class MiGA::Project

MiGA representation of a project

@package MiGA @license Artistic-2.0

Attributes

do_not_save[RW]

If true, it doesn't save changes

metadata[R]

Information about the project as MiGA::Metadata

path[R]

Absolute path to the project folder

Public Class Methods

DISTANCE_TASKS() click to toggle source

# File lib/miga/project/base.rb, line 25
def DISTANCE_TASKS
  @@DISTANCE_TASKS
end

INCLADE_TASKS() click to toggle source

# File lib/miga/project/base.rb, line 21
def INCLADE_TASKS
  @@INCLADE_TASKS
end

KNOWN_TYPES() click to toggle source

# File lib/miga/project/base.rb, line 29
def KNOWN_TYPES
  @@KNOWN_TYPES
end

RESULT_DIRS() click to toggle source

# File lib/miga/project/base.rb, line 33
def RESULT_DIRS
  @@RESULT_DIRS
end

exist?(path) click to toggle source

Does the project at path exist?

# File lib/miga/project/base.rb, line 8
def exist?(path)
  Dir.exist?(path) and File.exist?("#{path}/miga.project.json")
end

load(path) click to toggle source

Load the project at path. Returns MiGA::Project if project exists, nil otherwise.

# File lib/miga/project/base.rb, line 15
def load(path)
  return nil unless exist? path

  new path
end

new(path, update = false) click to toggle source

Create a new MiGA::Project at path, if it doesn't exist and update is false, or load an existing one.

# File lib/miga/project.rb, line 31
def initialize(path, update = false)
  @datasets = {}
  @do_not_save = false
  @path = File.absolute_path(path)
  self.create if not update and not Project.exist? self.path
  self.load if self.metadata.nil?
  self.metadata[:type] = :mixed if type.nil?
  raise "Unrecognized project type: #{type}." if @@KNOWN_TYPES[type].nil?
end

Public Instance Methods

create() click to toggle source

Create an empty project

# File lib/miga/project.rb, line 43
def create
  unless MiGA::MiGA.initialized?
    raise 'Impossible to create project in uninitialized MiGA.'
  end

  dirs = [path] + @@FOLDERS.map { |d| "#{path}/#{d}" } +
         @@DATA_FOLDERS.map { |d| "#{path}/data/#{d}" }
  dirs.each { |d| Dir.mkdir(d) unless Dir.exist? d }
  @metadata = MiGA::Metadata.new(
    File.expand_path('miga.project.json', path),
    { datasets: [], name: File.basename(path) }
  )
  d_path = File.expand_path('daemon/daemon.json', path)
  File.open(d_path, 'w') { |fh| fh.puts '{}' } unless File.exist? d_path
  pull_hook :on_create
  self.load
end

is_clade?() click to toggle source

Is this a clade project?

# File lib/miga/project.rb, line 100
def is_clade?
  type == :clade
end

is_multi?() click to toggle source

Is this a project for multi-organism datasets?

# File lib/miga/project.rb, line 106
def is_multi?
  @@KNOWN_TYPES[type][:multi]
end

load() click to toggle source

(Re-)load project data and metadata

# File lib/miga/project.rb, line 77
def load
  @datasets = {}
  @dataset_names_hash = nil
  @metadata = MiGA::Metadata.load "#{path}/miga.project.json"
  raise "Couldn't find project metadata at #{path}" if metadata.nil?

  pull_hook :on_load
end

name() click to toggle source

Name of the project

# File lib/miga/project.rb, line 88
def name
  metadata[:name]
end

save() click to toggle source

Save any changes persistently. Do nothing if do_not_save is true

# File lib/miga/project.rb, line 63
def save
  save! unless do_not_save
end

save!() click to toggle source

Save any changes persistently, regardless of do_not_save

# File lib/miga/project.rb, line 69
def save!
  metadata.save
  pull_hook :on_save
  self.load
end

type() click to toggle source

Type of project

# File lib/miga/project.rb, line 94
def type
  metadata[:type]
end