Class: Labimotion::Import

Inherits:
Object
  • Object
show all
Defined in:
lib/labimotion/utils/import.rb

Class Method Summary collapse

Class Method Details

.import_datasets(data, instances, gt, current_user_id, &update_instances) ⇒ Object 



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# File 'lib/labimotion/utils/import.rb', line 43

def self.import_datasets(data, instances, gt, current_user_id, &update_instances)
  begin
    data.fetch('Labimotion::Dataset', {}).each do |uuid, fields|
      klass_id = fields['dataset_klass_id']
      dk_obj = data.fetch('Labimotion::DatasetKlass', {})[klass_id]
      dk_id = dk_obj['identifier']
      element_uuid = fields.fetch('element_id')
      element_type = fields.fetch('element_type')
      element = instances.fetch(element_type).fetch(element_uuid)

      dataset_klass = Labimotion::DatasetKlass.find_by(identifier: dk_id)
      next if gt == true && dataset_klass.nil?

      dkr = Labimotion::DatasetKlassesRevision.find_by(uuid: fields.fetch('klass_uuid'))
      dataset_klass = dkr.dataset_klass if dataset_klass.nil? && dkr.present?
      next if dataset_klass.nil? || dataset_klass.ols_term_id != dk_obj['ols_term_id']

      dataset_klass = Labimotion::DatasetKlass.find_by(ols_term_id: dk_obj['ols_term_id']) if dataset_klass.nil?
      next if dataset_klass.nil?

      dataset = Labimotion::Dataset.create!(
        fields.slice(
          'properties', 'properties_release'
        ).merge(
          ## created_by: current_user_id,
          element: element,
          dataset_klass: dataset_klass,
          uuid: SecureRandom.uuid,
          klass_uuid: dkr&.uuid || dataset_klass.uuid
        )
      )
      update_instances.call(uuid, dataset)
    end
  rescue StandardError => e
    Rails.logger.error(e.backtrace)
    raise
  end
end

.import_repo_segment_props(instances, attachments, attachable_uuid, fields) ⇒ Object 



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# File 'lib/labimotion/utils/import.rb', line 6

def self.import_repo_segment_props(instances, attachments, attachable_uuid, fields)
  primary_store = Rails.configuration.storage.primary_store
  attachable = instances.fetch('Labimotion::Segment').fetch(attachable_uuid)
  attachment = Attachment.where(id: attachments, filename: fields.fetch('identifier')).first
  attachment.update!(
    attachable_id: attachable.id,
    attachable_type: 'SegmentProps',
    con_state: Labimotion::ConState::NONE,
    transferred: true,
    aasm_state: fields.fetch('aasm_state'),
    filename: fields.fetch('filename'),
    content_type: fields.fetch('content_type'),
    storage: primary_store
    # checksum: fields.fetch('checksum'),
    # created_at: fields.fetch('created_at'),
    # updated_at: fields.fetch('updated_at')
  )

  properties = attachable.properties
  properties['layers'].keys.each do |key|
    layer = properties['layers'][key]
    field_uploads = layer['fields'].select { |ss| ss['type'] == 'upload' }
    field_uploads&.each do |upload|
      idx = properties['layers'][key]['fields'].index(upload)
      files = upload["value"] && upload["value"]["files"]
      files&.each_with_index do |fi, fdx|
        if properties['layers'][key]['fields'][idx]['value']['files'][fdx]['uid'] == fields.fetch('identifier')
          properties['layers'][key]['fields'][idx]['value']['files'][fdx]['aid'] = attachment.id
          properties['layers'][key]['fields'][idx]['value']['files'][fdx]['uid'] = attachment.identifier
        end
      end
    end
  end
  attachable.update!(properties: properties)
  attachment
end

.import_segments(data, instances, gt, current_user_id, &update_instances) ⇒ Object 



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# File 'lib/labimotion/utils/import.rb', line 82

def self.import_segments(data, instances, gt, current_user_id, &update_instances)
  begin
    data.fetch('Labimotion::Segment', {}).each do |uuid, fields|
      klass_id = fields["segment_klass_id"]
      sk_obj = data.fetch('Labimotion::SegmentKlass', {})[klass_id]
      sk_id = sk_obj["identifier"]
      ek_obj = data.fetch('Labimotion::ElementKlass').fetch(sk_obj["element_klass_id"])
      element_klass = Labimotion::ElementKlass.find_by(name: ek_obj['name']) if ek_obj.present?
      next if element_klass.nil? || ek_obj.nil? || ek_obj['is_generic'] == true
      element_uuid = fields.fetch('element_id')
      element_type = fields.fetch('element_type')
      element = instances.fetch(element_type).fetch(element_uuid)
      segment_klass = Labimotion::SegmentKlass.find_by(identifier: sk_id)
      next if gt == true && segment_klass.nil?

      skr = Labimotion::SegmentKlassesRevision.find_by(uuid: fields.fetch('klass_uuid'))
      segment_klass = skr.segment_klass if segment_klass.nil? && skr.present?

