Class: MiGA::RemoteDataset

Inherits:
MiGA
  • Object
show all
Includes:
Base, Download
Defined in:
lib/miga/remote_dataset.rb,
lib/miga/remote_dataset/base.rb,
lib/miga/remote_dataset/download.rb

Overview

MiGA representation of datasets with data in remote locations.

Defined Under Namespace

Modules: Base, Download

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 Download

#download

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(ids, db, universe) ⇒ RemoteDataset

Initialize MiGA::RemoteDataset with ids in database db from universe.



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

def initialize(ids, db, universe)
  ids = [ids] unless ids.is_a? Array
  @ids = (ids.is_a?(Array) ? ids : [ids])
  @db = db.to_sym
  @universe = universe.to_sym
  @metadata = {}
  @metadata[:"#{universe}_#{db}"] = ids.join(',')
  @@UNIVERSE.keys.include?(@universe) or
    raise "Unknown Universe: #{@universe}. Try: #{@@UNIVERSE.keys}"
  @@UNIVERSE[@universe][:dbs].include?(@db) or
    raise "Unknown Database: #{@db}. Try: #{@@UNIVERSE[@universe][:dbs].keys}"
  @_ncbi_asm_json_doc = nil
  # FIXME: Part of the +map_to+ support:
  # unless @@UNIVERSE[@universe][:dbs][@db][:map_to].nil?
  #   MiGA::RemoteDataset.download
  # end
end

Instance Attribute Details

#db ⇒ Object (readonly)

Database storing the dataset.



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

def db
  @db
end

#ids ⇒ Object (readonly)

Array of IDs of the entries composing the dataset.



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# File 'lib/miga/remote_dataset.rb', line 34

def ids
  @ids
end

#metadata ⇒ Object (readonly)

Internal metadata hash



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# File 'lib/miga/remote_dataset.rb', line 36

def metadata
  @metadata
end

#universe ⇒ Object (readonly)

Universe of the dataset.



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# File 'lib/miga/remote_dataset.rb', line 30

def universe
  @universe
end

Class Method Details

.download(universe, db, ids, format, file = nil, extra = [], obj = nil) ⇒ Object

Download data from the universe in the database db with IDs ids and in format. If passed, it saves the result in file. Additional parameters specific to the download method can be passed using extra. Returns String. The obj can also be passed as MiGA::RemoteDataset or MiGA::Dataset.



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# File 'lib/miga/remote_dataset/download.rb', line 14

def download(universe, db, ids, format, file = nil, extra = [], obj = nil)
  ids = [ids] unless ids.is_a? Array
  getter = @@UNIVERSE[universe][:dbs][db][:getter] || :download
  method = @@UNIVERSE[universe][:method]
  opts = {
    universe: universe,
    db: db,
    ids: ids,
    format: format,
    file: file,
    extra: extra,
    obj: obj
  }
  doc = send("#{getter}_#{method}", opts)
  unless opts[:file].nil?
    ofh = File.open(opts[:file], 'w')
    ofh.print doc.force_encoding('UTF-8')
    ofh.close
  end
  doc
end

.download_rest(opts) ⇒ Object Also known as: download_net

Download data using the REST method. Supported opts (Hash) include: universe (mandatory): Symbol db (mandatory): Symbol ids (mandatory): Array of String format: String extra: Array



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# File 'lib/miga/remote_dataset/download.rb', line 82

def download_rest(opts)
  u = @@UNIVERSE[opts[:universe]]
  url = sprintf(
    u[:url], opts[:db], opts[:ids].join(','), opts[:format], *opts[:extra]
  )
  url = u[:api_key][url] unless u[:api_key].nil?
  download_url url
end

.download_url(url) ⇒ Object

Download the given url and return the result regardless of response code. Attempts download up to three times before raising Net::ReadTimeout.



