Module: MiGA::Dataset::Result

Includes:
Common::WithResult, Base
Included in:
MiGA::Dataset
Defined in:
lib/miga/dataset/result.rb

Overview

Helper module including specific functions to add dataset results

Instance Method Summary collapse

Methods included from Common::WithResult

#add_result, #each_result, #get_result, #next_task, #recalculate_tasks, #result, #result_dirs, #results

Instance Method Details

#cleanup_distances! ⇒ Object

Clean-up all the stored distances, removing values for datasets no longer in the project as reference datasets.



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# File 'lib/miga/dataset/result.rb', line 138

def cleanup_distances!
  r = get_result(:distances)
  return if r.nil?

  require 'miga/sqlite'
  ref = project.datasets.select(&:ref?).select(&:active?).map(&:name)
  %i[haai_db aai_db ani_db].each do |db_type|
    db = r.file_path(db_type)
    next if db.nil? || !File.size?(db)

    sqlite_db = MiGA::SQLite.new(db)
    table = db_type[-6..-4]
    val = sqlite_db.run("select seq2 from #{table}")
    next if val.empty?

    (val.map(&:first) - ref).each do |extra|
      sqlite_db.run("delete from #{table} where seq2=?", extra)
    end
  end
end

#done_preprocessing?(save = false) ⇒ Boolean

Are all the dataset-specific tasks done? Passes save to #add_result

Returns:

  • (Boolean) 


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# File 'lib/miga/dataset/result.rb', line 86

def done_preprocessing?(save = false)
  !first_preprocessing(save).nil? && next_preprocessing(save).nil?
end

#first_preprocessing(save = false) ⇒ Object

Returns the key symbol of the first registered result (sorted by the execution order). This typically corresponds to the result used as the initial input. Passes save to #add_result.



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# File 'lib/miga/dataset/result.rb', line 70

def first_preprocessing(save = false)
  @first_processing ||= @@PREPROCESSING_TASKS.find do |t|
    !add_result(t, save).nil?
  end
end

#ignore_task?(task) ⇒ Boolean

Should I ignore task for this dataset?

Returns:

  • (Boolean) 


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# File 'lib/miga/dataset/result.rb', line 24

def ignore_task?(task)
  why_ignore(task) != :execute
end

#next_preprocessing(save = false) ⇒ Object

Returns the key symbol of the next task that needs to be executed or nil. Passes save to #add_result.



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# File 'lib/miga/dataset/result.rb', line 79

def next_preprocessing(save = false)
  first_preprocessing(save) if save
  next_task(nil, save)
end

#profile_advance(save = false) ⇒ Object

Returns an array indicating the stage of each task (sorted by execution order). The values are integers:

  • 0 for an undefined result (a task before the initial input).

  • 1 for a registered result (a completed task).

  • 2 for a queued result (a task yet to be executed).

It passes save to #add_result



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# File 'lib/miga/dataset/result.rb', line 97

def profile_advance(save = false)
  first_task = first_preprocessing(save)
  return Array.new(@@PREPROCESSING_TASKS.size, 0) if first_task.nil?

  adv = []
  state = 0
  next_task = next_preprocessing(save)
  @@PREPROCESSING_TASKS.each do |task|
    state = 1 if first_task == task
    state = 2 if !next_task.nil? && next_task == task
    adv << state
  end
  adv
end

#result_base ⇒ Object

Return the basename for results



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# File 'lib/miga/dataset/result.rb', line 18

def result_base
  name
end

#result_status(task) ⇒ Object

Returns the status of task. The status values are symbols:

  • -: the task is upstream from the initial input

  • ignore_*: the task is to be ignored, see codes in #why_ignore

  • complete: a task with registered results

  • pending: a task queued to be performed



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# File 'lib/miga/dataset/result.rb', line 125

def result_status(task)
  reason = why_ignore(task)
  case reason
  when :upstream; :-
  when :execute; :pending
  when :complete; :complete
  else; :"ignore_#{reason}"
  end
end

#results_status ⇒ Object

Returns a Hash with tasks as key and status as value. See result_status for possible values



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# File 'lib/miga/dataset/result.rb', line 115

def results_status
  Hash[@@PREPROCESSING_TASKS.map { |task| [task, result_status(task)] }]
end

#why_ignore(task) ⇒ Object

Return a code explaining why a task is ignored. The values are symbols:

  • empty: the dataset has no data

  • inactive: the dataset is inactive

  • upstream: the task is upstream from dataset’s input

  • force: forced to ignore by metadata

  • project: incompatible project

  • noref: incompatible dataset, only for reference

  • multi: incompatible dataset, only for multi

  • nonmulti: incompatible dataset, only for nonmulti

  • complete: the task is already complete

  • execute: do not ignore, execute the task



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# File 'lib/miga/dataset/result.rb', line 41

def why_ignore(task)
  if !get_result(task).nil?
    :complete
  elsif !active?
    :inactive
  elsif first_preprocessing.nil?
    :empty
  elsif @@PREPROCESSING_TASKS.index(task) <
        @@PREPROCESSING_TASKS.index(first_preprocessing)
    :upstream
  elsif !metadata["run_#{task}"].nil?
    metadata["run_#{task}"] ? :execute : :force
  elsif task == :taxonomy && project.option(:ref_project).nil?
    :project
  elsif @@_EXCLUDE_NOREF_TASKS_H[task] && !ref?
    :noref
  elsif @@_ONLY_MULTI_TASKS_H[task] && !multi?
    :multi
  elsif @@_ONLY_NONMULTI_TASKS_H[task] && !nonmulti?
    :nonmulti
  else
    :execute
  end
end