Class: MiGA::Dataset

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

Overview

Dataset representation in MiGA

Defined Under Namespace

Modules: Base, Hooks, Result, Status

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_recalculate_status, #hook_run_cmd

Methods included from Common::Hooks

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

Methods included from Status

#recalculate_status, #status

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, #next_task, #recalculate_tasks, #result, #result_dirs, #results

Methods included from Common::WithOption

#all_options, #assert_has_option, #assert_valid_option_value, #option, #option?, #option_by_default, #option_by_metadata, #option_from_string, #set_option

Methods inherited from MiGA

CITATION, CITATION_ARRAY, DEBUG, DEBUG_OFF, DEBUG_ON, DEBUG_TRACE_OFF, DEBUG_TRACE_ON, FULL_VERSION, LONG_VERSION, VERSION, VERSION_DATE, #advance, debug?, debug_trace?, initialized?, #like_io?, #num_suffix, rc_path, #result_files_exist?, #say

Methods included from Common::Path

#root_path, #script_path

Methods included from Common::Format

#clean_fasta_file, #seqs_length, #tabulate

Methods included from Common::Net

#download_file_ftp, #known_hosts, #remote_connection

Methods included from Common::SystemCall

#run_cmd, #run_cmd_opts

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 53

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

  save
  pull_hook :on_create
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 46

def name
  @name
end

#project ⇒ Object (readonly)

MiGA::Project that contains the dataset



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# File 'lib/miga/dataset.rb', line 42

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 27

def exist?(project, name)
  !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 33

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 14

def KNOWN_TYPES
  @@KNOWN_TYPES
end

.OPTIONS ⇒ Object 



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

def OPTIONS
  @@OPTIONS
end

.PREPROCESSING_TASKS ⇒ Object 



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

def PREPROCESSING_TASKS
  @@PREPROCESSING_TASKS
end

.RESULT_DIRS ⇒ Object 



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

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 116

def activate!
  metadata[:inactive] = nil
  metadata[:warn] = nil if metadata[:warn] && metadata[:warn] =~ /^Inactive: /
  metadata.save
  project.recalculate_tasks("Reference dataset activated: #{name}") if ref?
  pull_hook :on_activate
end

#active? ⇒ Boolean Also known as: is_active?

Is this dataset active?

Returns:

  • (Boolean) 


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# File 'lib/miga/dataset.rb', line 162

def active?
  metadata[:inactive].nil? or !metadata[:inactive]
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 193

def closest_relatives(how_many = 1, ref_project = false)
  return nil if (ref? != ref_project) || multi?

  r = result(ref_project ? :taxonomy : :distances)
  return nil if r.nil?

  require 'miga/sqlite'
  MiGA::SQLite.new(r.file_path(:aai_db)).run(
    'SELECT seq2, aai FROM aai WHERE seq2 != ? ' \
    'GROUP BY seq2 ORDER BY aai DESC LIMIT ?', [name, how_many]
  )
end

#inactivate!(reason = nil) ⇒ Object

Inactivate a dataset. This halts automated processing by the daemon

If given, the reason string is saved as a metadata :warn entry



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# File 'lib/miga/dataset.rb', line 106

def inactivate!(reason = nil)
  metadata[:warn] = "Inactive: #{reason}" unless reason.nil?
  metadata[:inactive] = true
  metadata.save
  project.recalculate_tasks("Reference dataset inactivated: #{name}") if ref?
  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 126

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

#metadata ⇒ Object

MiGA::Metadata with information about the dataset



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# File 'lib/miga/dataset.rb', line 71

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

#multi? ⇒ Boolean Also known as: is_multi?

Is this dataset known to be multi-organism?

Returns:

  • (Boolean) 


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# File 'lib/miga/dataset.rb', line 146

def multi?
  return false if metadata[:type].nil? || @@KNOWN_TYPES[type].nil?

  @@KNOWN_TYPES[type][:multi]
end

#nonmulti? ⇒ Boolean Also known as: is_nonmulti?

Is this dataset known to be single-organism?

Returns:

  • (Boolean) 


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# File 'lib/miga/dataset.rb', line 154

def nonmulti?
  return false if metadata[:type].nil? || @@KNOWN_TYPES[type].nil?

  !@@KNOWN_TYPES[type][:multi]
end

#query? ⇒ Boolean Also known as: is_query?

Is this dataset a query (non-reference)?

Returns:

  • (Boolean) 


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# File 'lib/miga/dataset.rb', line 140

def query?
  !metadata[:ref]
end

#ref? ⇒ Boolean Also known as: is_ref?

Is this dataset a reference?

Returns:

  • (Boolean) 


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# File 'lib/miga/dataset.rb', line 134

def ref?
  !query?
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 96

def remove!
  results.each(&:remove!)
  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 81

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 89

def type
  metadata[:type]
end