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, DEBUG, DEBUG_OFF, DEBUG_ON, DEBUG_TRACE_OFF, DEBUG_TRACE_ON, FULL_VERSION, LONG_VERSION, VERSION, VERSION_DATE, initialized?, #result_files_exist?

Methods included from Common::Path

#root_path, #script_path

Methods included from Common::Format

#clean_fasta_file, #seqs_length, #tabulate

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 25

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]}"
  # 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 17

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 19

def ids
  @ids
end

#metadata ⇒ Object (readonly)

Internal metadata hash



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# File 'lib/miga/remote_dataset.rb', line 21

def metadata
  @metadata
end

#universe ⇒ Object (readonly)

Universe of the dataset.



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

def universe
  @universe
end

Class Method Details

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



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

def download(universe, db, ids, format, file = nil, extra = [])
  ids = [ids] unless ids.is_a? Array
  case @@UNIVERSE[universe][:method]
  when :rest
    doc = download_rest(universe, db, ids, format, extra)
  when :net
    doc = download_net(universe, db, ids, format, extra)
  end
  unless file.nil?
    ofh = File.open(file, 'w')
    ofh.print doc
    ofh.close
  end
  doc
end

.download_rest(universe, db, ids, format, extra = []) ⇒ Object Also known as: download_net

Download data using a REST method from the universe in the database db with IDs ids and in format. Additional URL parameters can be passed using extra. Returns the doc as String.



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

def download_rest(universe, db, ids, format, extra = [])
  u = @@UNIVERSE[universe]
  url = sprintf(u[:url], db, ids.join(","), format, *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 50

def download_url(url)
  doc = ''
  @timeout_try = 0
  begin
    open(url, read_timeout: 600) { |f| doc = f.read }
  rescue => e
    @timeout_try += 1
    raise e if @timeout_try >= 3
    retry
  end
  doc
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 66

def ncbi_map(id, dbfrom, db)
  doc = download(:ncbi_map, dbfrom, id, :json, nil, [db])
  return if doc.empty?
  tree = JSON.parse(doc, symbolize_names: 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 9

def UNIVERSE ; @@UNIVERSE ; end

Instance Method Details

#get_metadata(metadata_def = {}) ⇒ Object

Get metadata from the remote location.



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# File 'lib/miga/remote_dataset.rb', line 77

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
  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 89

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 108

def get_ncbi_taxonomy
  tax_id = get_ncbi_taxid
  lineage = {}
  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::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 96

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

#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.



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# File 'lib/miga/remote_dataset.rb', line 45

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(',')
  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
  dataset = MiGA::Dataset.new(project, name, is_ref, metadata)
  project.add_dataset(dataset.name)
  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
  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 69

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