Module: MiGA::Dataset::Result

Includes:
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

Instance Method Details

#add_result(result_type, save = true, opts = {}) ⇒ Object

Look for the result with symbol key result_type and register it in the dataset. If save is false, it doesn’t register the result, but it still returns a result if the expected files are complete. The opts hash controls result creation (if necessary). Supported values include:

  • is_clean: A Boolean indicating if the input files are clean.

  • force: A Boolean indicating if the result must be re-indexed. If true, it implies save=true.

Returns MiGA::Result or nil.



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

def add_result(result_type, save=true, opts={})
  dir = @@RESULT_DIRS[result_type]
  return nil if dir.nil?
  base = File.expand_path("data/#{dir}/#{name}", project.path)
  if opts[:force]
    FileUtils.rm("#{base}.json") if File.exist?("#{base}.json")
  else
    r_pre = MiGA::Result.load("#{base}.json")
    return r_pre if (r_pre.nil? and not save) or not r_pre.nil?
  end
  r = File.exist?("#{base}.done") ?
      self.send("add_result_#{result_type}", base, opts) : nil
  r.save unless r.nil?
  r
end

#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 117

def cleanup_distances!
  r = get_result(:distances)
  return if r.nil?
  [:haai_db, :aai_db, :ani_db].each do |db_type|
    db = r.file_path(db_type)
    next if db.nil? or not File.size? db
    sqlite_db = SQLite3::Database.new db
    table = db_type[-6..-4]
    val = sqlite_db.execute "select seq2 from #{table}"
    next if val.empty?
    (val.map{ |i| i.first } - project.dataset_names).each do |extra|
      sqlite_db.execute "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 89

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

#each_result(&blk) ⇒ Object

For each result executes the 2-ary blk block: key symbol and MiGA::Result.



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# File 'lib/miga/dataset/result.rb', line 26

def each_result(&blk)
  @@RESULT_DIRS.keys.each do |k|
    blk.call(k, result(k)) unless result(k).nil?
  end
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 66

def first_preprocessing(save=false)
  @@PREPROCESSING_TASKS.find do |t|
    not ignore_task?(t) and not add_result(t, save).nil?
  end
end

#get_result(result_type) ⇒ Object

Gets a result as MiGA::Result for the datasets with result_type. This is equivalent to add_result(result_type, false).



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# File 'lib/miga/dataset/result.rb', line 60

def get_result(result_type) ; add_result(result_type, false) ; end

#next_preprocessing(save = false) ⇒ Object

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



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# File 'lib/miga/dataset/result.rb', line 75

def next_preprocessing(save=false)
  after_first = false
  first = first_preprocessing(save)
  return nil if first.nil?
  @@PREPROCESSING_TASKS.each do |t|
    next if ignore_task? t
    return t if after_first and add_result(t, save).nil?
    after_first = (after_first or (t==first))
  end
  nil
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 100

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? and next_task==task
    adv << state
  end
  adv
end

#result(k) ⇒ Object

Get the result MiGA::Result in this dataset identified by the symbol k.



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# File 'lib/miga/dataset/result.rb', line 14

def result(k)
  return nil if @@RESULT_DIRS[k.to_sym].nil?
  MiGA::Result.load(
    "#{project.path}/data/#{@@RESULT_DIRS[k.to_sym]}/#{name}.json" )
end

#results ⇒ Object

Get all the results (Array of MiGA::Result) in this dataset.



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# File 'lib/miga/dataset/result.rb', line 22

def results ; @@RESULT_DIRS.keys.map{ |k| result k }.compact ; end