Class: MiGA::Json

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

Overview

Taxonomic classifications in MiGA.

Constant Summary

Constants included from MiGA

CITATION, VERSION, VERSION_DATE, VERSION_NAME

Instance Attribute Summary

Attributes included from Common::Net

#remote_connection_uri

Class 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, #http_request, #known_hosts, #main_server, #net_method, #normalize_encoding, #remote_connection

Methods included from Common::SystemCall

#run_cmd, #run_cmd_opts

Class Method Details

.default_opts(opts = {}) ⇒ Object

Default parsing options. Supported opts keys:

  • :contents: If true, the input is assumed to be the contents to parse, not the path to a JSON file.

  • :default: A base to attach the parsed hash. A Hash or a String (path).

  • :additions: If addition classes should be parsed. By default is false.

  • :symbolize: If names should be symbolized. By default it’s true if additions is false, or false otherwise. They can both be false, but an exception will be raised if both are true

  • :large_file: If passed, the file is treated as a file with very long lines (possibly a single long line)



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

def default_opts(opts = {})
  opts[:contents] ||= false
  opts[:additions] ||= false
  opts[:symbolize] = !opts[:additions] if opts[:symbolize].nil?
  if opts[:additions] and opts[:symbolize]
    raise 'JSON additions are not supported with symbolized names'
  end

  opts
end

.generate(obj, path = nil) ⇒ Object

Generates and returns prettyfied JSON to represent obj. If path is passed, it saves the JSON in that file.



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# File 'lib/miga/json.rb', line 82

def generate(obj, path = nil)
  generate_generic(:pretty_generate, obj, path)
end

.generate_fast(obj, path = nil) ⇒ Object

Generates and returns plain JSON to represent obj without checking for circular references. If path is passed, it saves the JSON in that file.



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

def generate_fast(obj, path = nil)
  generate_generic(:fast_generate, obj, path)
end

.generate_plain(obj, path = nil) ⇒ Object

Generates and returns plain JSON to represent obj. If path is passed, it saves the JSON in that file.



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# File 'lib/miga/json.rb', line 89

def generate_plain(obj, path = nil)
  generate_generic(:generate, obj, path)
end

.parse(path, opts = {}) ⇒ Object

Parse a JSON file in path and return a hash. Optionally, use default as the base to attach the parsed hash. default can be a Hash or a String (path). See default_opts for supported opts.



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

def parse(path, opts = {})
  opts = default_opts(opts)

  # Read JSON
  cont = path
  if opts[:large_file]
    cont = ''
    File.open(path, 'r') do |fh|
      cont += fh.read(2 ** 16) until fh.eof?
    end
  elsif !opts[:contents]
    12.times do
      cont = File.read(path)
      break unless cont.empty?
      sleep 1 # Wait up to 12 seconds for racing processes (iff empty file)
    end
  end
  raise "Empty descriptor: #{opts[:contents] ? "''" : path}" if cont.empty?

  # Parse JSON
  params = {
    symbolize_names: opts[:symbolize],
    create_additions: opts[:additions]
  }
  y = JSON.parse(cont, params)

  # Add defaults
  unless opts[:default].nil?
    opts[:default] = parse(opts[:default]) if opts[:default].is_a? String
    y.each { |k, v| opts[:default][k] = v }
    y = opts[:default]
  end

  # Return
  y
end