scinote-web/app/datatables/sample_datatable.rb

require 'active_record'

class SampleDatatable < CustomDatatable
  include ActionView::Helpers::TextHelper
  include SamplesHelper
  include InputSanitizeHelper
  include Rails.application.routes.url_helpers
  include ActionView::Helpers::UrlHelper
  include ApplicationHelper
  include ActiveRecord::Sanitization::ClassMethods

  ASSIGNED_SORT_COL = 'assigned'

  SAMPLES_TABLE_DEFAULT_STATE = {
    'time' => 0,
    'start' => 0,
    'length' => 10,
    'order' => [[2, 'desc']],
    'search' => { 'search' => '',
                  'smart' => true,
                  'regex' => false,
                  'caseInsensitive' => true },
    'columns' => [],
    'assigned' => 'all',
    'ColReorder' => [*0..6]
  }
  7.times do
    SAMPLES_TABLE_DEFAULT_STATE['columns'] << {
      'visible' => true,
      'search' => { 'search' => '',
                    'smart' => true,
                    'regex' => false,
                    'caseInsensitive' => true }
    }
  end
  SAMPLES_TABLE_DEFAULT_STATE.freeze

  def initialize(view,
                 team,
                 project = nil,
                 my_module = nil,
                 experiment = nil,
                 user = nil)
    super(view)
    @team = team
    @project = project
    @my_module = my_module
    @experiment = experiment
    @user = user
  end

  # Define sortable columns, so 1st column will be sorted
  # by attribute in sortable_columns[0]
  def sortable_columns
    sort_array = [
      ASSIGNED_SORT_COL,
      'Sample.name',
      'SampleType.name',
      'SampleGroup.name',
      'Sample.created_at',
      'User.full_name'
    ]

    sort_array.push(*custom_fields_sort_by)

    @sortable_columns = sort_array
  end

  # Define attributes on which we perform search
  def searchable_columns
    search_array = [
      'Sample.name',
      'SampleType.name',
      'SampleGroup.name',
      'Sample.created_at',
      'User.full_name'
    ]

    search_array.push(*custom_fields_sort_by)
    @searchable_columns ||= filter_search_array search_array
  end

  private

  # filters the search array by checking if the the column is visible
  def filter_search_array(input_array)
    param_index = 2
    filtered_array = []
    input_array.each do |col|
      next if dt_params.to_a[param_index].nil?
      params_col =
        columns_params.to_a.find { |v| v[1]['data'] == param_index.to_s }
      filtered_array.push(col) unless params_col[1]['searchable'] == 'false'
      param_index += 1
    end
    filtered_array
  end

  # Get array of columns to sort by (for custom fields)
  def custom_fields_sort_by
    num_cf = CustomField.where(team_id: @team).count
    array = []

    num_cf.times do
      array << 'SampleCustomField.value'
    end
    array
  end

  # Returns json of current samples (already paginated)
  def data
    records.map do |record|
      sample = {
        'DT_RowId': record.id,
        '1': assigned_cell(record),
        '2': escape_input(record.name),
        '3': if record.sample_type.nil?
               I18n.t('samples.table.no_type')
             else
               escape_input(record.sample_type.name)
             end,
        '4': sample_group_cell(record),
        '5': I18n.l(record.created_at, format: :full),
        '6': escape_input(record.user.full_name),
        'sampleInfoUrl':
          Rails.application.routes.url_helpers.sample_path(record.id),
        'sampleEditUrl':
          Rails.application.routes.url_helpers.edit_sample_path(record.id),
        'sampleUpdateUrl':
          Rails.application.routes.url_helpers.sample_path(record.id)
      }

      # Add custom attributes
      record.sample_custom_fields.each do |scf|
        sample[@cf_mappings[scf.custom_field_id]] =
          custom_auto_link(scf.value, simple_format: true, team: @team)
      end
      sample
    end
  end

  def assigned_cell(record)
    if @assigned_samples.include?(record)
      "<span class='circle'>&nbsp;</span>"
    else
      "<span class='circle disabled'>&nbsp;</span>"
    end
  end

  def sample_group_cell(record)
    if record.sample_group.nil?
      "<span class='fas fa-asterisk'></span> " \
        "#{I18n.t('samples.table.no_group')}"
    else
      "<span class='fas fa-asterisk' " \
        "style='color: #{escape_input(record.sample_group.color)}'></span> " \
        "#{escape_input(record.sample_group.name)}"
    end
  end

