Class: Sample

Inherits:
ApplicationRecord show all
Extended by:
EventfulRecord, Metadata, ValidationStateGuard
Includes:
Aliquot::Aliquotable, Api::SampleIo::Extensions, Commentable, ModelExtensions::Sample, Role::Authorized, SharedBehaviour::Named, StandardNamedScopes, Uuid::Uuidable
Defined in:
app/models/sample.rb

Overview

A Sample is an abstract concept, with represents the life of a sample of DNA/RNA as it moves through our processes. As a result, a sample may exist in multiple receptacles at the same time, in the form of an Aliquot. As a result Sample is mainly concerned with dealing with aspects which are always true, such as tracking where it originally came from.

An individual sample may be subject to library creation and sequencing multiple different times. These processes may be different each time.

Sample Creation

Samples can enter Sequencescape via a number of different routes. Such as: - SampleManifest: Large spreadsheets of sample information are generated. When uploaded samples are created in the corresponding Receptacle. - Heron: Heron samples get registered via the Api::V2::Heron::PlatesController - Special samples: Samples such as PhiX are generated internally

Defined Under Namespace

Classes: Current, Metadata

Constant Summary collapse

GC_CONTENTS = 
['Neutral', 'High AT', 'High GC'].freeze
GENDERS = 
['Male', 'Female', 'Mixed', 'Hermaphrodite', 'Unknown', 'Not Applicable'].freeze
DNA_SOURCES = 
[
  'Genomic',
  'Whole Genome Amplified',
  'Blood',
  'Cell Line',
  'Saliva',
  'Brain',
  'FFPE',
  'Amniocentesis Uncultured',
  'Amniocentesis Cultured',
  'CVS Uncultured',
  'CVS Cultured',
  'Fetal Blood',
  'Tissue'
].freeze
SRA_HOLD_VALUES = 
%w[Hold Public Protect].freeze
AGE_REGEXP = 
'\d+(?:\.\d+|\-\d+|\.\d+\-\d+\.\d+|\.\d+\-\d+\.\d+)?\s+(?:second|minute|day|week|month|year)s?|Not Applicable|N/A|To be provided'
DOSE_REGEXP =

rubocop:enable Layout/LineLength

'\d+(?:\.\d+)?\s+\w+(?:\/\w+)?|Not Applicable|N/A|To be provided'
REMAPPED_ATTRIBUTES =

The spreadsheets that people upload contain various fields that could be mistyped. Here we ensure that the capitalisation of these is correct.

{
  gc_content: GC_CONTENTS,
  gender: GENDERS,
  dna_source: DNA_SOURCES,
  sample_sra_hold: SRA_HOLD_VALUES
}.transform_values { |v| v.index_by { |b| b.downcase } }

Constants included from Metadata

Metadata::SECTION_FIELDS

Constants included from StandardNamedScopes

StandardNamedScopes::SORT_FIELDS, StandardNamedScopes::SORT_ORDERS

Instance Attribute Summary collapse

Instance Method Summary collapse

Methods included from EventfulRecord

has_many_events, has_many_lab_events, has_one_event_with_family

Methods included from ValidationStateGuard

validation_guard, validation_guarded_by

Methods included from Metadata

has_metadata

Methods included from Commentable

#after_comment_addition

Methods included from Aliquot::Aliquotable

included

Methods included from SharedBehaviour::Named

included

Methods included from StandardNamedScopes

included

Methods included from Uuid::Uuidable

included, #unsaved_uuid!, #uuid

Methods included from Api::SampleIo::Extensions

included, #json_root

Methods inherited from ApplicationRecord

alias_association, convert_labware_to_receptacle_for, find_by_id_or_name, find_by_id_or_name!

Methods included from Squishify

extended

Instance Attribute Details

#current_user ⇒ Object

For attributing accessioning changes recorded in the SS events table



282
283
284
 
# File 'app/models/sample.rb', line 282

def current_user
  @current_user
end

#empty_supplier_sample_name ⇒ Boolean

Deprecated.

Only set on older samples where samples were created at manifest generation, rather than upload

Returns true if the customer didn't fill in the supplier_sample_name. Indicating that there is actually no sample in the well.

Returns:

  • (Boolean) —

    Returns true if the customer didn't fill in the supplier_sample_name. Indicating that there is actually no sample in the well.




# File 'app/models/sample.rb', line 77

Instance Method Details

#accession(event_user) ⇒ Object 



519
520
521
522
523
524
525
526
527
528
529
530
531
 
# File 'app/models/sample.rb', line 519

def accession(event_user)
  # Check if study is present and allowed to be accessioned
  return unless ena_study&.accession_required?

  # Flag set in the deployment project to allow per-environment enabling of accessioning
  unless configatron.accession_samples
    raise AccessionService::AccessioningDisabledError, 'Accessioning is not enabled in this environment.'
  end

  accessionable = build_accessionable
  validate_accessionable!(accessionable)
  enqueue_accessioning_job!(accessionable, event_user)
end

#accession_and_handle_validation_errors ⇒ Object 



533
534
535
536
537
538
539
540
 
# File 'app/models/sample.rb', line 533

def accession_and_handle_validation_errors
  event_user = current_user # the event_user for this sample must be set from the calling controller
  accession(event_user)
  Rails.logger.info("Accessioning passed for sample '#{name}'")
rescue AccessionService::AccessionServiceError => e
  # Save error messages for later feedback to the user in a flash message
  errors.add(:base, e.message)
end

#accession_number? ⇒ Boolean

Returns:

  • (Boolean) 


