scinote-web/app/models/my_module.rb

class MyModule < ActiveRecord::Base
  include ArchivableModel, SearchableModel

  before_create :create_blank_protocol

  auto_strip_attributes :name, :description, nullify: false
  validates :name,
            length: { minimum: NAME_MIN_LENGTH, maximum: NAME_MAX_LENGTH }
  validates :description, length: { maximum: 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'
  belongs_to :last_modified_by, foreign_key: 'last_modified_by_id', class_name: 'User'
  belongs_to :archived_by, foreign_key: 'archived_by_id', class_name: 'User'
  belongs_to :restored_by, foreign_key: 'restored_by_id', class_name: 'User'
  belongs_to :experiment, inverse_of: :my_modules
  belongs_to :my_module_group, inverse_of: :my_modules
  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 :my_module_comments, inverse_of: :my_module, :dependent => :destroy
  has_many :comments, through: :my_module_comments
  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 :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)
    exp_ids =
      Experiment
      .search(user, include_archived, nil, SHOW_ALL_RESULTS)
      .select("id")

    if query
      a_query = query.strip
      .gsub("_","\\_")
      .gsub("%","\\%")
      .split(/\s+/)
      .map {|t|  "%" + t + "%" }
    else
      a_query = query
    end

    if include_archived
      new_query = MyModule
        .distinct
        .where("my_modules.experiment_id IN (?)", exp_ids)
        .where_attributes_like([:name, :description], a_query)
    else
      new_query = MyModule
        .distinct
        .where("my_modules.experiment_id IN (?)", exp_ids)
        .where("my_modules.archived = ?", false)
        .where_attributes_like([:name, :description], a_query)
    end

    # Show all results if needed
    if page == SHOW_ALL_RESULTS
      new_query
    else
      new_query
        .limit(SEARCH_LIMIT)
        .offset((page - 1) * 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(organization_id: experiment.project.organization).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 = 20)
    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 = 20)
    last_id = 9999999999999 if last_id <= 1
    comments = Comment.joins(:my_module_comment)
                      .where(my_module_comments: { my_module_id: id })
                      .where('comments.id <  ?', last_id)
                      .order(created_at: :desc)
                      .limit(per_page)
    comments.reverse
  end

  def last_activities(last_id = 1, count = 20)
    last_id = 9999999999999 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 = 20)
    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

  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

  # Writes to user log.
  def log(message)
    final = "[%s] %s" % [name, message]
    experiment.project.log(final)
  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

  private

  def create_blank_protocol
    protocols << Protocol.new_blank_for_module(self)
  end
end