Class: Study

Inherits:
ApplicationRecord show all
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 collapse

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'
ALL_DATA_RELEASE_TIMINGS =

The list of all possible data release timings

[
  DATA_RELEASE_TIMING_STANDARD,
  DATA_RELEASE_TIMING_NEVER,
  DATA_RELEASE_TIMING_DELAYED,
  DATA_RELEASE_TIMING_IMMEDIATE,
  DATA_RELEASE_TIMING_PUBLICATION
].freeze
DATA_RELEASE_TIMINGS_FOR_OPEN_RELEASE =

Release timings for open studies

[
  DATA_RELEASE_TIMING_STANDARD,
  DATA_RELEASE_TIMING_IMMEDIATE,
  DATA_RELEASE_TIMING_DELAYED,
  DATA_RELEASE_TIMING_PUBLICATION
].freeze
DATA_RELEASE_TIMINGS_FOR_MANAGED_RELEASE =

Release timings for managed studies

[
  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 collapse

  




  
    

      Instance Method Summary
      collapse
    


    
  


  
  
  
  
  
  
  
  
  
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.



  





  



  

    
      


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# File 'app/models/study.rb', line 144

def approval
  @approval
end

    		
  





    
      
      
      

  

  
    #run_count  ⇒ Object 
  

  

  


  

    

Returns the value of attribute run_count.



  





  



  

    
      


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# File 'app/models/study.rb', line 144

def run_count
  @run_count
end

    		
  





    
      
      
      

  

  
    #total_price  ⇒ Object 
  

  

  


  

    

Returns the value of attribute total_price.



  





  



  

    
      


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# File 'app/models/study.rb', line 144

def total_price
  @total_price
end

    		
  





    
  



  

    
Instance Method Details


    
      

  

  
    #abbreviation  ⇒ Object 
  

  

  


  

    
      


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# File 'app/models/study.rb', line 611

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

    		
  





    
      

  

  
    #accession_all_samples(event_user)  ⇒ void 
  

  

  


  

    
This method returns an undefined value.


Accession all samples in the study.



If the study does not have an accession number, adds an error to the study and returns. Otherwise, iterates through each sample in the study and attempts to accession it, unless the sample already has an accession number. If an Accession::Error occurs for a sample, adds the error message to the study's errors.



NOTE: this does not check if the current user has permission to accession samples in this study



  





  



  

    
      


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

def accession_all_samples(event_user)
  return errors.add(:base, 'Please accession the study before accessioning samples') unless accession_number?

  unless samples_accessionable?
    return errors.add(:base,
                      'Study cannot accession samples, see Study Accessioning tab for details')
  end

  samples.find_each do |sample|
    Accession.accession_sample(sample, event_user) unless sample.accession_number?
  rescue Accession::Error => e
    errors.add(:base, e.message)
  end
end

    		
  





    
      

  

  
    #accession_number?  ⇒ Boolean 
  

  

  


  

    

  





  

Returns:


    
  
    
  • 
      
      
        (Boolean)
      
      
      
    
    • 
  





  

    
      


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# File 'app/models/study.rb', line 561

def accession_number?
  ebi_accession_number.present?
end

    		
  





    
      

  

  
    #approved?  ⇒ Boolean 
  

  

  


  

    

  





  

Returns:


    
  
    
  • 
      
      
        (Boolean)
      
      
      
    
    • 
  





  

    
      


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# File 'app/models/study.rb', line 620

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))
      
      
      
    
    • 
  





  

    
      


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

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

    		
  





    
      

  

  
    #completed  ⇒ Object 
  

  

  


  

    
      


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# File 'app/models/study.rb', line 484

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 
  

  

  


  

    
      


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# File 'app/models/study.rb', line 553

def dac_accession_number
  study_metadata.ega_dac_accession_number
end

    		
  





    
      

  

  
    #dac_refname  ⇒ Object 
  

  

  


  

    
      


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# File 'app/models/study.rb', line 522

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
    

    
      
    
    • 
  





  

    
      


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# File 'app/models/study.rb', line 663

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
    

    
      
    
    • 
  





  

    
      


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# File 'app/models/study.rb', line 650

