Class: Study

Inherits:

ApplicationRecord

• Object
• ActiveRecord::Base
• ApplicationRecord
• Study

Extended by:

Attributable::Association::Target, EventfulRecord, Metadata

Includes:

AASM, Api::StudyIo::Extensions, Commentable, DataRelease, EventfulRecord, ModelExtensions::Study, ReferenceGenome::Associations, Role::Authorized, SampleManifest::Associations, SharedBehaviour::Named, StudyReport::StudyDetails, Uuid::Uuidable

Defined in:

app/models/study.rb

Overview

Note:

This is really quite convoluted, and couples together administrative organization alongside accessioning and data-access rules. It results in samples being tied to an EGAS/ERP far too early in their lifecycle, and as a result we often need to perform 'sample moves'. Although we do need to know if samples are open(ENA) or managed(EGA) at the point of accessioning.

A Study is a collection of various samples and the work done on them. They are perhaps slightly overloaded, and provide: - A means of grouping together samples for administrative purposes - A means of generating EGAS/ERP study accession numbers at the ENA/EGA - @see Accessionable::Study - These accession numbers are used at data release to group samples together for publication - For managed/EGA studies, also ties the data to an Accessionable::Dac and Accessionable::Policy - A means of generating the aforementioned Accessionable::Dac and Accessionable::Policy @note These should DEFINITELY be separate entities - A means of tying data to internal data-release timings - A means to apply internal data access policies to released sequencing data - A means to tie interested parties to the samples and the work done on them - A way of specifying common ways of filtering/processing generated data. eg. filter human sequence - The service with which a Sample will be accessioned (eg. EGA/ENA)

When a Sample enters Sequencescape it will usually be associated with a single Study, usually determined by the Study associated with the SampleManifest. This study will be recorded on the Aliquot in the stock Receptacle, and additionally a StudySample will record this association.

When work is requested an Order will be created, specifying a list of receptacles and the Study for which this work is being performed. This will set initial study id on request and in turn will be recorded on any downstream aliquots. Critically, it is the study specified on the Aliquot in the Lane which will influence processes like data release and data access.

Defined Under Namespace

Classes: Metadata

Constant Summary

STOCK_PLATE_PURPOSES =

Constants

['Stock Plate', 'Stock RNA Plate'].freeze

YES =

'Yes'

NO =

'No'

YES_OR_NO =

[YES, NO].freeze

OTHER_TYPE =

'Other'

STUDY_SRA_HOLDS =

%w[Hold Public].freeze

DATA_RELEASE_STRATEGY_OPEN =

'open'

DATA_RELEASE_STRATEGY_MANAGED =

'managed'

DATA_RELEASE_STRATEGY_NOT_APPLICABLE =

'not applicable'

DATA_RELEASE_STRATEGIES =

[
  DATA_RELEASE_STRATEGY_OPEN,
  DATA_RELEASE_STRATEGY_MANAGED,
  DATA_RELEASE_STRATEGY_NOT_APPLICABLE
].freeze

DATA_RELEASE_TIMING_STANDARD =

'standard'

DATA_RELEASE_TIMING_NEVER =

'never'

DATA_RELEASE_TIMING_DELAYED =

'delayed'

DATA_RELEASE_TIMING_IMMEDIATE =

'immediate'

DATA_RELEASE_TIMING_PUBLICATION =

'delay until publication'

DATA_RELEASE_TIMINGS =

[
  DATA_RELEASE_TIMING_STANDARD,
  DATA_RELEASE_TIMING_IMMEDIATE,
  DATA_RELEASE_TIMING_DELAYED
].freeze

OLD_DATA_RELEASE_PREVENTION_REASONS =

['data validity', 'legal', 'replication of data subset'].freeze

DATA_RELEASE_PREVENTION_REASON_OTHER =

'Other (please specify)'

DATA_RELEASE_PREVENTION_REASONS =

[
  'Pilot or validation studies - DAC approval not required',
  'Collaborators will share data in a research repository - DAC approval not required',
  'Prevent harm (e.g sensitive studies or biosecurity) - DAC approval required',
  'Protecting IP - DAC approval required',
  DATA_RELEASE_PREVENTION_REASON_OTHER
].freeze

OLD_DATA_RELEASE_DELAY_FOR_OTHER =

'other'

DATA_RELEASE_DELAY_FOR_OTHER =

'Other (please specify below)'

OLD_DATA_RELEASE_DELAY_REASONS =

['other', 'phd study'].freeze

DATA_RELEASE_DELAY_REASONS_STANDARD =

[
  'PhD study',
  'Capacity building',
  'Intellectual property protection',
  'Additional time to make data FAIR',
  DATA_RELEASE_DELAY_FOR_OTHER
].freeze