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# File 'lib/miga/remote_dataset/download.rb', line 98

def download_url(url)
  doc = ''
  @timeout_try = 0
  begin
    DEBUG 'GET: ' + url
    URI.parse(url).open(read_timeout: 600) { |f| doc = f.read }
  rescue => e
    @timeout_try += 1
    raise e if @timeout_try >= 3

    sleep 5 # <- For: 429 Too Many Requests
    DEBUG "RETRYING after: #{e}"
    retry
  end
  doc
end

.ncbi_asm_acc2id(acc) ⇒ Object 



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# File 'lib/miga/remote_dataset.rb', line 15

def ncbi_asm_acc2id(acc)
  return acc if acc =~ /^\d+$/

  search_doc = MiGA::Json.parse(
    download(:ncbi_search, :assembly, acc, :json),
    symbolize: false, contents: true
  )
  (search_doc['esearchresult']['idlist'] || []).first
end

.ncbi_asm_rest(opts) ⇒ Object

Download data from NCBI Assembly database using the REST method. Supported opts (Hash) include: obj (mandatory): MiGA::RemoteDataset ids (mandatory): String or Array of String file: String, passed to download extra: Array, passed to download format: String, passed to download



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# File 'lib/miga/remote_dataset/download.rb', line 44

def ncbi_asm_rest(opts)
  url_dir = opts[:obj].ncbi_asm_json_doc['ftppath_genbank']
  if url_dir.nil? || url_dir.empty?
    raise MiGA::RemoteDataMissingError.new(
      "Missing ftppath_genbank in NCBI Assembly JSON"
    )
  end

  url = "#{url_dir}/#{File.basename url_dir}_genomic.fna.gz"
  download(
    :web, :assembly_gz, url,
    opts[:format], opts[:file], opts[:extra], opts[:obj]
  )
end

.ncbi_gb_rest(opts) ⇒ Object

Download data from NCBI GenBank (nuccore) database using the REST method. Supported opts (Hash) are the same as #download_rest and #ncbi_asm_rest.



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# File 'lib/miga/remote_dataset/download.rb', line 62

def ncbi_gb_rest(opts)
  o = download_rest(opts)
  return o unless o.strip.empty?

  MiGA::MiGA.DEBUG 'Empty sequence, attempting download from NCBI assembly'
  opts[:format] = :fasta_gz
  if opts[:file]
    File.unlink(opts[:file]) if File.exist? opts[:file]
    opts[:file] = "#{opts[:file]}.gz"
  end
  ncbi_asm_rest(opts)
end

.ncbi_map(id, dbfrom, db) ⇒ Object

Looks for the entry id in dbfrom, and returns the linked identifier in db (or nil).



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# File 'lib/miga/remote_dataset/download.rb', line 118

def ncbi_map(id, dbfrom, db)
  doc = download(:ncbi_map, dbfrom, id, :json, nil, [db])
  return if doc.empty?

  tree = MiGA::Json.parse(doc, contents: true)
  [:linksets, 0, :linksetdbs, 0, :links, 0].each do |i|
    tree = tree[i]
    break if tree.nil?
  end
  tree
end

.UNIVERSE ⇒ Object 



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# File 'lib/miga/remote_dataset/base.rb', line 7

def UNIVERSE
  @@UNIVERSE
end

Instance Method Details

#get_gtdb_taxonomy ⇒ Object

Get GTDB taxonomy as MiGA::Taxonomy



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

def get_gtdb_taxonomy
  gtdb_genome = metadata[:gtdb_assembly] or return

  doc = MiGA::Json.parse(
    MiGA::RemoteDataset.download(
      :gtdb, :genome, gtdb_genome, 'taxon-history', nil, ['']
    ),
    contents: true
  )
  lineage = { ns: 'gtdb' }
  lineage.merge!(doc.first) # Get only the latest available classification
  release = lineage.delete(:release)
  @metadata[:gtdb_release] = release
  lineage.transform_values! { |v| v.gsub(/^\S__/, '') }
  MiGA.DEBUG "Got lineage from #{release}: #{lineage}"
  MiGA::Taxonomy.new(lineage)
end

#get_metadata(metadata_def = {}) ⇒ Object

Get metadata from the remote location.



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

def get_metadata(metadata_def = {})
  metadata_def.each { |k, v| @metadata[k] = v }
  case universe
  when :ebi, :ncbi, :web
    # Get taxonomy
    @metadata[:tax] = get_ncbi_taxonomy
  when :gtdb
    # Get taxonomy
    @metadata[:tax] = get_gtdb_taxonomy
  end
  @metadata = get_type_status(metadata)
end

#get_ncbi_taxid ⇒ Object

Get NCBI Taxonomy ID.