  # Query database for records (this will be later paginated and filtered)
  # after that "data" function will return json
  def get_raw_records
    samples = Sample
              .includes(
                :sample_type,
                :sample_group,
                :user,
                :sample_custom_fields
              )
              .references(
                :sample_type,
                :sample_group,
                :user,
                :sample_custom_fields
              )
              .where(
                team: @team
              )

    if @my_module
      @assigned_samples = @my_module.samples

      samples = samples.joins("LEFT OUTER JOIN sample_my_modules ON
                              (samples.id = sample_my_modules.sample_id AND
                              (sample_my_modules.my_module_id =
                              #{@my_module.id} OR
                              sample_my_modules.id IS NULL))")
                       .references(:sample_my_modules)
      if dt_params[:assigned] == 'assigned'
        samples = samples.where('"sample_my_modules"."id" > 0')
      end
    elsif @project
      @assigned_samples = @project.assigned_samples
      ids = @project.my_modules_ids

      if ids.blank?
        samples = samples.joins('LEFT OUTER JOIN sample_my_modules ON
                                (samples.id = sample_my_modules.sample_id AND
                                sample_my_modules.id IS NULL)')
                         .references(:sample_my_modules)
      else
        samples = samples.joins("LEFT OUTER JOIN sample_my_modules ON
                                (samples.id = sample_my_modules.sample_id AND
                                (sample_my_modules.my_module_id IN (#{ids}) OR
                                sample_my_modules.id IS NULL))")
                         .references(:sample_my_modules)
      end
      if dt_params[:assigned] == 'assigned'
        samples = samples.joins('LEFT OUTER JOIN "my_modules" ON
                                "my_modules"."id" =
                                "sample_my_modules"."my_module_id"')
                         .joins('LEFT OUTER JOIN "experiments" ON
                                "experiments"."id" =
                                "my_modules"."experiment_id"')
                         .where('"experiments"."project_id" = ?', @project.id)
                         .where('"my_modules"."nr_of_assigned_samples" > 0')
      end
    elsif @experiment
      @assigned_samples = @experiment.assigned_samples
      ids = @experiment.my_modules.select(:id)

      samples = samples.joins("LEFT OUTER JOIN sample_my_modules ON
                          (samples.id = sample_my_modules.sample_id AND
                          (sample_my_modules.my_module_id IN (#{ids.to_sql}) OR
                          sample_my_modules.id IS NULL))")
                       .references(:sample_my_modules)
      if dt_params[:assigned] == 'assigned'
        samples = samples.joins('LEFT OUTER JOIN "my_modules" ON
                                "my_modules"."id" =
                                "sample_my_modules"."my_module_id"')
                         .where('"my_modules"."experiment_id" = ?',
                                @experiment.id)
                         .where('"my_modules"."nr_of_assigned_samples" > 0')
      end
    end

    # Make mappings of custom fields, so we have same id for every column
    i = 7
    @cf_mappings = {}
    all_custom_fields.each do |cf|
      @cf_mappings[cf.id] = i.to_s
      i += 1
    end

    samples
  end

  # Override default behaviour
  # Don't filter and paginate records when sorting by custom column - everything
  # is done in sort_records method - you might ask why, well if you want the
  # number of samples/all samples it's dependant upon sort_record query
  def fetch_records
    records = get_raw_records
    records = sort_records(records) if order_params.present?
    escape_special_chars
    unless sorting_by_custom_column
      records = filter_records(records) if dt_params[:search].present?
      records = paginate_records(records) unless dt_params[:length].present? &&
                                                 dt_params[:length] == '-1'
    end
    records
  end

  # Override default sort method if needed
  def sort_records(records)
    if sort_column(order_params) == ASSIGNED_SORT_COL
      # If "assigned" column is sorted
      if @my_module
        # Depending on the sort, order nulls first or
        # nulls last on sample_my_modules association
        records.order(
          "sample_my_modules.id NULLS #{sort_null_direction(order_params)}"
        )
      elsif @experiment
        # A very elegant solution to sort assigned samples at a experiment level
        # grabs the ids of samples which has a modules that belongs
        # to this project
        assigned =
          Sample
          .joins('LEFT OUTER JOIN "sample_my_modules" ' \
                 'ON "sample_my_modules"."sample_id" = "samples"."id"')
          .joins('LEFT OUTER JOIN "my_modules" ' \
                 'ON "my_modules"."id" = "sample_my_modules"."my_module_id"')
          .where('"my_modules"."experiment_id" = ?', @experiment.id)
          .where('"my_modules"."nr_of_assigned_samples" > 0')
          .select('"samples"."id"')
          .distinct

