wwood-bioruby 1.2.11

data/lib/bio/io/flatfile/splitter.rb

@@ -0,0 +1,297 @@
+#
+# = bio/io/flatfile/splitter.rb - input data splitter for FlatFile
+#
+#   Copyright (C) 2001-2008 Naohisa Goto <ng@bioruby.org>
+#
+# License:: The Ruby License
+#
+#  $Id:$
+#
+#
+# See documents for Bio::FlatFile::Splitter and Bio::FlatFile.
+#
+
+require 'bio/io/flatfile'
+
+module Bio
+
+  class FlatFile
+
+    # The Bio::FlatFile::Splitter is a namespace for flatfile splitters.
+    # Each splitter is a class to get entries from a buffered input stream.
+    #
+    # It is internally called in Bio::FlatFile.
+    # Normally, users do not need to use it directly.
+    module Splitter
+
+      # This is a template of splitter.
+      class Template
+        # Creates a new splitter.
+        def initialize(klass, bstream)
+          @dbclass = klass
+          @stream = bstream
+          @entry_pos_flag = nil
+        end
+
+        # skips leader of the entry.
+        def skip_leader
+          raise NotImplementedError
+        end
+
+        # rewind the stream
+        def rewind
+          @stream.rewind
+        end
+
+        # Gets entry as a string. (String)
+        def get_entry
+          raise NotImplementedError
+        end
+
+        # Gets entry as a data class's object
+        def get_parsed_entry
+          ent = get_entry
+          if ent then
+            self.parsed_entry = dbclass.new(ent)
+          else
+            self.parsed_entry = ent
+          end
+          parsed_entry
+        end
+
+        # the last entry string read from the stream (String)
+        attr_reader :entry
+
+        # The last parsed entry read from the stream (entry data class).
+        # Note that it is valid only after get_parsed_entry is called,
+        # and the get_entry may not affect the parsed_entry attribute.
+        attr_reader :parsed_entry
+
+        # a flag to write down entry start and end positions
+        attr_accessor :entry_pos_flag
+
+        # start position of the entry
+        attr_reader :entry_start_pos
+
+        # (end position of the entry) + 1
+        attr_reader :entry_ended_pos
+
+        #--
+        #private
+        #
+        ## to prevent warning message "warning: private attribute?",
+        ## private attributes are explicitly declared.
+        #++
+
+        # entry data class
+        attr_reader :dbclass
+        private     :dbclass
+
+        # input stream
+        attr_reader :stream
+        private     :stream
+
+        # the last entry string read from the stream
+        attr_writer :entry
+        private     :entry=
+
+        # the last entry as a parsed data object
+        attr_writer :parsed_entry
+        private     :parsed_entry=
+
+        # start position of the entry
+        attr_writer :entry_start_pos
+        private     :entry_start_pos=
+
+        # (end position of the entry) + 1
+        attr_writer :entry_ended_pos
+        private     :entry_ended_pos=
+
+        # Does stream.pos if entry_pos_flag is not nil.
+        # Otherwise, returns nil.
+        def stream_pos
+          entry_pos_flag ? stream.pos : nil
+        end
+        private :stream_pos
+      end #class Template
+
+      # Default splitter.
+      # It sees following constants in the given class.
+      # DELIMITER:: (String) delimiter indicates the end of a entry.
+      # FLATFILE_HEADER:: (String) start of a entry, located on head of a line.
+      # DELIMITER_OVERRUN:: (Integer) excess read size included in DELIMITER.
+      #
+      class Default < Template
+        # Creates a new splitter.
+        # klass:: database class
+        # bstream:: input stream. It must be a BufferedInputStream object.
+        def initialize(klass, bstream)
+          super(klass, bstream)
+
+          @delimiter = klass::DELIMITER rescue nil
+          @header = klass::FLATFILE_HEADER rescue nil
+          # for specific classes' benefit
+          unless header
+            if (defined?(Bio::GenBank) and klass == Bio::GenBank) or
+                (defined?(Bio::GenPept) and klass == Bio::GenPept)
+              @header = 'LOCUS '
+            end
+          end
+          @delimiter_overrun = klass::DELIMITER_OVERRUN rescue nil
+        end
+
+        # (String) delimiter indicates the end of a entry.
+        attr_accessor :delimiter
+
+        # (String) start of a entry, located on head of a line.
+        attr_accessor :header
+
+        # (Integer) excess read data size included in delimiter.
+        attr_accessor :delimiter_overrun
+        
+        # Skips leader of the entry.
