SysMO-DB/seek

require 'grouped_pagination'


class Sample < ActiveRecord::Base
  include Subscribable

  acts_as_scalable if Seek::Config.is_virtualliver
  include Seek::Rdf::RdfGeneration
  include BackgroundReindexing

  acts_as_authorized
  acts_as_favouritable
  acts_as_uniquely_identifiable

  grouped_pagination

  attr_accessor :parent_name
  attr_accessor :from_biosamples

  belongs_to :specimen
  belongs_to :age_at_sampling_unit, :class_name => 'Unit', :foreign_key => "age_at_sampling_unit_id"
  belongs_to :institution

  has_and_belongs_to_many :assays
  has_and_belongs_to_many :tissue_and_cell_types
  has_many :sample_assets, :dependent => :destroy
  has_many :treatments, :dependent=>:destroy

  has_many :data_files, :class_name => "DataFile::Version", :finder_sql => Proc.new { self.asset_sql("DataFile") }
  has_many :models, :class_name => "Model::Version", :finder_sql => Proc.new{self.asset_sql("Model")}
  has_many :sops, :class_name => "Sop::Version", :finder_sql => Proc.new { self.asset_sql("Sop") }
  has_many :data_file_masters, :through => :sample_assets, :source => :asset, :source_type => 'DataFile'
  has_many :model_masters, :through => :sample_assets, :source => :asset, :source_type => 'Model'
  has_many :sop_masters, :through => :sample_assets, :source => :asset, :source_type => 'Sop'

  accepts_nested_attributes_for :specimen
  alias_attribute :description, :comments

  validates_uniqueness_of :title

  validates_presence_of :title
  validates_presence_of :specimen, :lab_internal_number
  validates_presence_of :donation_date, :if => "Seek::Config.is_virtualliver"
  validates_presence_of :projects, :unless => "Seek::Config.is_virtualliver"

  scope :default_order, order("title")

  include Seek::Search::BiosampleFields

  searchable(:auto_index=>false) do
    text :specimen do
      if specimen
        text=[]
        text << specimen.lab_internal_number
        text << specimen.provider_name
        text << specimen.title
        text << specimen.provider_id
        text
      end
    end

    text :strain do
      if (specimen.strain)
        text = []
        text << specimen.strain.info
        text << specimen.strain.try(:organism).try(:title).to_s
        text
      end
    end
  end if Seek::Config.solr_enabled

  HUMANIZED_COLUMNS = {:title => "Sample name", :lab_internal_number=> "Sample lab internal identifier", :provider_id => "Provider's sample identifier"}

  ["data_file","sop","model"].each do |type|
     eval <<-END_EVAL
       #related items hash will use data_file_masters instead of data_files, etc. (sops, models)
       def related_#{type.pluralize}
         #{type}_masters
       end
     END_EVAL
  end



  def self.sop_sql()
    'SELECT sop_versions.* FROM sop_versions ' +
        'INNER JOIN sample_sops ' +
        'ON sample_sops.sop_id = sop_versions.sop_id ' +
        'WHERE (sample_sops.sop_version = sop_versions.version ' +
        "AND sample_sops.sample_id = #{self.id})"
  end

  def asset_sql(asset_class)
    asset_class_underscored = asset_class.underscore
    'SELECT ' + asset_class_underscored + '_versions.* FROM ' + asset_class_underscored + '_versions ' +
        'INNER JOIN sample_assets ' +
        'ON sample_assets.asset_id= '+ asset_class_underscored + '_id ' +
        'AND sample_assets.asset_type=\'' + asset_class + '\' ' +
        'WHERE (sample_assets.version= ' + asset_class_underscored + '_versions.version ' +
        "AND sample_assets.sample_id= #{self.id})"
  end

  def state_allows_delete? *args
    assays.empty? && super
  end

  def self.user_creatable?
    Seek::Config.biosamples_enabled
  end

  def associate_tissue_and_cell_type tissue_and_cell_type_id,tissue_and_cell_type_title
       tissue_and_cell_type=nil
    if !tissue_and_cell_type_title.blank?
      if ( tissue_and_cell_type_id =="0" )
          found = TissueAndCellType.where(:title => tissue_and_cell_type_title).first
          unless found
          tissue_and_cell_type = TissueAndCellType.create!(:title=> tissue_and_cell_type_title)
          end
      else
          tissue_and_cell_type = TissueAndCellType.find_by_id(tissue_and_cell_type_id)
      end

      if tissue_and_cell_type
       existing = false
       self.tissue_and_cell_types.each do |t|
         if t == tissue_and_cell_type
           existing = true
           break
         end
       end
       unless existing
         self.tissue_and_cell_types << tissue_and_cell_type
       end
      end
    end
  end

  def associate_asset asset
    sample_asset = sample_assets.detect { |sa| sa.asset == asset }

    unless sample_asset
      sample_asset = SampleAsset.new
      sample_asset.sample = self
      sample_asset.asset = asset
    end

    sample_asset.version = asset.version
    sample_asset.save if sample_asset.changed?

    return sample_asset
  end

  def create_or_update_assets asset_ids, asset_class_name
    asset_class = eval asset_class_name
    existing_sample_assets = sample_assets.select { |sa| sa.asset_type == asset_class_name }
    asset_ids_to_destroy = existing_sample_assets.map(&:asset_id) - asset_ids.map(&:to_i)

    #destroy old,redundant sample_assets
    existing_sample_assets.select { |sa| asset_ids_to_destroy.include? sa.asset_id }.each &:destroy

    #update/create new sample assets
    asset_ids.each do |id|
      asset = asset_class.find id
      associate_asset asset if asset.can_view?
    end
  end

  def clone_with_associations
    new_object= self.dup
    new_object.policy = self.policy.deep_copy
    new_object.data_file_masters = self.data_file_masters.select(&:can_view?)
   new_object.model_masters = self.model_masters.select(&:can_view?)  
    new_object.sop_masters = self.sop_masters.select(&:can_view?)
   new_object.tissue_and_cell_types = self.try(:tissue_and_cell_types)
    new_object.project_ids = self.project_ids
    return new_object
  end

  def self.human_attribute_name(attribute, options = {})
    HUMANIZED_COLUMNS[attribute.to_sym] || super
  end

  def sampling_date_info
    if sampling_date.nil?
      ''
    else
      if try(:sampling_date).hour == 0 and try(:sampling_date).min == 0 and try(:sampling_date).sec == 0 then
        try(:sampling_date).strftime('%d/%m/%Y')
      else
        try(:sampling_date).strftime('%d/%m/%Y @ %H:%M:%S')
      end

    end
  end

  def provider_name_info
    provider_name.blank? ? contributor.try(:person).try(:name) : provider_name
  end

  def specimen_info
    specimen.nil? ? '' : (I18n.t 'biosamples.sample_parent_term').capitalize + ': ' + specimen.title
  end

  def age_at_sampling_info
    unless age_at_sampling.blank? || age_at_sampling_unit.blank?
      "#{age_at_sampling} (#{age_at_sampling_unit.title || age_at_sampling_unit.symbol}s)"
    else
      ''
    end
  end
end