DATA_RELEASE_DELAY_REASONS_ASSAY =

['assay of no other use'].freeze

DATA_RELEASE_DELAY_PERIODS =

['3 months', '6 months', '9 months', '12 months', '18 months'].freeze

EBI_LIBRARY_STRATEGY_OPTIONS =

EBI_LIBRARY_SOURCE_OPTIONS =

EBI_LIBRARY_SELECTION_OPTIONS =

REMAPPED_ATTRIBUTES =

{
  contaminated_human_dna: YES_OR_NO,
  remove_x_and_autosomes: YES_OR_NO,
  study_sra_hold: STUDY_SRA_HOLDS,
  contains_human_dna: YES_OR_NO,
  commercially_available: YES_OR_NO
}.transform_values { |v| v.index_by { |b| b.downcase } }

Constants included from Metadata

Metadata::SECTION_FIELDS

Constants included from StudyReport::StudyDetails

StudyReport::StudyDetails::BATCH_SIZE

Instance Attribute Summary

• #approval ⇒ Object

  Returns the value of attribute approval.

• #run_count ⇒ Object

  Returns the value of attribute run_count.

• #total_price ⇒ Object

  Returns the value of attribute total_price.

Instance Method Summary

• #abbreviation ⇒ Object
• #accession_all_samples ⇒ Object
• #accession_number? ⇒ Boolean
• #accession_service ⇒ Object
• #approved? ⇒ Boolean
• #asset_progress(assets = nil) {|initial_requests.asset_statistics(wheres)| ... } ⇒ Object

  Yields information on the state of all assets in a convenient fashion for displaying in a table.

• #completed ⇒ Object
• #dac_accession_number ⇒ Object
• #dac_refname ⇒ Object
• #data_release_delay_options(assay_option: false) ⇒ Array<String>

  Helper method for edit dropdowns to support backwards compatibility with old options.

• #data_release_prevention_options ⇒ Array<String>

  Helper method for edit dropdowns to support backwards compatibility with old options.

• #dehumanise_abbreviated_name ⇒ Object
• #each_well_for_qc_report_in_batches(exclude_existing, product_criteria, plate_purposes = nil) ⇒ Object
• #ebi_accession_number ⇒ Object
• #ethical_approval_required? ⇒ Boolean
• #locale ⇒ Object
• #mailing_list_of_managers ⇒ Object
• #mark_active ⇒ Object
• #mark_deactive ⇒ Object
• #owner ⇒ Object

  Returns the study owner (user) if exists or nil TODO - Should be “owners” and return all owners or empty array - done TODO - Look into this is the person that created it really the owner? If so, then an owner should be created when a study is created.

• #policy_accession_number ⇒ Object
• #rebroadcast ⇒ Object
• #request_progress {|@stats_cache ||= initial_requests.progress_statistics| ... } ⇒ Object

  Yields information on the state of all request types in a convenient fashion for displaying in a table.

• #sample_progress(samples = nil) ⇒ Object

  Yields information on the state of all samples in a convenient fashion for displaying in a table.

• #send_samples_to_service? ⇒ Boolean
• #study ⇒ Object

  Used by EventfulMailer.

• #study_status ⇒ Object
• #subject_type ⇒ Object
• #text_comments ⇒ Object
• #unprocessed_submissions? ⇒ Boolean
• #validate_ena_required_fields! ⇒ Object
• #validate_ethically_approved ⇒ Object

  Instance methods.

• #warnings ⇒ Object

Methods included from EventfulRecord

has_many_events, has_many_lab_events, has_one_event_with_family

Methods included from Metadata

has_metadata

Methods included from Attributable::Association::Target

default, extended, for_select_association

Methods included from SampleManifest::Associations

included

Methods included from ReferenceGenome::Associations

included

Methods included from SharedBehaviour::Named

included

Methods included from Commentable

#after_comment_addition

Methods included from DataRelease

#accession_required?, #do_not_enforce_accessioning, #for_array_express?, #valid_data_release_properties?

Methods included from Uuid::Uuidable

included, #unsaved_uuid!, #uuid

Methods included from Api::StudyIo::Extensions

included, #render_class

Methods included from StudyReport::StudyDetails

#each_stock_well_id_in_study_in_batches, #progress_report_header, #progress_report_on_all_assets

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

#approval ⇒ Object

Returns the value of attribute approval.

# File 'app/models/study.rb', line 128

def approval
  @approval
end

#run_count ⇒ Object

Returns the value of attribute run_count.

# File 'app/models/study.rb', line 128

def run_count
  @run_count
end

#total_price ⇒ Object

Returns the value of attribute total_price.