+        #
+        # If @header is not nil, it reads till the contents of @header
+        # comes at the head of a line.
+        # If correct FLATFILE_HEADER is found, returns true.
+        # Otherwise, returns nil.
+        def skip_leader
+          if @header then
+            data = ''
+            while s = stream.gets(@header)
+              data << s
+              if data.split(/[\r\n]+/)[-1] == @header then
+                stream.ungets(@header)
+                return true
+              end
+            end
+            # @header was not found. For safety,
+            # pushes back data with removing white spaces in the head.
+            data.sub(/\A\s+/, '')
+            stream.ungets(data)
+            return nil
+          else
+            stream.skip_spaces
+            return nil
+          end
+        end
+
+        # gets a entry
+        def get_entry
+          p0 = stream_pos()
+          e  = stream.gets(@delimiter)
+          if e and @delimiter_overrun then
+            if e[-@delimiter.size, @delimiter.size ] == @delimiter then
+              overrun = e[-@delimiter_overrun, @delimiter_overrun]
+              e[-@delimiter_overrun, @delimiter_overrun] = ''
+              stream.ungets(overrun)
+            end
+          end
+          p1 = stream_pos()
+          self.entry_start_pos = p0
+          self.entry = e
+          self.entry_ended_pos = p1
+          return entry
+        end
+      end #class Defalult
+
+
+      # A splitter for line oriented text data.
+      #
+      # The given class's object must have following methods.
+      #   Klass#add_header_line(line)
+      #   Klass#add_line(line)
+      # where 'line' is a string. They normally returns self.
+      # If the line is not suitable to add to the current entry,
+      # nil or false should be returned.
+      # Then, the line is treated as (for add_header_line) the entry data
+      # or (for add_line) the next entry's data.
+      #
+      class LineOriented < Template
+        # Creates a new splitter.
+        # klass:: database class
+        # bstream:: input stream. It must be a BufferedInputStream object.
+        def initialize(klass, bstream)
+          super(klass, bstream)
+          self.flag_to_fetch_header = true
+        end
+
+        # do nothing
+        def skip_leader
+          nil
+        end
+
+        # get an entry and return the entry as a string
+        def get_entry
+          if e = get_parsed_entry then
+            entry
+          else
+            e
+          end
+        end
+
+        # get an entry and return the entry as a data class object
+        def get_parsed_entry
+          p0 = stream_pos()
+          ent = @dbclass.new()
+
+          lines = []
+          line_overrun = nil
+
+          if flag_to_fetch_header then
+            while line = stream.gets("\n")
+              unless ent.add_header_line(line) then
+                line_overrun = line
+                break
+              end
+              lines.push line
+            end
+            stream.ungets(line_overrun) if line_overrun
+            line_overrun = nil
+            self.flag_to_fetch_header = false
+          end
+              
+          while line = stream.gets("\n")
+            unless ent.add_line(line) then
+              line_overrun = line
+              break
+            end
+            lines.push line
+          end
+          stream.ungets(line_overrun) if line_overrun
+          p1 = stream_pos()
+
+          return nil if lines.empty?
+
+          self.entry_start_pos = p0
+          self.entry = lines.join('')
+          self.parsed_entry = ent
+          self.entry_ended_pos = p1
+
+          return ent
+        end
+
+        # rewinds the stream
+        def rewind
+          ret = super
+          self.flag_to_fetch_header = true
+          ret
+        end
+
+        #--
+        #private methods / attributes
+        #++
+
+        # flag to fetch header
+        attr_accessor :flag_to_fetch_header
+        private       :flag_to_fetch_header
+        private       :flag_to_fetch_header=
+
+      end #class LineOriented
+
+    end #module Splitter
+
+  end #class FlatFile
+end #module Bio
+
+

data/lib/bio/io/higet.rb

@@ -0,0 +1,73 @@
+#
+# = bio/io/higet.rb - SOAP interface for HGC HiGet
+#
+# Copyright::  Copyright (C) 2005 Toshiaki Katayama <k@bioruby.org>
+#
+# $Id: higet.rb,v 1.3 2006/09/19 05:46:22 k Exp $
+#
+
+require 'bio/io/soapwsdl'
+
+module Bio
+class HGC
+
+# == Description
+#
+# Interface for the HiGet service provided by Human Genome Center (HGC), Japan.
+# HiGet performs full-text search against various biological databases.
