Class: Bio::TogoWS::REST

Inherits:
Object show all
Includes:
AccessWait
Defined in:
lib/bio/io/togows.rb

Overview

Description

Bio::TogoWS::REST is a REST client for the TogoWS web service.

Details of the service are desribed in the following URI.

Examples

For light users, class methods can be used.

print Bio::TogoWS::REST.entry('genbank', 'AF237819')
print Bio::TogoWS::REST.search('uniprot', 'lung cancer')

For heavy users, an instance of the REST class can be created, and using the instance is more efficient than using class methods.

t = Bio::TogoWS::REST.new
print t.entry('genbank', 'AF237819')
print t.search('uniprot', 'lung cancer')

References

Constant Summary collapse

BASE_URI =

URI of the TogoWS REST service

'http://togows.dbcls.jp/'.freeze
DEFAULT_RETRIEVAL_DATABASES =

preset default databases used by the retrieve method.

%w( genbank uniprot embl ddbj dad )

Constants included from AccessWait

AccessWait::TOGOWS_ACCESS_WAIT, AccessWait::TOGOWS_ACCESS_WAIT_MAX

Instance Attribute Summary collapse

Class Method Summary collapse

Instance Method Summary collapse

Constructor Details

#initialize(uri = BASE_URI) ⇒ REST

Creates a new object.

Arguments:

  • (optional) uri: String or URI object

Returns

new object



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# File 'lib/bio/io/togows.rb', line 141

def initialize(uri = BASE_URI)
  uri = URI.parse(uri) unless uri.kind_of?(URI)
  @pathbase = uri.path
  @pathbase = '/' + @pathbase unless /\A\// =~ @pathbase
  @pathbase = @pathbase + '/' unless /\/\z/ =~ @pathbase
  @http = Bio::Command.new_http(uri.host, uri.port)
  @header = {
    'User-Agent' => "BioRuby/#{Bio::BIORUBY_VERSION_ID}"
  }
  @debug = false
end

Instance Attribute Details

#debug ⇒ Object

If true, shows debug information to $stderr.



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# File 'lib/bio/io/togows.rb', line 154

def debug
  @debug
end

Class Method Details

.convert(*arg) ⇒ Object

The same as Bio::TogoWS::REST#convert.



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# File 'lib/bio/io/togows.rb', line 345

def self.convert(*arg)
  self.new.convert(*arg)
end

.entry(*arg) ⇒ Object

The same as Bio::TogoWS::REST#entry.



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# File 'lib/bio/io/togows.rb', line 335

def self.entry(*arg)
  self.new.entry(*arg)
end

.entry_database_list(*arg) ⇒ Object

The same as Bio::TogoWS::REST#entry_database_list



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# File 'lib/bio/io/togows.rb', line 355

def self.entry_database_list(*arg)
  self.new.entry_database_list(*arg)
end

.retrieve(*arg) ⇒ Object

The same as Bio::TogoWS::REST#retrieve.



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# File 'lib/bio/io/togows.rb', line 350

def self.retrieve(*arg)
  self.new.retrieve(*arg)
end

.search(*arg) ⇒ Object

The same as Bio::TogoWS::REST#search.



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# File 'lib/bio/io/togows.rb', line 340

def self.search(*arg)
  self.new.search(*arg)
end

.search_database_list(*arg) ⇒ Object

The same as Bio::TogoWS::REST#search_database_list



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# File 'lib/bio/io/togows.rb', line 360

def self.search_database_list(*arg)
  self.new.search_database_list(*arg)
end

Instance Method Details

#convert(data, inputformat, format) ⇒ Object

Data format conversion.

Example:

t = Bio::TogoWS::REST.new
blast_string = File.read('test.blastn')
t.convert(blast_string, 'blast', 'gff')

Arguments:

  • (required) text: (String) input data

  • (required) inputformat: (String) data source format

  • (required) format: (String) output format

Returns

String or nil



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# File 'lib/bio/io/togows.rb', line 310

def convert(data, inputformat, format)
  response = post_data(data, 'convert', "#{inputformat}.#{format}")

  prepare_return_value(response)
end

#entry(database, ids, format = nil, field = nil) ⇒ Object

Retrieves entries corresponding to the specified IDs.

Example:

t = Bio::TogoWS::REST.new
kuma = t.entry('genbank', 'AF237819')
# multiple IDs at a time
misc = t.entry('genbank', [ 'AF237819', 'AF237820' ])
# with format change
p53 = t.entry('uniprot', 'P53_HUMAN', 'fasta')

Arguments:

  • (required) database: (String) database name

  • (required) ids: (String) an entry ID, or (Array containing String) IDs. Note that strings containing “,” are regarded as multiple IDs.

