.sample_type.present? sample_json << sample.sample_type.name else sample_json << I18n.t("samples.table.no_type") end if sample.sample_group.present? sample_json << sample.sample_group.name else sample_json << I18n.t("samples.table.no_group") end sample_json << I18n.l(sample.created_at, format: :full) sample_json << sample.user.full_name data << sample_json end # Prepare column headers headers = [ I18n.t("samples.table.sample_name"), I18n.t("samples.table.sample_type"), I18n.t("samples.table.sample_group"), I18n.t("samples.table.added_on"), I18n.t("samples.table.added_by") ] { data: data, headers: headers } end # Generate the repository rows belonging to this module # in JSON form, suitable for display in handsontable.js def repository_json_hot(repository_id, order) data = [] repository_rows .where(repository_id: repository_id) .order(created_at: order).find_each do |row| row_json = [] row_json << row.name row_json << I18n.l(row.created_at, format: :full) row_json << row.created_by.full_name data << row_json end # Prepare column headers headers = [ I18n.t('repositories.table.row_name'), I18n.t('repositories.table.added_on'), I18n.t('repositories.table.added_by') ] { data: data, headers: headers } end def deep_clone(current_user) deep_clone_to_experiment(current_user, experiment) end def deep_clone_to_experiment(current_user, experiment) # Copy the module clone = MyModule.new( name: self.name, experiment: experiment, description: self.description, x: self.x, y: self.y) clone.save # Remove the automatically generated protocol, # & clone the protocol instead clone.protocol.destroy clone.reload # Update the cloned protocol if neccesary clone.protocols << self.protocol.deep_clone_my_module(self, current_user) clone.reload # fixes linked protocols clone.protocols.each do |protocol| next unless protocol.linked? protocol.updated_at = protocol.parent_updated_at protocol.save end return clone end # Find an empty position for the restored module. It's # basically a first empty row with empty space inside x=[0, 32). def get_new_position return { x: 0, y: 0 } if experiment.blank? # Get all modules position that overlap with first column, [0, WIDTH) and # sort them by y coordinate. positions = experiment.active_modules.collect { |m| [m.x, m.y] } .select { |x, _| x >= 0 && x < WIDTH } .sort_by { |_, y| y } return { x: 0, y: 0 } if positions.empty? || positions.first[1] >= HEIGHT # It looks we'll have to find a gap between the modules if it exists (at # least 2*HEIGHT wide ind = positions.each_cons(2).map { |f, s| s[1] - f[1] } .index { |y| y >= 2 * HEIGHT } return { x: 0, y: positions[ind][1] + HEIGHT } if ind # We lucked out, no gaps, therefore we need to add it after the last element { x: 0, y: positions.last[1] + HEIGHT } end def completed? state == 'completed' end # Check if my_module is ready to become completed def check_completness_status if protocol && protocol.steps.count > 0 completed = true protocol.steps.find_each do |step| completed = false unless step.completed end return true if completed end false end def complete self.state = 'completed' self.completed_on = DateTime.now end def uncomplete self.state = 'uncompleted' self.completed_on = nil end private def create_blank_protocol protocols << Protocol.new_blank_for_module(self) end end