# File 'app/models/study.rb', line 128

def total_price
  @total_price
end

Instance Method Details

#abbreviation ⇒ Object

# File 'app/models/study.rb', line 562

def abbreviation
  abbreviation = study_metadata.study_name_abbreviation
  abbreviation.presence || "#{id}STDY"
end

#accession_all_samples ⇒ Object

# File 'app/models/study.rb', line 558

def accession_all_samples
  samples.find_each(&:accession) if accession_number?
end

#accession_number? ⇒ Boolean

Returns:

• (Boolean)

# File 'app/models/study.rb', line 554

def accession_number?
  ebi_accession_number.present?
end

#accession_service ⇒ Object

# File 'app/models/study.rb', line 581

def accession_service
  case data_release_strategy
  when 'open'
    EnaAccessionService.new
  when 'managed'
    EgaAccessionService.new
  else
    NoAccessionService.new(self)
  end
end

#approved? ⇒ Boolean

Returns:

• (Boolean)

# File 'app/models/study.rb', line 571

def approved?
  # TODO: remove
  true
end

#asset_progress(assets = nil) {|initial_requests.asset_statistics(wheres)| ... } ⇒ Object

Yields information on the state of all assets in a convenient fashion for displaying in a table.

Yields:

• (initial_requests.asset_statistics(wheres))

# File 'app/models/study.rb', line 492

def asset_progress(assets = nil)
  wheres = {}
  wheres = { asset_id: assets.map(&:id) } if assets.present?
  yield(initial_requests.asset_statistics(wheres))
end

#completed ⇒ Object

# File 'app/models/study.rb', line 477

def completed
  counts = requests.standard.group('state').count
  total = counts.values.sum
  failed = counts['failed'] || 0
  cancelled = counts['cancelled'] || 0
  (total - failed - cancelled) > 0 ? (counts.fetch('passed', 0) * 100) / (total - failed - cancelled) : 0
end

#dac_accession_number ⇒ Object

# File 'app/models/study.rb', line 546

def dac_accession_number
  study_metadata.ega_dac_accession_number
end

#dac_refname ⇒ Object

# File 'app/models/study.rb', line 515

def dac_refname
  "DAC for study - #{name} - ##{id}"
end

#data_release_delay_options(assay_option: false) ⇒ Array<String>

Helper method for edit dropdowns to support backwards compatibility with old options.

Parameters:

• assay_option (Boolean) (defaults to: false) —

  • whether to include assay-specific options

Returns:

• (Array<String>) —

  the list of options for the data release delay reason dropdown

# File 'app/models/study.rb', line 629

def data_release_delay_options(assay_option: false)
  # If the current value is an old one, then we need to include it in the list of options
  additional_options = []
  if OLD_DATA_RELEASE_DELAY_REASONS.include? study_metadata.data_release_delay_reason
    additional_options << study_metadata.data_release_delay_reason
  end

  additional_options.concat(DATA_RELEASE_DELAY_REASONS_ASSAY) if assay_option
  DATA_RELEASE_DELAY_REASONS_STANDARD + additional_options
end

#data_release_prevention_options ⇒ Array<String>

Helper method for edit dropdowns to support backwards compatibility with old options.

Returns:

• (Array<String>) —

  the list of options for the data release prevention reason dropdown

# File 'app/models/study.rb', line 616

def data_release_prevention_options
  additional_options = []
  if OLD_DATA_RELEASE_PREVENTION_REASONS.include? study_metadata.data_release_prevention_reason
    additional_options << study_metadata.data_release_prevention_reason
  end

  DATA_RELEASE_PREVENTION_REASONS + additional_options
end

#dehumanise_abbreviated_name ⇒ Object

# File 'app/models/study.rb', line 567

def dehumanise_abbreviated_name
  abbreviation.downcase.gsub(/ +/, '_')
end

#each_well_for_qc_report_in_batches(exclude_existing, product_criteria, plate_purposes = nil) ⇒ Object

# File 'app/models/study.rb', line 442

def each_well_for_qc_report_in_batches(exclude_existing, product_criteria, plate_purposes = nil)
  # @note We include aliquots here, despite the fact they are only needed if we have to set a poor-quality flag
  #       as in some cases failures are not as rare as you may imagine, and it can cause major performance issues.
  base_scope =
    Well
      .on_plate_purpose_included(PlatePurpose.where(name: plate_purposes || STOCK_PLATE_PURPOSES))
      .for_study_through_aliquot(self)
      .without_blank_samples
      .includes(:well_attribute, :aliquots, :map, samples: :sample_metadata)
      .readonly(true)
  scope = exclude_existing ? base_scope.without_report(product_criteria) : base_scope
  scope.find_in_batches { |wells| yield wells }
end

#ebi_accession_number ⇒ Object

# File 'app/models/study.rb', line 542

def ebi_accession_number
  study_metadata.study_ebi_accession_number
end

#ethical_approval_required? ⇒ Boolean

Returns:

• (Boolean)