+#
+# == References
+#
+# * http://higet.hgc.jp/
+#
+class HiGet < Bio::SOAPWSDL
+
+  SERVER_URI = "http://higet.hgc.jp/soap/higet.wsdl"
+
+  def initialize(wsdl = nil)
+    super(wsdl || SERVER_URI)
+  end
+
+  def higet_in_fasta(db, entries)
+    self.higet(db, entries, "-d fasta")
+  end
+
+  def higet_in_xml(db, entries)
+    self.higet(db, entries, "-d xml")
+  end
+
+end
+
+end # HGC
+end # Bio
+
+
+if __FILE__ == $0
+
+  begin
+    require 'pp'
+    alias p pp
+  rescue LoadError
+  end
+
+  puts ">>> Bio::HGC::HiGet"
+  serv = Bio::HGC::HiGet.new
+  serv.log = STDERR
+
+  puts "### HiFind"
+  puts serv.hifind("genbank", "human kinase", "-l 10")
+
+  puts "### HiGet"
+  puts serv.higet("genbank", "S40289", "")
+
+  puts "### HiGet (FASTA)"
+  puts serv.higet("genbank", "S40289", "-d fasta")
+
+  puts "### HiGet higet_in_fasta"
+  puts serv.higet_in_fasta("genbank", "S40289")
+
+  puts "### HiGet higet_in_xml"
+  puts serv.higet_in_xml("genbank", "S40289")
+
+end
+

data/lib/bio/io/hinv.rb

@@ -0,0 +1,442 @@
+#
+# = bio/io/hinv.rb - H-invDB web service (REST) client module
+#
+# Copyright::  Copyright (C) 2008 Toshiaki Katayama <k@bioruby.org>
+# License::    The Ruby License
+#
+# $Id:$
+#
+
+require 'bio/command'
+require 'rexml/document'
+
+module Bio
+
+  # = Bio::Hinv
+  #
+  # Accessing the H-invDB web services.
+  #
+  # * http://www.h-invitational.jp/
+  # * http://www.jbirc.aist.go.jp/hinv/hws/doc/index.html
+  #
+  class Hinv
+
+    BASE_URI = "http://www.jbirc.aist.go.jp/hinv/hws/"
+
+    module Common
+      def query(options = nil)
+        response = Bio::Command.post_form(@url, options)
+        @result = response.body
+        @xml = REXML::Document.new(@result)
+      end
+    end
+
+
+    # Bio::Hinv.acc2hit("BC053657")  # => "HIT000053961"
+    def self.acc2hit(acc)
+      serv = Acc2hit.new
+      serv.query("acc" => acc)
+      serv.result
+    end
+
+    # Bio::Hinv.hit2acc("HIT000022181")  # => "AK097327"
+    def self.hit2acc(hit)
+      serv = Hit2acc.new
+      serv.query("hit" => hit)
+      serv.result
+    end
+
+    # Bio::Hinv.hit_cnt  # => 187156
+    def self.hit_cnt
+      serv = HitCnt.new
+      serv.query
+      serv.result
+    end
+
+    # Bio::Hinv.hit_definition("HIT000000001")  # => "Rho guanine ..."
+    def self.hit_definition(hit)
+      serv = HitDefinition.new
+      serv.query("hit" => hit)
+      serv.result
+    end
+
+    # Bio::Hinv.hit_pubmedid("HIT000053961")  # => [7624364, 11279095, ... ]
+    def self.hit_pubmedid(hit)
+      serv = HitPubmedId.new
+      serv.query("hit" => hit)
+      serv.result
+    end
+
+    # Bio::Hinv.hit_xml("HIT000000001")  # => "<?xml version="1.0" ..."