      # segment_klass = Labimotion::SegmentKlass.create!(sk_obj.slice(
      #     'label',
      #     'desc',
      #     'properties_template',
      #     'is_active',
      #     'place',
      #     'properties_release',
      #     'uuid',
      #     'identifier',
      #     'sync_time'
      #   ).merge(
      #     element_klass: element_klass,
      #     created_by: current_user_id,
      #     released_at: DateTime.now
      #   )
      # ) if segment_klass.nil?

      next if segment_klass.nil?

      segment = Labimotion::Segment.create!(
        fields.slice(
          'properties', 'properties_release'
        ).merge(
          created_by: current_user_id,
          element: element,
          segment_klass: segment_klass,
          uuid: SecureRandom.uuid,
          klass_uuid: skr&.uuid || segment_klass.uuid
        )
      )

      properties = segment.properties
      properties['layers'].keys.each do |key|
        layer = properties['layers'][key]
        field_molecules = layer['fields'].select { |ss| ss['type'] == 'drag_molecule' }
        field_molecules.each do |field|
          idx = properties['layers'][key]['fields'].index(field)
          id = field["value"] && field["value"]["el_id"] unless idx.nil?
          mol = Molecule.find_or_create_by_molfile(data.fetch('Molecule')[id]['molfile']) unless id.nil?
          unless mol.nil?
            properties['layers'][key]['fields'][idx]['value']['el_id'] = mol.id
            properties['layers'][key]['fields'][idx]['value']['el_tip'] = "#{mol.inchikey}@@#{mol.cano_smiles}"
            properties['layers'][key]['fields'][idx]['value']['el_label'] = mol.iupac_name
          end
        end

        field_tables = layer['fields'].select { |ss| ss['type'] == 'table' }
        field_tables&.each do |field|
          tidx = layer['fields'].index(field)
          next unless field['sub_values'].present? && field['sub_fields'].present?

          field_table_molecules = field['sub_fields'].select { |ss| ss['type'] == 'drag_molecule' }
          if field_table_molecules.present?
            col_ids = field_table_molecules.map { |x| x.values[0] }
            col_ids.each do |col_id|
              field['sub_values'].each_with_index do |sub_value, vdx|
                next unless sub_value[col_id].present? && sub_value[col_id]['value'].present? && sub_value[col_id]['value']['el_id'].present?

                svalue = sub_value[col_id]['value']
                next unless svalue['el_id'].present? && svalue['el_inchikey'].present?

                tmol = Molecule.find_or_create_by_molfile(data.fetch('Molecule')[svalue['el_id']]['molfile']) unless svalue['el_id'].nil?
                unless tmol.nil?
                  properties['layers'][key]['fields'][tidx]['sub_values'][vdx][col_id]['value']['el_id'] = tmol.id
                  properties['layers'][key]['fields'][tidx]['sub_values'][vdx][col_id]['value']['el_tip'] = "#{tmol.inchikey}@@#{tmol.cano_smiles}"
                  properties['layers'][key]['fields'][tidx]['sub_values'][vdx][col_id]['value']['el_label'] = tmol.cano_smiles
                  properties['layers'][key]['fields'][tidx]['sub_values'][vdx][col_id]['value']['el_smiles'] = tmol.cano_smiles
                  properties['layers'][key]['fields'][tidx]['sub_values'][vdx][col_id]['value']['el_iupac'] = tmol.iupac_name
                  properties['layers'][key]['fields'][tidx]['sub_values'][vdx][col_id]['value']['el_inchikey'] = tmol.inchikey
                  properties['layers'][key]['fields'][tidx]['sub_values'][vdx][col_id]['value']['el_svg'] = File.join('/images', 'molecules', tmol.molecule_svg_file)
                  properties['layers'][key]['fields'][tidx]['sub_values'][vdx][col_id]['value']['el_molecular_weight'] = tmol.molecular_weight
                end
              end
            end
          end
        end
      end
      segment.update!(properties: properties)
      update_instances.call(uuid, segment)
    end
  rescue StandardError => e
    Rails.logger.error(e.backtrace)
    raise
  end
end