  • (optional) format: (String) format. nil means the default format (differs depending on the database).

  • (optional) field: (String) gets only the specified field if not nil

Returns

String or nil



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# File 'lib/bio/io/togows.rb', line 241

def entry(database, ids, format = nil, field = nil)
  begin
    a = ids.to_ary
  rescue NoMethodError
    ids = ids.to_s
  end

  arg = [ 'entry', database ]
  if a then
    b = a.dup
    (a.size - 1).downto(1) { |i| b.insert(i, :",") }
    arg.concat b
  else
    arg.push ids
  end

  arg.push field if field
  arg[-1] = "#{arg[-1]}.#{format}" if format
  response = get(*arg)

  prepare_return_value(response)
end

#entry_database_list ⇒ Object

Returns list of available databases in the entry service.

Returns

Array containing String



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# File 'lib/bio/io/togows.rb', line 319

def entry_database_list
  database_list('entry')
end

#internal_http ⇒ Object

Debug purpose only. Returns Net::HTTP object used inside the object. The method will be changed in the future if the implementation of this class is changed.



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# File 'lib/bio/io/togows.rb', line 160

def internal_http
  @http
end

#retrieve(ids, hash = {}) ⇒ Object

Intelligent version of the entry method. If two or more databases are specified, sequentially tries them until valid entry is obtained.

If database is not specified, preset default databases are used. See DEFAULT_RETRIEVAL_DATABASES for details.

When multiple IDs and multiple databases are specified, sequentially tries each IDs. Note that results with no hits found or with server errors are regarded as void strings. Also note that data format of the result entries can be different from entries to entries.

Arguments:

  • (required) ids: (String) an entry ID, or (Array containing String) IDs. Note that strings containing “,”

  • (optional) hash: (Hash) options below can be passed as a hash.

    • (optional) :database: (String) database name, or (Array containing String) database names.

    • (optional) :format: (String) format

    • (optional) :field: (String) gets only the specified field

Returns

String or nil



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# File 'lib/bio/io/togows.rb', line 186

def retrieve(ids, hash = {})
  begin
    a = ids.to_ary
  rescue NoMethodError
    ids = ids.to_s
  end
  ids = a.join(',') if a
  ids = ids.split(',')

  dbs = hash[:database] || DEFAULT_RETRIEVAL_DATABASES
  begin
    dbs.to_ary
  rescue NoMethodError
    dbs = dbs.to_s.empty? ? [] : [ dbs.to_s ]
  end
  return nil if dbs.empty? or ids.empty?

  if dbs.size == 1 then
    return entry(dbs[0], ids, hash[:format], hash[:field])
  end

  results = []
  ids.each do |idstr|
    dbs.each do |dbstr|
      r = entry(dbstr, idstr, hash[:format], hash[:field])
      if r and !r.strip.empty? then
        results.push r
        break
      end
    end #dbs.each
  end #ids.each
  
  results.join('')
end

#search(database, query, offset = nil, limit = nil, format = nil) ⇒ Object

Database search. Format of the search term string follows the Common Query Language.

Example:

t = Bio::TogoWS::REST.new
print t.search('uniprot', 'lung cancer')
# only get the 10th and 11th hit ID
print t.search('uniprot', 'lung cancer', 10, 2)
# with json format
print t.search('uniprot', 'lung cancer', 10, 2, 'json')

Arguments:

  • (required) database: (String) database name

  • (required) query: (String) query string

  • (optional) offset: (Integer) offset in search results.

  • (optional) limit: (Integer) max. number of returned results. If offset is not nil and the limit is nil, it is set to 1.

  • (optional) format: (String) format. nil means the default format.

Returns

String or nil



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# File 'lib/bio/io/togows.rb', line 285

def search(database, query, offset = nil, limit = nil, format = nil)
  arg = [ 'search', database, query ]
  if offset then
    limit ||= 1
    arg.concat [ "#{offset}", :",", "#{limit}" ]
  end
  arg[-1] = "#{arg[-1]}.#{format}" if format
  response = get(*arg)

  prepare_return_value(response)
end

#search_database_list ⇒ Object

Returns list of available databases in the search service.

Returns

Array containing String



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# File 'lib/bio/io/togows.rb', line 326

def search_database_list
  database_list('search')
end