# File 'app/models/study.rb', line 576

def ethical_approval_required?
  study_metadata.contains_human_dna == Study::YES && study_metadata.contaminated_human_dna == Study::NO &&
    study_metadata.commercially_available == Study::NO
end

#locale ⇒ Object

# File 'app/models/study.rb', line 538

def locale
  funding_source
end

#mailing_list_of_managers ⇒ Object

# File 'app/models/study.rb', line 600

def mailing_list_of_managers
  configured_managers = managers.pluck(:email).compact.uniq
  configured_managers.empty? ? configatron.fetch(:ssr_emails, User.all_administrators_emails) : configured_managers
end

#mark_active ⇒ Object

# File 'app/models/study.rb', line 469

def mark_active
  logger.warn "Study activation failed! #{errors.map(&:to_s)}" unless active?
end

#mark_deactive ⇒ Object

# File 'app/models/study.rb', line 465

def mark_deactive
  logger.warn "Study deactivation failed! #{errors.map(&:to_s)}" unless inactive?
end

#owner ⇒ Object

Returns the study owner (user) if exists or nil TODO - Should be “owners” and return all owners or empty array - done TODO - Look into this is the person that created it really the owner? If so, then an owner should be created when a study is created.

# File 'app/models/study.rb', line 534

def owner
  owners.first
end

#policy_accession_number ⇒ Object

# File 'app/models/study.rb', line 550

def policy_accession_number
  study_metadata.ega_policy_accession_number
end

#rebroadcast ⇒ Object

# File 'app/models/study.rb', line 609

def rebroadcast
  broadcast
end

#request_progress {|@stats_cache ||= initial_requests.progress_statistics| ... } ⇒ Object

Yields information on the state of all request types in a convenient fashion for displaying in a table. Used initial requests, which won't capture cross study sequencing requests.

Yields:

• (@stats_cache ||= initial_requests.progress_statistics)

# File 'app/models/study.rb', line 487

def request_progress
  yield(@stats_cache ||= initial_requests.progress_statistics) if block_given?
end

#sample_progress(samples = nil) ⇒ Object

Yields information on the state of all samples in a convenient fashion for displaying in a table.

# File 'app/models/study.rb', line 499

def sample_progress(samples = nil)
  if samples.blank?
    requests.sample_statistics_new
  else
    # Rubocop suggests this changes as it allows MySQL to perform a single query, which is usually better
    # however in this case we've actually already loaded the samples. If we do try passing in the
    # samples themselves, then things top working as intended. (Performance tanks in some places, and
    # we generate invalid SQL in others)
    yield(requests.where(aliquots: { sample_id: samples.pluck(:id) }).sample_statistics_new)
  end
end

#send_samples_to_service? ⇒ Boolean

Returns:

• (Boolean)

# File 'app/models/study.rb', line 592

def send_samples_to_service?
  accession_service.no_study_accession_needed || (!study_metadata.never_release? && accession_number?)
end

#study ⇒ Object

Used by EventfulMailer

# File 'app/models/study.rb', line 525

def study
  self
end

#study_status ⇒ Object

# File 'app/models/study.rb', line 511

def study_status
  inactive? ? 'closed' : 'open'
end

#subject_type ⇒ Object

# File 'app/models/study.rb', line 605

def subject_type
  'study'
end

#text_comments ⇒ Object

# File 'app/models/study.rb', line 473

def text_comments
  comments.each_with_object([]) { |c, array| array << c.description if c.description.present? }.join(', ')
end

#unprocessed_submissions? ⇒ Boolean

Returns:

• (Boolean)

# File 'app/models/study.rb', line 519

def unprocessed_submissions?
  # TODO[mb14] optimize if needed
  study.orders.any? { |o| o.submission.nil? || o.submission.unprocessed? }
end

#validate_ena_required_fields! ⇒ Object

# File 'app/models/study.rb', line 596

def validate_ena_required_fields!
  valid?(:accession) or raise ActiveRecord::RecordInvalid, self
end

#validate_ethically_approved ⇒ Object

Instance methods

# File 'app/models/study.rb', line 429

def validate_ethically_approved
  return true if valid_ethically_approved?

  message =
    if ethical_approval_required?
      'should be either true or false for this study.'
    else
      'should be not applicable (null) not false.'
    end
  errors.add(:ethically_approved, message)
  false
end

#warnings ⇒ Object

# File 'app/models/study.rb', line 456

def warnings
  # These studies are now invalid, but the warning should remain until existing studies are fixed.
  if study_metadata.managed? && study_metadata.data_access_group.blank?
    # rubocop:todo Layout/LineLength
    'No user group specified for a managed study. Please specify a valid Unix user group to ensure study data is visible to the correct people.'
    # rubocop:enable Layout/LineLength
  end
end