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

Attributes included from Common::Net

#remote_connection_uri

Class Method Summary collapse

Instance Method Summary collapse

Methods included from Download

#database_hash, #download, #download_headers, #download_opts, #download_params, #download_payload, #download_uri, #universe_hash

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

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 131

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 121

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 123

def ids
  @ids
end

#metadata ⇒ Object (readonly)

Internal metadata hash



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# File 'lib/miga/remote_dataset.rb', line 125

def metadata
  @metadata
end

#universe ⇒ Object (readonly)

Universe of the dataset.



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# File 'lib/miga/remote_dataset.rb', line 119

def universe
  @universe
end

Class Method Details

.download(*params) ⇒ Object

Returns String. The prequired parameters (params) are identical to those of download_opts (see for details)



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# File 'lib/miga/remote_dataset/download.rb', line 37

def download(*params)
  opts = download_opts(*params)
  doc = send(opts[:_fun], opts)

  unless opts[:file].nil?
    ofh = File.open(opts[:file], 'w')
    unless opts[:file] =~ /\.([gb]?z|tar|zip|rar)$/i
      doc = normalize_encoding(doc)
    end
    ofh.print doc
    ofh.close
  end
  doc
end

.download_ftp(opts) ⇒ Object

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



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# File 'lib/miga/remote_dataset/download.rb', line 150

def download_ftp(opts)
  u = @@UNIVERSE[opts[:universe]]
  net_method(:ftp, u[:uri][opts])
end

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

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



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# File 'lib/miga/remote_dataset/download.rb', line 123

def download_get(opts)
  u = @@UNIVERSE[opts[:universe]]
  download_uri(u[:uri][opts], u[:headers] ? u[:headers][opts] : {})
end

.download_net(opts) ⇒ Object

Redirects to download_get or download_ftp, depending on the URI’s protocol



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# File 'lib/miga/remote_dataset/download.rb', line 158

def download_net(opts)
  u = @@UNIVERSE[opts[:universe]]
  if u[:scheme][opts] == 'ftp'
    download_ftp(opts)
  else
    download_get(opts)
  end
end

.download_opts(universe, db, ids, format, file = nil, extra = {}, obj = nil) ⇒ Object

Return hash of options used internally for the getter methods, including by download. The prepared request is for 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. The obj can also be passed as MiGA::RemoteDataset or MiGA::Dataset



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

def download_opts(
      universe, db, ids, format, file = nil, extra = {}, obj = nil)
  universe_hash = @@UNIVERSE[universe]
  database_hash = universe_hash.dig(:dbs, db)
  getter = database_hash[:getter] || :download
  action = database_hash[:method] || universe_hash[:method]

  # Clean IDs
  ids = 

  # Return options
  {
    universe: universe,  db:   db,    ids: ids.is_a?(Array) ? ids : [ids],
    format:   format,    file: file,  obj: obj,
    extra:    (database_hash[:extra] || {}).merge(extra),
    _fun:     :"#{getter}_#{action}"
  }
end

.download_post(opts) ⇒ Object

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



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# File 'lib/miga/remote_dataset/download.rb', line 135

def download_post(opts)
  u = @@UNIVERSE[opts[:universe]]
  uri = u[:uri][opts]
  payload = u[:payload] ? u[:payload][opts] : ''
  headers = u[:headers] ? u[:headers][opts] : {}
  net_method(:post, uri, payload, headers)
end

.download_uri(uri, headers = {}) ⇒ Object

Download the given URI 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 174

def download_uri(uri, headers = {})
  net_method(:get, uri, headers)
end

.download_url(url, headers = {}) ⇒ 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 181

def download_url(url, headers = {})
  download_uri(URI.parse(url), headers)
end

.longest_common_prefix(strs) ⇒ Object

From: github.com/isisAnchalee/Algorithms



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# File 'lib/miga/remote_dataset/download.rb', line 207

def longest_common_prefix(strs)
  return '' if strs.empty?
  min, max = strs.minmax
  idx = min.size.times { |i| break i if min[i] != max[i] }
  min[0...idx]
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 83

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_get(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 (mandatory): String, assembly saved here extra: Hash, passed to download format: String, ignored



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# File 'lib/miga/remote_dataset/download.rb', line 60

def ncbi_asm_get(opts)
  require 'tempfile'
  require 'zip'

  zipped = download(
    :ncbi_datasets_download, :genome, opts[:ids],
    :zip, nil, opts[:extra], opts[:obj]
  )
  zip_tmp = Tempfile.new(['asm', '.zip'], encoding: zipped.encoding.to_s)
  zip_tmp.print(zipped)
  zip_tmp.close

  o = ''
  ofh = opts[:file] ? File.open(opts[:file], 'w') : nil
  Zip::File.open(zip_tmp.path) do |zfh|
    zfh.each do |entry|
      if entry.file? && entry.name =~ /_genomic\.fna$/
        DEBUG "Extracting: #{entry.name}"
        entry.get_input_stream do |ifh|
          cont = MiGA::MiGA.normalize_encoding(ifh.read).chomp + "\n"
          ofh&.print(cont)
          o += cont
        end
      end
    end
  end
  ofh&.close
  File.unlink(zip_tmp.path)
  o
end

.ncbi_gb_get(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_get.



