Class: MiGA::Cli::Action::Add

Inherits:
MiGA::Cli::Action show all
Defined in:
lib/miga/cli/action/add.rb

Constant Summary collapse

@@INPUT_TYPES = 
{
  raw_reads_single:
    ['Single raw reads in a single FastQ file',
     :raw_reads, %w[.1.fastq]],
  raw_reads_paired:
    ['Paired raw reads in two FastQ files',
     :raw_reads, %w[.1.fastq .2.fastq]],
  trimmed_reads_single:
    ['Single trimmed reads in a single FastA file',
     :trimmed_fasta, %w[.SingleReads.fa]],
  trimmed_reads_paired:
    ['Paired trimmed reads in two FastA files',
     :trimmed_fasta, %w[.1.fasta .2.fasta]],
  trimmed_reads_interleaved:
    ['Paired trimmed reads in a single FastA file',
     :trimmed_fasta, %w[.CoupledReads.fa]],
  assembly:
    ['Assembled contigs or scaffolds in FastA format',
     :assembly, %w[.LargeContigs.fna]]
}

Constants included from MiGA

MiGA::CITATION, VERSION, VERSION_DATE, VERSION_NAME

Instance Attribute Summary

Attributes inherited from MiGA::Cli::Action

#cli

Attributes included from MiGA::Common::Net

#remote_connection_uri

Class Method Summary collapse

Instance Method Summary collapse

Methods inherited from MiGA::Cli::Action

#complete, #empty_action, #initialize, #launch, load, #name

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 MiGA::Common::Path

#root_path, #script_path

Methods included from MiGA::Common::Format

#clean_fasta_file, #seqs_length, #tabulate

Methods included from MiGA::Common::Net

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

Methods included from MiGA::Common::SystemCall

#run_cmd, #run_cmd_opts

Constructor Details

This class inherits a constructor from MiGA::Cli::Action

Class Method Details

.INPUT_TYPES ⇒ Object 



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# File 'lib/miga/cli/action/add.rb', line 101

def INPUT_TYPES
  @@INPUT_TYPES
end

Instance Method Details

#parse_cli ⇒ Object 



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# File 'lib/miga/cli/action/add.rb', line 7

def parse_cli
  cli.expect_files = true
  cli.defaults = { ref: true, ignore_dups: false }
  cli.parse do |opt|
    opt.separator 'You can create multiple datasets with a single command; ' \
      'simply pass all the files at the end: {FILES...}'
    opt.separator 'If -D is passed, only one dataset will be added. ' \
      'Otherwise, dataset names will be determined by the file paths (see -R)'
    opt.separator ''
    cli.opt_object(opt, [:project, :dataset_opt, :dataset_type_req])
    opt.on(
      '-q', '--query',
      'Register the dataset as a query, not a reference dataset'
    ) { |v| cli[:ref] = !v }
    opt.on(
      '-d', '--description STRING',
      'Description of the dataset'
    ) { |v| cli[:description] = v }
    opt.on(
      '-c', '--comments STRING',
      'Comments on the dataset'
    ) { |v| cli[:comments] = v }
    opt.on(
      '-m', '--metadata STRING',
      'Metadata as key-value pairs separated by = and delimited by comma',
      'Values are saved as strings except for booleans (true / false) or nil'
    ) { |v| cli[:metadata] = v }
    opt.on(
      '-R', '--name-regexp REGEXP', Regexp,
      'Regular expression indicating how to extract the name from the path',
      'By default for paired files:',
      "'#{MiGA::Cli.FILE_REGEXP(true)}'",
      'By default for other files:',
      "'#{MiGA::Cli.FILE_REGEXP}'"
    ) { |v| cli[:regexp] = v }
    opt.on(
      '--prefix STRING',
      'Prefix to all the dataset names'
    ) { |v| cli[:prefix] = v }
    opt.on(
      '-i', '--input-type STRING',
      'Type of input data, one of the following:',
      *self.class.INPUT_TYPES.map { |k, v| "~ #{k}: #{v[0]}" }
    ) { |v| cli[:input_type] = v.downcase.to_sym }
    opt.on(
      '--ignore-dups',
      'Continue with a warning if a dataset already exists'
    ) { |v| cli[:ignore_dups] = v }
  end
end

#perform ⇒ Object 



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# File 'lib/miga/cli/action/add.rb', line 58

def perform
  p = cli.load_project
  cli.ensure_par(type: '-t')
  files, file_type = get_files_and_type

  paired = cli[:input_type].to_s.include?('_paired')
  cli[:regexp] ||= MiGA::Cli.FILE_REGEXP(paired)

  cli.say 'Creating datasets:'
  files.each do |file|
    d = create_dataset(file, p)
    next if d.nil?

    copy_file_to_project(file, file_type, d, p)
    cli.add_metadata(d)
    p.add_dataset(d.name)
    res = d.first_preprocessing(true)
    cli.say "  result: #{res}"
  end
end