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# File 'lib/miga/remote_dataset.rb', line 116

def get_ncbi_taxid
  origin = (universe == :ncbi and db == :assembly) ? :web : universe
  send("get_ncbi_taxid_from_#{origin}")
end

#get_ncbi_taxonomy ⇒ Object

Get NCBI taxonomy as MiGA::Taxonomy



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

def get_ncbi_taxonomy
  tax_id = get_ncbi_taxid or return

  lineage = { ns: 'ncbi' }
  doc = MiGA::RemoteDataset.download(:ncbi, :taxonomy, tax_id, :xml)
  doc.scan(%r{<Taxon>(.*?)</Taxon>}m).map(&:first).each do |i|
    name = i.scan(%r{<ScientificName>(.*)</ScientificName>}).first.to_a.first
    rank = i.scan(%r{<Rank>(.*)</Rank>}).first.to_a.first
    rank = nil if rank == 'no rank' or rank.empty?
    rank = 'dataset' if lineage.empty? and rank.nil?
    lineage[rank] = name unless rank.nil? or rank.nil?
  end
  MiGA.DEBUG "Got lineage: #{lineage}"
  MiGA::Taxonomy.new(lineage)
end

#get_type_status(metadata) ⇒ Object

Get the type material status and return an (updated) metadata hash.



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# File 'lib/miga/remote_dataset.rb', line 124

def get_type_status(metadata)
  if metadata[:ncbi_asm]
    get_type_status_ncbi_asm metadata
  elsif metadata[:ncbi_nuccore]
    get_type_status_ncbi_nuccore metadata
  else
    metadata
  end
end

#ncbi_asm_json_doc ⇒ Object

Get the JSON document describing an NCBI assembly entry.



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# File 'lib/miga/remote_dataset.rb', line 174

def ncbi_asm_json_doc
  return @_ncbi_asm_json_doc unless @_ncbi_asm_json_doc.nil?

  if db == :assembly && %i[ncbi gtdb].include?(universe)
    metadata[:ncbi_asm] ||= ids.first
  end
  return nil unless metadata[:ncbi_asm]

  ncbi_asm_id = self.class.ncbi_asm_acc2id metadata[:ncbi_asm]
  txt = nil
  3.times do
    txt = self.class.download(:ncbi_summary, :assembly, ncbi_asm_id, :json)
    txt.empty? ? sleep(1) : break
  end
  doc = MiGA::Json.parse(txt, symbolize: false, contents: true)
  return if doc.nil? || doc['result'].nil? || doc['result'].empty?

  @_ncbi_asm_json_doc = doc['result'][ doc['result']['uids'].first ]
end

#save_to(project, name = nil, is_ref = true, metadata_def = {}) ⇒ Object

Save dataset to the MiGA::Project project identified with name. is_ref indicates if it should be a reference dataset, and contains metadata_def. If metadata_def includes metadata_only: true, no input data is downloaded.



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# File 'lib/miga/remote_dataset.rb', line 65

def save_to(project, name = nil, is_ref = true, metadata_def = {})
  name ||= ids.join('_').miga_name
  project = MiGA::Project.new(project) if project.is_a? String
  MiGA::Dataset.exist?(project, name) and
    raise "Dataset #{name} exists in the project, aborting..."
  @metadata = get_metadata(metadata_def)
  udb = @@UNIVERSE[universe][:dbs][db]
  @metadata["#{universe}_#{db}"] = ids.join(',')
  unless @metadata[:metadata_only]
    respond_to?("save_#{udb[:stage]}_to", true) or
      raise "Unexpected error: Unsupported stage #{udb[:stage]} for #{db}."
    send "save_#{udb[:stage]}_to", project, name, udb
  end
  dataset = MiGA::Dataset.new(project, name, is_ref, metadata)
  project.add_dataset(dataset.name)
  unless @metadata[:metadata_only]
    result = dataset.add_result(udb[:stage], true, is_clean: true)
    result.nil? and
      raise 'Empty dataset: seed result not added due to incomplete files.'
    result.clean!
    result.save
  end
  dataset
end

#update_metadata(dataset, metadata = {}) ⇒ Object

Updates the MiGA::Dataset dataset with the remotely available metadata, and optionally the Hash metadata.



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

def update_metadata(dataset, metadata = {})
  metadata = get_metadata(metadata)
  metadata.each { |k, v| dataset.metadata[k] = v }
  dataset.save
end