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 
  

  

  


  

    
      


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

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

    		
  





    
      

  

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

  

  


  

    
      


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# File 'app/models/study.rb', line 449

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 
  

  

  


  

    
      


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# File 'app/models/study.rb', line 549

def ebi_accession_number
  study_metadata.study_ebi_accession_number
end

    		
  





    
      

  

  
    #ethical_approval_required?  ⇒ Boolean 
  

  

  


  

    

  





  

Returns:


    
  
    
  • 
      
      
        (Boolean)
      
      
      
    
    • 
  





  

    
      


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# File 'app/models/study.rb', line 625

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 
  

  

  


  

    
      


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# File 'app/models/study.rb', line 545

def locale
  funding_source
end

    		
  





    
      

  

  
    #mailing_list_of_managers  ⇒ Object 
  

  

  


  

    
      


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# File 'app/models/study.rb', line 634

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 
  

  

  


  

    
      


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# File 'app/models/study.rb', line 476

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

    		
  





    
      

  

  
    #mark_deactive  ⇒ Object 
  

  

  


  

    
      


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# File 'app/models/study.rb', line 472

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.



  





  



  

    
      


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# File 'app/models/study.rb', line 541

def owner
  owners.first
end

    		
  





    
      

  

  
    #policy_accession_number  ⇒ Object 
  

  

  


  

    
      


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# File 'app/models/study.rb', line 557

def policy_accession_number
  study_metadata.ega_policy_accession_number
end

    		
  





    
      

  

  
    #rebroadcast  ⇒ Object 
  

  

  


  

    
      


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# File 'app/models/study.rb', line 643

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)
      
      
      
    
    • 
  





  

    
      


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# File 'app/models/study.rb', line 494

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.



  





  



  

    
      


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# File 'app/models/study.rb', line 506

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

    		
  





    
      

  

  
    #samples_accessionable?  ⇒ Boolean 
  

  

  


  

    

Returns true if the samples in this study are eligible for accessioning



A study's samples are eligible for accessioning if: - the study is active - the study's data release strategy open or managed - the study is not set to never release - the study requires accessioning - the study has an accession number



  





  

Returns:


    
  
    
  • 
      
      
        (Boolean)
      
      
      
        —
        
    

    true if the samples in this study are eligible for accessioning, false otherwise
    

    
      
    
    • 
  





  

    
      


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# File 'app/models/study.rb', line 575

def samples_accessionable?
  # If updating this method, please also update app/views/studies/information/_study_accession_status.html.erb
  [
    active?,
    !study_metadata.strategy_not_applicable?,
    !study_metadata.never_release?,
    accession_required?,
    accession_number?
  ].all?
end

    		
  





    
      

  

  
    #study  ⇒ Object 
  

  

  


  

    

Used by EventfulMailer



  





  



  

    
      


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# File 'app/models/study.rb', line 532

def study
  self
end

    		
  





    
      

  

  
    #study_status  ⇒ Object 
  

  

  


  

    
      


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# File 'app/models/study.rb', line 518

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

    		
  





    
      

  

  
    #subject_type  ⇒ Object 
  

  

  


  

    
      


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# File 'app/models/study.rb', line 639

def subject_type
  'study'
end

    		
  





    
      

  

  
    #text_comments  ⇒ Object 
  

  

  


  

    
      


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# File 'app/models/study.rb', line 480

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

    		
  





    
      

  

  
    #unprocessed_submissions?  ⇒ Boolean 
  

  

  


  

    

  





  

Returns:


    
  
    
  • 
      
      
        (Boolean)
      
      
      
    
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# File 'app/models/study.rb', line 526

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

    		
  





    
      

  

  
    #validate_ethically_approved  ⇒ Object 
  

  

  


  

    

Instance methods



  





  



  

    
      


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# File 'app/models/study.rb', line 436

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

    		
  





    
      

  

  
    #validate_study_for_accessioning!  ⇒ Object 
  

  

  


  

    
      


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# File 'app/models/study.rb', line 630

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

    		
  





    
      

  

  
    #warnings  ⇒ Object 
  

  

  


  

    
      


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# File 'app/models/study.rb', line 463

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