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, #main_server, #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 67

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 57

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 59

def ids
  @ids
end

#metadata ⇒ Object (readonly)

Internal metadata hash



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# File 'lib/miga/remote_dataset.rb', line 61

def metadata
  @metadata
end

#universe ⇒ Object (readonly)

Universe of the dataset.



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# File 'lib/miga/remote_dataset.rb', line 55

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 83

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 99

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, retrials = 3) ⇒ Object

Translate an NCBI Assembly Accession (acc) to corresponding internal NCBI ID, with up to retrials retrials if the returned JSON document does not conform to the expected format



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# File 'lib/miga/remote_dataset.rb', line 19

def ncbi_asm_acc2id(acc, retrials = 3)
  return acc if acc =~ /^\d+$/

  search_doc = MiGA::Json.parse(
    download(:ncbi_search, :assembly, acc, :json),
    symbolize: false, contents: true
  )
  out = (search_doc['esearchresult']['idlist'] || []).first
  if out.nil?
    raise MiGA::RemoteDataMissingError.new(
      "NCBI Assembly Accession not found: #{acc}"
    )
  end
  return out
rescue JSON::ParserError, MiGA::RemoteDataMissingError => e
  # Note that +JSON::ParserError+ is being rescued because the NCBI backend
  # may in some cases return a malformed JSON response indicating that the
  # "Search Backend failed". The issue with the JSON payload is that it
  # includes two tab characters (\t\t) in the error message, which is not
  # allowed by the JSON specification and causes a parsing error
  # (see https://www.rfc-editor.org/rfc/rfc4627#page-4)

  if retrials <= 0
    raise e
  else
    MiGA::MiGA.DEBUG("#{self}.ncbi_asm_acc2id - RETRY #{retrials}")
    retrials -= 1
    retry
  end
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&.dig('ftppath_genbank')
  if url_dir.nil? || url_dir.empty?
    raise MiGA::RemoteDataMissingError.new(
      "Missing ftppath_genbank in NCBI Assembly JSON"
    )
  end

  url = '%s/%s_genomic.fna.gz' % [url_dir, File.basename(url_dir)]
  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)
  # Simply use defaults, but ensure that the URL can be properly formed
  o = download_rest(opts.merge(universe: :ncbi, db: :nuccore))
  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 119

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 191

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 126

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
  when :seqcode
    # Taxonomy already defined
    # Copy IDs over to allow additional metadata linked
    @metadata[:ncbi_asm] = @metadata[:seqcode_asm]
    @metadata[:ncbi_nuccore] = @metadata[:seqcode_nuccore]
  end

  if metadata[:get_ncbi_taxonomy]
    tax = get_ncbi_taxonomy
    tax&.add_alternative(@metadata[:tax].dup, false) if @metadata[:tax]
    @metadata[:tax] = tax
  end
  @metadata[:get_ncbi_taxonomy] = nil
  @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 154

def get_ncbi_taxid
  send("get_ncbi_taxid_from_#{universe}")
end

#get_ncbi_taxonomy ⇒ Object

Get NCBI taxonomy as MiGA::Taxonomy



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# File 'lib/miga/remote_dataset.rb', line 173

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 161

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 211

def ncbi_asm_json_doc
  return @_ncbi_asm_json_doc unless @_ncbi_asm_json_doc.nil?

  if db == :assembly && i[ncbi gtdb seqcode].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 ]
  url_dir = @_ncbi_asm_json_doc['ftppath_genbank']
  if url_dir
    metadata[:web_assembly_gz] ||=
      '%s/%s_genomic.fna.gz' % [url_dir, File.basename(url_dir)]
  end
  @_ncbi_asm_json_doc
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 90

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 118

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