Class: MiGA::Dataset

Inherits:
MiGA
  • Object
show all
Includes:
Hooks, Result
Defined in:
lib/miga/dataset/base.rb,
lib/miga/dataset.rb

Overview

Dataset representation in MiGA.

Defined Under Namespace

Modules: Base, Hooks, Result

Constant Summary

Constants included from MiGA

CITATION, VERSION, VERSION_DATE, VERSION_NAME

Instance Attribute Summary collapse

Class Method Summary collapse

Instance Method Summary collapse

Methods included from Hooks

#default_hooks, #hook__pull_result_hooks, #hook_clear_run_counts, #hook_run_cmd

Methods included from Common::Hooks

#add_hook, #default_hooks, #hook_run_lambda, #hooks, #pull_hook

Methods included from Result

#cleanup_distances!, #done_preprocessing?, #first_preprocessing, #ignore_task?, #next_preprocessing, #profile_advance, #result_base, #result_status, #results_status, #why_ignore

Methods included from Common::WithResult

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

Methods inherited from MiGA

CITATION, DEBUG, DEBUG_OFF, DEBUG_ON, DEBUG_TRACE_OFF, DEBUG_TRACE_ON, FULL_VERSION, LONG_VERSION, VERSION, VERSION_DATE, initialized?, #result_files_exist?

Methods included from Common::Path

#root_path, #script_path

Methods included from Common::Format

#clean_fasta_file, #seqs_length, #tabulate

Constructor Details

#initialize(project, name, is_ref = true, metadata = {}) ⇒ Dataset

Create a MiGA::Dataset object in a project MiGA::Project with a uniquely identifying name. is_ref indicates if the dataset is to be treated as reference (true, default) or query (false). Pass any additional metadata as a Hash.



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# File 'lib/miga/dataset.rb', line 47

def initialize(project, name, is_ref = true, metadata = {})
  unless name.miga_name?
    raise 'Invalid name, please use only alphanumerics and underscores: ' +
      name.to_s
  end
  @project = project
  @name = name
  @metadata = nil
  metadata[:ref] = is_ref
  @metadata_future = [
    File.expand_path("metadata/#{name}.json", project.path),
    metadata
  ]
  save unless File.exist? @metadata_future[0]
end

Instance Attribute Details

#name ⇒ Object (readonly)

Datasets are uniquely identified by name in a project.



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# File 'lib/miga/dataset.rb', line 40

def name
  @name
end

#project ⇒ Object (readonly)

MiGA::Project that contains the dataset.



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# File 'lib/miga/dataset.rb', line 36

def project
  @project
end

Class Method Details

.exist?(project, name) ⇒ Boolean

Does the project already have a dataset with that name?

Returns:

  • (Boolean) 


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# File 'lib/miga/dataset.rb', line 20

def exist?(project, name)
  not project.dataset_names_hash[name].nil?
end

.INFO_FIELDS ⇒ Object

Standard fields of metadata for datasets.



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

def INFO_FIELDS
  %w(name created updated type ref user description comments)
end

.KNOWN_TYPES ⇒ Object 



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# File 'lib/miga/dataset/base.rb', line 9

def KNOWN_TYPES ; @@KNOWN_TYPES ; end

.PREPROCESSING_TASKS ⇒ Object 



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# File 'lib/miga/dataset/base.rb', line 10

def PREPROCESSING_TASKS ; @@PREPROCESSING_TASKS ; end

.RESULT_DIRS ⇒ Object 



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# File 'lib/miga/dataset/base.rb', line 8

def RESULT_DIRS ; @@RESULT_DIRS ; end

Instance Method Details

#activate! ⇒ Object

Activate a dataset. This removes the :inactive flag.



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# File 'lib/miga/dataset.rb', line 104

def activate!
  self.metadata[:inactive] = nil
  self.metadata.save
  pull_hook :on_activate
end

#closest_relatives(how_many = 1, ref_project = false) ⇒ Object

Returns an Array of how_many duples (Arrays) sorted by AAI:

  • 0: A String with the name(s) of the reference dataset.

  • 1: A Float with the AAI.

This function is currently only supported for query datasets when ref_project is false (default), and only for reference dataset when ref_project is true. It returns nil if this analysis is not supported.



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# File 'lib/miga/dataset.rb', line 153

def closest_relatives(how_many = 1, ref_project = false)
  return nil if (is_ref? != ref_project) or is_multi?
  r = result(ref_project ? :taxonomy : :distances)
  return nil if r.nil?
  db = SQLite3::Database.new(r.file_path :aai_db)
  db.execute(
    'SELECT seq2, aai FROM aai WHERE seq2 != ? ' \
    'GROUP BY seq2 ORDER BY aai DESC LIMIT ?', [name, how_many])
end

#inactivate! ⇒ Object

Inactivate a dataset. This halts automated processing by the daemon.



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# File 'lib/miga/dataset.rb', line 96

def inactivate!
  self.metadata[:inactive] = true
  self.metadata.save
  pull_hook :on_inactivate
end

#info ⇒ Object

Get standard metadata values for the dataset as Array.



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# File 'lib/miga/dataset.rb', line 112

def info
  MiGA::Dataset.INFO_FIELDS.map do |k|
    (k == 'name') ? self.name : metadata[k.to_sym]
  end
end

#is_active? ⇒ Boolean

Is this dataset active?

Returns:

  • (Boolean) 


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# File 'lib/miga/dataset.rb', line 142

def is_active?
  metadata[:inactive].nil? or !metadata[:inactive]
end

#is_multi? ⇒ Boolean

Is this dataset known to be multi-organism?

Returns:

  • (Boolean) 


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# File 'lib/miga/dataset.rb', line 128

def is_multi?
  return false if metadata[:type].nil? or @@KNOWN_TYPES[type].nil?
  @@KNOWN_TYPES[type][:multi]
end

#is_nonmulti? ⇒ Boolean

Is this dataset known to be single-organism?

Returns:

  • (Boolean) 


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# File 'lib/miga/dataset.rb', line 135

def is_nonmulti?
  return false if metadata[:type].nil? or @@KNOWN_TYPES[type].nil?
  !@@KNOWN_TYPES[type][:multi]
end

#is_query? ⇒ Boolean

Is this dataset a query (non-reference)?

Returns:

  • (Boolean) 


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# File 'lib/miga/dataset.rb', line 124

def is_query? ; !metadata[:ref] ; end

#is_ref? ⇒ Boolean

Is this dataset a reference?

Returns:

  • (Boolean) 


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# File 'lib/miga/dataset.rb', line 120

def is_ref? ; !!metadata[:ref] ; end

#metadata ⇒ Object

MiGA::Metadata with information about the dataset



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# File 'lib/miga/dataset.rb', line 65

def metadata
  if @metadata.nil?
    @metadata = MiGA::Metadata.new(*@metadata_future)
    pull_hook :on_load
  end
  @metadata
end

#remove! ⇒ Object

Delete the dataset with all it’s contents (including results) and returns nil.



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# File 'lib/miga/dataset.rb', line 88

def remove!
  self.results.each{ |r| r.remove! }
  self.metadata.remove!
  pull_hook :on_remove
end

#save ⇒ Object

Save any changes you’ve made in the dataset.



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

def save
  MiGA.DEBUG "Dataset.metadata: #{metadata.data}"
  metadata.save
  pull_hook :on_save
end

#type ⇒ Object

Get the type of dataset as Symbol.



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# File 'lib/miga/dataset.rb', line 83

def type ; metadata[:type] ; end