scinote-web/app/models/repository.rb

class Repository < ActiveRecord::Base
  include SearchableModel

  belongs_to :team
  belongs_to :created_by, foreign_key: :created_by_id, class_name: 'User'
  has_many :repository_columns
  has_many :repository_rows
  has_many :repository_table_states,
           inverse_of: :repository, dependent: :destroy
  has_many :report_elements, inverse_of: :repository, dependent: :destroy

  auto_strip_attributes :name, nullify: false
  validates :name,
            presence: true,
            uniqueness: { scope: :team, case_sensitive: false },
            length: { maximum: Constants::NAME_MAX_LENGTH }
  validates :team, presence: true
  validates :created_by, presence: true

  def self.search(
    user,
    _include_archived,
    query = nil,
    page = 1,
    current_team = nil,
    options = {}
  )
    team_ids =
      if current_team
        current_team.id
      else
        Team.joins(:user_teams)
            .where('user_teams.user_id = ?', user.id)
            .distinct
            .pluck(:id)
      end

    row_ids = RepositoryRow
              .search(nil, query, Constants::SEARCH_NO_LIMIT, options)
              .select(:id)

    new_query = Repository
                .select('repositories.*, COUNT(repository_rows.id) AS counter')
                .joins(:team)
                .joins('LEFT OUTER JOIN repository_rows ON ' \
                       'repositories.id = repository_rows.repository_id')
                .where(team: team_ids)
                .where('repository_rows.id IN (?)', row_ids)
                .group('repositories.id')

    # 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

  def open_spreadsheet(file)
    filename = file.original_filename
    file_path = file.path

    if file.class == Paperclip::Attachment && file.is_stored_on_s3?
      fa = file.fetch
      file_path = fa.path
    end
    generate_file(filename, file_path)
  end

  def available_repository_fields
    fields = {}
    # First and foremost add record name
    fields['-1'] = I18n.t('repositories.default_column')
    # Add all other custom columns
    repository_columns.order(:created_at).each do |rc|
      fields[rc.id] = rc.name
    end
    fields
  end

  def copy(created_by, name)
    new_repo = nil

    begin
      Repository.transaction do
        # Clone the repository object
        new_repo = dup
        new_repo.created_by = created_by
        new_repo.name = name
        new_repo.save!

        # Clone columns (only if new_repo was saved)
        repository_columns.find_each do |col|
          new_col = col.dup
          new_col.repository = new_repo
          new_col.created_by = created_by
          new_col.save!
        end
      end
    rescue ActiveRecord::RecordInvalid
      return false
    end

    # If everything is okay, return new_repo
    new_repo
  end

  # Imports records
  def import_records(sheet, mappings, user)
    errors = false
    custom_fields = []
    name_index = -1
    total_nr = 0
    nr_of_added = 0

    mappings.each.with_index do |(_k, value), index|
      if value == '-1'
        # Fill blank space, so our indices stay the same
        custom_fields << nil
        name_index = index
      else
        cf = repository_columns.find_by_id(value)
        custom_fields << cf
      end
    end

    # Now we can iterate through record data and save stuff into db
    (2..sheet.last_row).each do |i|
      total_nr += 1
      cell_error = false
      record_row = RepositoryRow.new(name: sheet.row(i)[name_index],
                                 repository: self,
                                 created_by: user,
                                 last_modified_by: user)

      unless record_row.valid?
        errors = true
        next
      end
      sheet.row(i).each.with_index do |value, index|
        if custom_fields[index] && value
          rep_column = RepositoryTextValue.new(
            data: value,
            created_by: user,
            last_modified_by: user,
            repository_cell_attributes: {
              repository_row: record_row,
              repository_column: custom_fields[index]
            }
          )
          cell_error = true unless rep_column.save
        end
      end
      if cell_error
        errors = true
        record_row.destroy
      else
        nr_of_added += 1
        record_row.save
      end
    end

    if errors
      return { status: :error,
               nr_of_added: nr_of_added,
               total_nr: total_nr }
    end
    { status: :ok, nr_of_added: nr_of_added, total_nr: total_nr }
  end

  private

  def generate_file(filename, file_path)
    case File.extname(filename)
    when '.csv'
      Roo::CSV.new(file_path, extension: :csv)
    when '.tdv'
      Roo::CSV.new(file_path, nil, :ignore, csv_options: { col_sep: '\t' })
    when '.txt'
      # This assumption is based purely on biologist's habits
      Roo::CSV.new(file_path, csv_options: { col_sep: '\t' })
    when '.xls'
      Roo::Excel.new(file_path)
    when '.xlsx'
      Roo::Excelx.new(file_path)
    else
      raise TypeError
    end
  end
end