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# File 'lib/miga/remote_dataset/download.rb', line 94

def ncbi_gb_get(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?

  begin
    MiGA::MiGA.DEBUG 'Empty sequence, attempting download as NCBI assembly'
    opts[:format] = :fasta
    ncbi_asm_get(opts)
  rescue => e
    raise e unless opts[:obj]&.metadata&.dig(:ncbi_wgs)
    MiGA::MiGA.DEBUG e.to_s
  end

  MiGA::MiGA.DEBUG 'Empty sequence, attempting download as WGS records'
  a, b = opts[:obj].metadata[:ncbi_wgs].split('-', 2)
  pref = longest_common_prefix([a, b])
  rang = a[pref.size .. -1].to_i .. b[pref.size .. -1].to_i
  ids  = rang.map { |k| "%s%0#{a.size - pref.size}i" % [pref, k] }
  download_rest(opts.merge(universe: :ncbi, db: :nuccore, ids: ids))
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 188

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

  begin
    tree = MiGA::Json.parse(doc, contents: true)
  rescue => e
    sleep 5 # <- Usually caused by busy servers: BLOB ID IS NOT IMPLEMENTED
    DEBUG "RETRYING after: #{e}"
    doc = download(:ncbi_map, dbfrom, id, :json, nil, db: db)
    return if doc.empty?
    tree = MiGA::Json.parse(doc, contents: true)
  end

  tree&.dig(:linksets, 0, :linksetdbs, 0, :links, 0)
end

.ncbi_taxonomy_dump? ⇒ Boolean

Is a local NCBI Taxonomy dump available?

Returns:

  • (Boolean) 


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

def ncbi_taxonomy_dump?
  (@ncbi_taxonomy_names ||= nil) ? true : false
end

.taxonomy_from_ncbi_dump(id) ⇒ Object

Get the MiGA::Taxonomy object for the lineage of the taxon with TaxID id using the local NCBI Taxonomy dump.



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# File 'lib/miga/remote_dataset.rb', line 69

def taxonomy_from_ncbi_dump(id)
  id = id.to_i unless id.is_a? Integer
  MiGA::Taxonomy.new(ns: 'ncbi').tap do |tax|
    while @ncbi_taxonomy_names[id]
      tax << { @ncbi_taxonomy_names[id][1] => @ncbi_taxonomy_names[id][0] }
      id = @ncbi_taxonomy_names[id][2]
    end
  end
end

.UNIVERSE ⇒ Object 



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# File 'lib/miga/remote_dataset/base.rb', line 6

def UNIVERSE
  @@UNIVERSE
end

.use_ncbi_taxonomy_dump(path, cli = nil) ⇒ Object

Path to a directory with a recent NCBI Taxonomy dump to use instead of making API calls to NCBI servers, which can be obtained at: ftp.ncbi.nih.gov/pub/taxonomy/taxdump.tar.gz

The cli parameter, if passed, should be a MiGA::Cli object that will be used to report advance in the reading. Other objects can be passed, minimally supporting the MiGA::Cli#say and MiGA::Cli#advance method interfaces



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# File 'lib/miga/remote_dataset.rb', line 24

def use_ncbi_taxonomy_dump(path, cli = nil)
  raise "Directory doesn't exist: #{path}" unless File.directory?(path)

  # Structure: { TaxID => ["name", "rank", parent TaxID] }
  MiGA::MiGA.DEBUG "Loading NCBI Taxonomy dump: #{path}"
  @ncbi_taxonomy_names = {}

  # Read names.dmp
  File.open(file = File.join(path, 'names.dmp')) do |fh|
    read = 0
    size = File.size(file)
    fh.each do |ln|
      cli&.advance('- names.dmp:', read += ln.size, size)
      row = ln.split(/\t\|\t?/)
      next unless row[3] == 'scientific name'
      @ncbi_taxonomy_names[row[0].to_i] = [row[1].strip]
    end
    cli&.say
  end

  # Read nodes.dmp
  File.open(file = File.join(path, 'nodes.dmp')) do |fh|
    read = 0
    size = File.size(file)
    fh.each do |ln|
      cli&.advance('- nodes.dmp:', read += ln.size, size)
      row = ln.split(/\t\|\t?/)
      child  = row[0].to_i
      parent = row[1].to_i
      @ncbi_taxonomy_names[child][1] = row[2]
      @ncbi_taxonomy_names[child][2] = parent unless parent == child
    end
    cli&.say
  end
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 260

def get_gtdb_taxonomy
  gtdb_genome = metadata[:gtdb_assembly] or return

  doc = MiGA::Json.parse(
    MiGA::RemoteDataset.download(
      :gtdb, :genome, gtdb_genome, 'taxon-history'
    ),
    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 190

def get_metadata(metadata_def = {})
  metadata_def.each { |k, v| @metadata[k] = v }
  return @metadata if @metadata[:bypass_metadata]

  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 219

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 238

def get_ncbi_taxonomy
  tax_id = get_ncbi_taxid or return

  if self.class.ncbi_taxonomy_dump?
    return self.class.taxonomy_from_ncbi_dump(tax_id)
  end

  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.nil? || rank == 'no rank' || rank.empty?
    rank = 'dataset' if lineage.size == 1 && rank.nil?
    lineage[rank] = name unless rank.nil? || name.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 226

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 280

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 154

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 182

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