module MiGA::Project::Dataset

add_dataset(name) click to toggle source

Add dataset identified by name and return MiGA::Dataset.

# File lib/miga/project/dataset.rb, line 49
def add_dataset(name)
  unless metadata[:datasets].include? name
    d = MiGA::Dataset.new(self, name)
    @metadata[:datasets] << name
    @dataset_names_hash = nil # Ensure loading even if +do_not_save+ is true
    save
    if d.ref? && d.active?
      recalculate_tasks("Reference dataset added: #{d.name}")
    end
    pull_hook(:on_add_dataset, name)
  end
  dataset(name)
end

dataset(name) click to toggle source

Returns MiGA::Dataset

# File lib/miga/project/dataset.rb, line 28
def dataset(name)
  name = name.miga_name
  return nil unless MiGA::Dataset.exist?(self, name)

  @datasets ||= {}
  @datasets[name] ||= MiGA::Dataset.new(self, name)
  @datasets[name]
end

dataset_names() click to toggle source

Returns Array of String (without evaluating dataset objects).

# File lib/miga/project/dataset.rb, line 15
def dataset_names
  metadata[:datasets]
end

dataset_names_hash() click to toggle source

Returns Hash of Strings => true. Similar to dataset_names but as Hash for efficiency.

# File lib/miga/project/dataset.rb, line 22
def dataset_names_hash
  @dataset_names_hash ||= Hash[dataset_names.map { |i| [i, true] }]
end

datasets() click to toggle source

Returns Array of MiGA::Dataset.

# File lib/miga/project/dataset.rb, line 9
def datasets
  metadata[:datasets].map { |name| dataset(name) }
end

done_preprocessing?(save = false) click to toggle source

Are all the datasets in the project preprocessed? Save intermediate results if save (until the first incomplete dataset is reached).

# File lib/miga/project/dataset.rb, line 143
def done_preprocessing?(save = false)
  !each_dataset.any? do |d|
    d.ref? && d.active? && !d.done_preprocessing?(save)
  end
end

each_dataset(&blk) click to toggle source

Iterate through datasets (MiGA::Dataset)

# File lib/miga/project/dataset.rb, line 39
def each_dataset(&blk)
  if block_given?
    metadata[:datasets].each { |name| blk.call(dataset(name)) }
  else
    to_enum(:each_dataset)
  end
end

each_dataset_profile_advance(&blk) click to toggle source

Call blk passing the result of MiGA::Dataset::Result#profile_advance for each registered dataset.

# File lib/miga/project/dataset.rb, line 165
def each_dataset_profile_advance(&blk)
  each_dataset { |ds| blk.call(ds.profile_advance) }
end

import_dataset(ds, method = :hardlink) click to toggle source

Import the dataset ds, a MiGA::Dataset, using method which is any method supported by File#generic_transfer.

# File lib/miga/project/dataset.rb, line 81
def import_dataset(ds, method = :hardlink)
  raise "Impossible to import dataset, it already exists: #{ds.name}." if
    MiGA::Dataset.exist?(self, ds.name)

  # Import dataset results
  ds.each_result do |task, result|
    # import result files
    result.each_file do |file|
      File.generic_transfer(
        File.join(result.dir, file),
        File.join(path, 'data', MiGA::Dataset.RESULT_DIRS[task], file),
        method
      )
    end
    # import result metadata
    %w(json start done).each do |suffix|
      if File.exist? File.join(result.dir, "#{ds.name}.#{suffix}")
        File.generic_transfer(
          File.join(result.dir, "#{ds.name}.#{suffix}"),
          File.join(
            path, 'data', MiGA::Dataset.RESULT_DIRS[task],
            "#{ds.name}.#{suffix}"
          ),
          method
        )
      end
    end
  end
  # Import dataset metadata
  File.generic_transfer(
    File.join(ds.project.path, 'metadata', "#{ds.name}.json"),
    File.join(self.path, 'metadata', "#{ds.name}.json"),
    method
  )
  # Save dataset
  self.add_dataset(ds.name)
end

profile_datasets_advance() click to toggle source

Returns a two-dimensional matrix (Array of Array) where the first index corresponds to the dataset, the second index corresponds to the dataset task, and the value corresponds to:

0: Before execution.
1: Done (or not required).
2: To do.

# File lib/miga/project/dataset.rb, line 156
def profile_datasets_advance
  advance = []
  each_dataset_profile_advance { |adv| advance << adv }
  advance
end

unlink_dataset(name) click to toggle source

Unlink dataset identified by name and return MiGA::Dataset.

# File lib/miga/project/dataset.rb, line 65
def unlink_dataset(name)
  d = dataset(name)
  return nil if d.nil?

  self.metadata[:datasets].delete(name)
  save
  if d.ref? && d.active?
    recalculate_tasks("Reference dataset unlinked: #{d.name}")
  end
  pull_hook(:on_unlink_dataset, name)
  d
end

unregistered_datasets() click to toggle source

Find all datasets with (potential) result files but are yet unregistered.

# File lib/miga/project/dataset.rb, line 121
def unregistered_datasets
  datasets = []
  MiGA::Dataset.RESULT_DIRS.values.each do |dir|
    dir_p = "#{path}/data/#{dir}"
    next unless Dir.exist? dir_p

    Dir.entries(dir_p).each do |file|
      next unless
        file =~ %r{
          \.(fa(a|sta|stqc?)?|fna|solexaqa|gff[23]?|done|ess)(\.gz)?$
        }

      m = /([^\.]+)/.match(file)
      datasets << m[1] unless m.nil? or m[1] == "miga-project"
    end
  end
  datasets.uniq - metadata[:datasets]
end

Public Instance Methods