        # grabs the ids that are not the previous one but are still
        # of the same team
        unassigned = Sample.where('"samples"."team_id" = ?', @team.id)
                           .where('"samples"."id" NOT IN (?)', assigned)
                           .select('"samples"."id"')
                           .distinct

        # check the input param and merge the two arrays of ids
        if order_params['dir'] == 'asc'
          ids = assigned + unassigned
        elsif order_params['dir'] == 'desc'
          ids = unassigned + assigned
        end
        ids = ids.collect(&:id)

        # order the records by input ids
        order_by_index = ActiveRecord::Base.__send__(
          :sanitize_sql_array,
          ["position((',' || samples.id || ',') in ?)", ids.join(',') + ',']
        )

        records.where(id: ids).order(order_by_index)
      elsif @project
        # A very elegant solution to sort assigned samples at a project level
        # grabs the ids of samples which has a modules
        # that belongs to this project
        assigned =
          Sample
          .joins('LEFT OUTER JOIN "sample_my_modules" ' \
                 'ON "sample_my_modules"."sample_id" = "samples"."id"')
          .joins('LEFT OUTER JOIN "my_modules" ' \
                 'ON "my_modules"."id" = "sample_my_modules"."my_module_id"')
          .joins('LEFT OUTER JOIN "experiments" ' \
                 'ON "experiments"."id" = "my_modules"."experiment_id"')
          .where('"experiments"."project_id" = ?', @project.id)
          .where('"my_modules"."nr_of_assigned_samples" > 0')
          .select('"samples"."id"')
          .distinct

        # grabs the ids that are not the previous ones
        # but are still of the same team
        unassigned = Sample
                     .where('"samples"."team_id" = ?', @team.id)
                     .where('"samples"."id" NOT IN (?)', assigned)
                     .select('"samples"."id"')
                     .distinct

        # check the input param and merge the two arrays of ids
        if order_params['dir'] == 'asc'
          ids = assigned + unassigned
        elsif order_params['dir'] == 'desc'
          ids = unassigned + assigned
        end
        ids = ids.collect(&:id)

        # order the records by input ids
        order_by_index = ActiveRecord::Base.__send__(
          :sanitize_sql_array,
          ["position((',' || samples.id || ',') in ?)", ids.join(',') + ',']
        )
        records.where(id: ids).order(order_by_index)
      end
    elsif sorting_by_custom_column
      # Check if have to filter samples first
      if dt_params[:search].present? && dt_params[:search][:value].present?
        # Couldn't force ActiveRecord to yield the same query as below because
        # Rails apparently forgets to join stuff in subqueries -
        # #justrailsthings
        conditions = build_conditions_for(dt_params[:search][:value])
        filter_query = %(SELECT "samples"."id" FROM "samples"
          LEFT OUTER JOIN "sample_custom_fields" ON
          "sample_custom_fields"."sample_id" = "samples"."id"
          LEFT OUTER JOIN "sample_types" ON
          "sample_types"."id" = "samples"."sample_type_id"
          LEFT OUTER JOIN "sample_groups"
          ON "sample_groups"."id" = "samples"."sample_group_id"
          LEFT OUTER JOIN "users" ON "users"."id" = "samples"."user_id"
          WHERE "samples"."team_id" = #{@team.id} AND #{conditions.to_sql})

        records = records.where("samples.id IN (#{filter_query})")
      end

      ci = sortable_displayed_columns[
        order_params[:column].to_i - 1
      ]
      cf_id = @cf_mappings.key((ci.to_i + 1).to_s)
      dir = sort_direction(order_params)

      # Because samples can have multiple sample custom fields, we first group
      # them by samples.id and inside that group we sort them by cf_id. Because
      # we sort them ASC, sorted columns will be on top. Distinct then only
      # takes the first row and cuts the rest of every group and voila we have
      # 1 row for every sample, which are not sorted yet ...
      records =
        records
        .select('DISTINCT ON (samples.id) *')
        .order("samples.id, CASE WHEN sample_custom_fields.custom_field_id = " \
               "#{cf_id} THEN 1 ELSE 2 END ASC")

