Class: MiGA::Metadata

Inherits:
MiGA
  • Object
show all
Defined in:
lib/miga/metadata.rb

Overview

Metadata associated to objects like MiGA::Project, MiGA::Dataset, and MiGA::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 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(path, defaults = {}) ⇒ Metadata

Initiate a MiGA::Metadata object with description in path. It will create it if it doesn’t exist.



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# File 'lib/miga/metadata.rb', line 32

def initialize(path, defaults = {})
  @data = nil
  @path = File.absolute_path(path)
  unless File.exist? path
    @data = {}
    defaults.each { |k, v| self[k] = v }
    create
  end
end

Instance Attribute Details

#path ⇒ Object (readonly)

Path to the JSON file describing the metadata



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# File 'lib/miga/metadata.rb', line 27

def path
  @path
end

Class Method Details

.exist?(path) ⇒ Boolean

Does the metadata described in path already exist?

Returns:

  • (Boolean) 


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# File 'lib/miga/metadata.rb', line 12

def self.exist?(path) File.exist? path end

.load(path) ⇒ Object

Load the metadata described in path and return MiGA::Metadata if it exists, or nil otherwise.



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# File 'lib/miga/metadata.rb', line 17

def self.load(path)
  return nil unless Metadata.exist? path

  MiGA::Metadata.new(path)
end

Instance Method Details

#[](k) ⇒ Object

Return the value of k in #data



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# File 'lib/miga/metadata.rb', line 107

def [](k)
  if k.to_s =~ /(.+):(.+)/
    data[$1.to_sym]&.fetch($2)
  else
    data[k.to_sym]
  end
end

#[]=(k, v) ⇒ Object

Set the value of k to v



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# File 'lib/miga/metadata.rb', line 117

def []=(k, v)
  self.load if @data.nil?
  k = k.to_sym
  return @data.delete(k) if v.nil?

  case k
  when :name
    # Protect the special field :name
    v = v.miga_name
  when :type
    # Symbolize the special field :type
    v = v.to_sym if k == :type
  end

  @data[k] = v
end

#create ⇒ Object

Reset :created field and save the current data



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# File 'lib/miga/metadata.rb', line 51

def create
  self[:created] = Time.now.to_s
  save
end

#created ⇒ Object

Time of creation



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# File 'lib/miga/metadata.rb', line 148

def created
  Time.parse(self[:created]) unless self[:created].nil?
end

#data ⇒ Object

Parsed data as a Hash



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# File 'lib/miga/metadata.rb', line 44

def data
  self.load if @data.nil?
  @data
end

#each(&blk) ⇒ Object

Iterate blk for each data with 2 arguments: key and value



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# File 'lib/miga/metadata.rb', line 136

def each(&blk)
  data.each { |k, v| blk.call(k, v) }
end

#load ⇒ Object

(Re-)load metadata stored in #path



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# File 'lib/miga/metadata.rb', line 80

def load
  sleeper = 0.0
  while File.exist? lock_file
    sleeper += 0.1 if sleeper <= 10.0
    sleep(sleeper.to_i)
  end
  tmp = MiGA::Json.parse(path, additions: true)
  @data = {}
  tmp.each { |k, v| self[k] = v }
end

#lock_file ⇒ Object

Lock file for the metadata



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# File 'lib/miga/metadata.rb', line 101

def lock_file
  "#{path}.lock"
end

#remove! ⇒ Object

Delete file at #path



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# File 'lib/miga/metadata.rb', line 93

def remove!
  MiGA.DEBUG "Metadata.remove! #{path}"
  File.unlink(path)
  nil
end

#save ⇒ Object

Save the metadata into #path



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# File 'lib/miga/metadata.rb', line 58

def save
  return if self[:never_save]

  MiGA::MiGA.DEBUG "Metadata.save #{path}"
  self[:updated] = Time.now.to_s
  json = to_json
  wait_for_lock
  FileUtils.touch(lock_file)
  ofh = File.open("#{path}.tmp", 'w')
  ofh.puts json
  ofh.close

  unless File.exist?("#{path}.tmp") && File.exist?(lock_file)
    raise "Lock-racing detected for #{path}"
  end

  File.rename("#{path}.tmp", path)
  File.unlink(lock_file)
end

#to_json ⇒ Object

Show contents in JSON format as a String



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

def to_json
  MiGA::Json.generate(data)
end

#updated ⇒ Object

Time of last update



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

def updated
  Time.parse(self[:updated]) unless self[:updated].nil?
end