488
489
490
 
# File 'app/models/sample.rb', line 488

def accession_number?
  ebi_accession_number.present?
end

#accession_service ⇒ Object

Return the highest priority accession service



508
509
510
511
512
513
514
515
516
517
 
# File 'app/models/sample.rb', line 508

def accession_service
  services = studies.group_by { |s| s.accession_service.priority }
  return AccessionService::UnsuitableService.new([]) if services.empty?

  highest_priority = services.keys.max
  suitable_study = services[highest_priority].detect(&:send_samples_to_service?)
  return suitable_study.accession_service if suitable_study

  AccessionService::UnsuitableService.new(services[highest_priority])
end

#can_be_included_in_submission? ⇒ Boolean

if sample is registered through sample manifest it should have supplier sample name (without it the row is considered empty) if sample was registered directly, only sample name is a required field, so supplier sample name can be empty but it is reasonably safe to assume that required metadata was provided

Returns:

  • (Boolean) 


598
599
600
 
# File 'app/models/sample.rb', line 598

def can_be_included_in_submission?
  registered_through_manifest? ? sample_metadata.supplier_name.present? : true
end

#control_formatted ⇒ Object 



602
603
604
605
606
607
608
609
 
# File 'app/models/sample.rb', line 602

def control_formatted
  return nil if control.nil?

  return 'No' if control == false

  type_text = control_type || 'type unspecified'
  "Yes (#{type_text})"
end

#current_accession_status ⇒ Object 



557
558
559
 
# File 'app/models/sample.rb', line 557

def current_accession_status
  accession_sample_statuses.last
end

#ebi_accession_number ⇒ Object 



484
485
486
 
# File 'app/models/sample.rb', line 484

def ebi_accession_number
  sample_metadata.sample_ebi_accession_number
end

#ena_study ⇒ Object 



546
547
548
 
# File 'app/models/sample.rb', line 546

def ena_study
  studies.first
end

#error ⇒ Object 



492
493
494
 
# File 'app/models/sample.rb', line 492

def error
  'Default error message'
end

#friendly_name ⇒ Object 



578
579
580
 
# File 'app/models/sample.rb', line 578

def friendly_name
  sanger_sample_id || name
end

#handle_update_event(user) ⇒ Object 



542
543
544
 
# File 'app/models/sample.rb', line 542

def handle_update_event(user)
  events.updated_using_sample_manifest!(user)
end

#name_unchanged ⇒ Object 



582
583
584
585
 
# File 'app/models/sample.rb', line 582

def name_unchanged
  errors.add(:name, 'cannot be changed') unless can_rename_sample
  can_rename_sample
end

#registered_through_manifest? ⇒ Boolean

sample can either be registered through sample manifest, historically through studies/:id/sample_registration or via external services like Heron

Returns:

  • (Boolean) 


590
591
592
 
# File 'app/models/sample.rb', line 590

def registered_through_manifest?
  sample_manifest.present?
end

#rename_to!(new_name) ⇒ Object

this method has to be before validation_guarded_by



377
378
379
 
# File 'app/models/sample.rb', line 377

def rename_to!(new_name)
  update!(name: new_name)
end

#sample_empty?(supplier_sample_name = name) ⇒ Boolean

Returns:

  • (Boolean) 


496
497
498
499
500
 
# File 'app/models/sample.rb', line 496

def sample_empty?(supplier_sample_name = name)
  return true if empty_supplier_sample_name

  sample_supplier_name_empty?(supplier_sample_name)
end

#sample_reference_genome ⇒ Object 



561
562
563
564
565
566
 
# File 'app/models/sample.rb', line 561

def sample_reference_genome
  return sample_metadata.reference_genome if sample_metadata.reference_genome.try(:name).present?
  return study_reference_genome if study_reference_genome.try(:name).present?

  nil
end

#sample_supplier_name_empty?(supplier_sample_name) ⇒ Boolean

Returns:

  • (Boolean) 


502
503
504
505
 
# File 'app/models/sample.rb', line 502

def sample_supplier_name_empty?(supplier_sample_name)
  supplier_sample_name.blank? ||
    ['empty', 'blank', 'water', 'no supplier name available', 'none'].include?(supplier_sample_name.downcase)
end

#shorten_sanger_sample_id ⇒ Object

Note:

This appears to be set up to handle legacy data. All currently generated Sanger sample ids will be meet criteria 1 or 2.

Truncates the sanger_sample_id for display on labels - Returns the sanger_sample_id AS IS if it is nil or less than 10 characters - Tries to truncate it to the last 7 digits, and returns that - If it cannot extract 7 digits, the full sanger_sample_id is returned Earlier implementations were supposed to fall back to the name in the absence of a sanger_sample_id, but the feature was incorrectly implemented, and would have thrown an exception.



471
472
473
474
475
476
477
478
479
480
481
482
 
# File 'app/models/sample.rb', line 471

def shorten_sanger_sample_id
  case sanger_sample_id
  when nil
    sanger_sample_id
  when sanger_sample_id.size < 10
    sanger_sample_id
  when /(\d{7})$/
    Regexp.last_match(1)
  else
    sanger_sample_id
  end
end

#subject_type ⇒ Object 



568
569
570
 
# File 'app/models/sample.rb', line 568

def subject_type
  'sample'
end

#validate_ena_required_fields! ⇒ Object 



550
551
552
553
554
555
 
# File 'app/models/sample.rb', line 550

def validate_ena_required_fields!
  (valid?(:accession) && valid?(accession_service.provider)) || raise(ActiveRecord::RecordInvalid, self)
rescue ActiveRecord::RecordInvalid => e
  ena_study.errors.full_messages.each { |message| errors.add(:base, "#{message} on study") } unless ena_study.nil?
  raise e
end