      # ... this little gem (pun intended) then takes the records query,
      # sorts it again and paginates it.
      # sq.t0_* are determined empirically and are crucial -
      # imagine A -> B -> C transitive relation but where A and C are the
      # same. Useless right? But not when you acknowledge that find_by_sql
      # method does some funky stuff when your query spans multiple queries -
      # Sample object might have id from SampleType, name from
      # User ... chaos ensues basically. If something changes in db this might
      # change.
      formated_date = I18n.t('time.formats.datatables_date')
                          .gsub!(/^\"|\"?$/, '')
      Sample.find_by_sql(
        "SELECT sq.t0_r0 as id, sq.t0_r1 as name, " \
        "to_char( sq.t0_r4, '#{formated_date}' ) as created_at, sq.t0_r5, " \
        "sq.t0_r6 as sample_group_id ,sq.t0_r7 as sample_type_id, sq.t0_r2 " \
        "as user_id, sq.custom_field_id FROM (#{records.to_sql}) " \
        "as sq ORDER BY CASE WHEN sq.custom_field_id = #{cf_id} THEN 1 " \
        "ELSE 2 END #{dir}, sq.value #{dir} LIMIT #{per_page} OFFSET #{offset}"
      )
    else
      super(records)
    end
  end

  # A hack that overrides the new_search_contition method default behavior
  # of the ajax-datatables-rails gem now the method checks
  # if the column is the created_at and generate a custom SQL to parse
  # it back to the caller method
  def new_search_condition(column, value)
    model, column = column.split('.')
    model = model.constantize
    formated_date = I18n.t('time.formats.datatables_date')
                        .gsub!(/^\"|\"?$/, '')
    if model == SampleCustomField
      # Find visible (searchable) custom field IDs, and only perform filter
      # on those custom fields
      searchable_cfs = columns_params.select do |_, v|
        v['searchable'] == 'true' && @cf_mappings.values.include?(v['data'])
      end
      cfmi = @cf_mappings.invert
      cf_ids = searchable_cfs.map { |_, v| cfmi[v['data']] }

      # Do an ILIKE on 'value', as well as make sure to only include
      # custom fields that have 'custom_field_id' among visible custom fields
      casted_column = ::Arel::Nodes::NamedFunction.new(
        'CAST',
        [model.arel_table[column.to_sym].as(typecast)]
      )
      casted_column = casted_column.matches("%#{value}%")
      casted_column = casted_column.and(
        model.arel_table['custom_field_id'].in(cf_ids)
      )
      casted_column
    elsif column == 'created_at'
      casted_column = ::Arel::Nodes::NamedFunction.new(
        'CAST',
        [Arel.sql(
          "to_char( samples.created_at, '#{formated_date}' ) AS VARCHAR"
        )]
      )
      casted_column.matches("%#{sanitize_sql_like(value)}%")
    else
      casted_column = ::Arel::Nodes::NamedFunction.new(
        'CAST',
        [model.arel_table[column.to_sym].as(typecast)]
      )
      casted_column.matches("%#{sanitize_sql_like(value)}%")
    end
  end

  def sort_null_direction(item)
    val = sort_direction(item)
    val == 'ASC' ? 'LAST' : 'FIRST'
  end

  def inverse_sort_direction(item)
    val = sort_direction(item)
    val == 'ASC' ? 'DESC' : 'ASC'
  end

  def sorting_by_custom_column
    sort_column(order_params) == 'sample_custom_fields.value'
  end

  # Escapes special characters in search query
  def escape_special_chars
    if dt_params[:search].present?
      dt_params[:search][:value] =
        ActiveRecord::Base.__send__(:sanitize_sql_like,
                                    dt_params[:search][:value])
    end
  end

  def new_sort_column(item)
    coli = item[:column].to_i - 1
    model, column = sortable_columns[sortable_displayed_columns[coli].to_i]
                    .split('.')

    return model if model == ASSIGNED_SORT_COL
    [model.constantize.table_name, column].join('.')
  end

  def generate_sortable_displayed_columns
    sort_order = SamplesTable.find_status(@user, @team)['ColReorder']

    sort_order.shift
    sort_order.map! { |i| (i.to_i - 1).to_s }

    @sortable_displayed_columns = sort_order
  end
end