+    def self.hit_xml(hit)
+      serv = Bio::Hinv::HitXML.new
+      serv.query("hit" => hit)
+      puts serv.result
+    end
+
+    # Bio::Hinv.hix2hit("HIX0000004")  # => ["HIT000012846", ... ]
+    def self.hix2hit(hix)
+      serv = Bio::Hinv::Hix2hit.new
+      serv.query("hix" => hix)
+      serv.result
+    end
+
+    # Bio::Hinv.hix_cnt  # => 36073
+    def self.hix_cnt
+      serv = HixCnt.new
+      serv.query
+      serv.result
+    end
+
+    # Bio::Hinv.hix_represent("HIX0000001")  # => "HIT000022181"
+    def self.hix_represent(hix)
+      serv = HixRepresent.new
+      serv.query("hix" => hix)
+      serv.result
+    end
+
+    # Bio::Hinv.id_search("HIT00002218*")  # => ["HIT000022181", ... ]
+    def self.id_search(query)
+      serv = IdSearch.new
+      serv.query("query" => query)
+      serv.result
+    end
+
+    # Bio::Hinv.keyword_search("HIT00002218*")  # => ["HIT000022181", ... ]
+    def self.keyword_search(query)
+      serv = KeywordSearch.new
+      serv.query("query" => query)
+      serv.result
+    end
+
+
+    # serv = Bio::Hinv::Acc2hit.new
+    # serv.query("acc" => "BC053657")
+    # puts serv.result
+    class Acc2hit
+      include Common
+
+      def initialize
+        @url = BASE_URI + "acc2hit.php"
+      end
+
+      # <?xml version='1.0' encoding='UTF-8'?>
+      # <H-Inv>
+      #  <H-INVITATIONAL-ID>HIT000053961</H-INVITATIONAL-ID>
+      # </H-Inv>
+      def result
+        @xml.elements['//H-INVITATIONAL-ID'].text
+      end
+    end
+
+    # serv = Bio::Hinv::Hit2acc.new
+    # serv.query("hit" => "HIT000022181")
+    # puts serv.result
+    class Hit2acc
+      include Common
+
+      def initialize
+        @url = BASE_URI + "hit2acc.php"
+      end
+
+      # <?xml version='1.0' encoding='UTF-8'?>
+      # <H-Inv>
+      #  <ACCESSION-NO>AK097327</ACCESSION-NO>
+      # </H-Inv>
+      def result
+        @xml.elements['//ACCESSION-NO'].text
+      end
+    end
+
+    # serv = Bio::Hinv::HitCnt.new
+    # serv.query
+    # puts serv.result
+    class HitCnt
+      include Common
+
+      def initialize
+        @url = BASE_URI + "hit_cnt.php"
+      end
+
+      # <?xml version='1.0' encoding='UTF-8'?>
+      # <H-Inv>
+      #  <TRANSCRIPT_CNT>187156</TRANSCRIPT_CNT>
+      # </H-Inv>
+      def result
+        @xml.elements['//TRANSCRIPT_CNT'].text.to_i
+      end
+    end
+
+    # serv = Bio::Hinv::HitDefinition.new
+    # serv.query("hit" => "HIT000000001")
+    # puts serv.result
+    # puts serv.data_source_definition
+    # puts serv.cdna_rep_h_invitational
+    # puts serv.cdna_splicing_isoform_curation
+    # puts serv.data_source_db_reference_protein_motif_id
+    # puts serv.data_source_identity
+    # puts serv.data_source_coverage
+    # puts serv.data_source_homologous_species
+    # puts serv.data_source_similarity_category
+    class HitDefinition
+      include Common
+
+      def initialize
+        @url = BASE_URI + "hit_definition.php"
+      end
+
+      # <?xml version='1.0' encoding='UTF-8'?>
+      # <H-Inv>
+      #  <HIT_FUNCTION>
+      #   <H-INVITATIONAL-ID>HIT000000001</H-INVITATIONAL-ID>
+      #   <DATA-SOURCE_DEFINITION>Rho guanine nucleotide exchange factor 10.</DATA-SOURCE_DEFINITION>
+      #   <CDNA_REP-H-INVITATIONAL>Representative transcript</CDNA_REP-H-INVITATIONAL>
+      #   <CDNA_SPLICING-ISOFORM_CURATION></CDNA_SPLICING-ISOFORM_CURATION>
+      #   <DATA-SOURCE_DB-REFERENCE_PROTEIN-MOTIF-ID>NP_055444</DATA-SOURCE_DB-REFERENCE_PROTEIN-MOTIF-ID>
+      #   <DATA-SOURCE_IDENTITY>100.0</DATA-SOURCE_IDENTITY>
+      #   <DATA-SOURCE_COVERAGE>100.0</DATA-SOURCE_COVERAGE>
+      #   <DATA-SOURCE_HOMOLOGOUS_SPECIES>Homo sapiens</DATA-SOURCE_HOMOLOGOUS_SPECIES>
+      #   <DATA-SOURCE_SIMILARITY-CATEGORY>Identical to known human protein(Category I).</DATA-SOURCE_SIMILARITY-CATEGORY>
+      #  </HIT_FUNCTION>
+      # </H-Inv>
+      def result
+        @xml.elements['//DATA-SOURCE_DEFINITION'].text
+      end
+      alias :data_source_definition :result
+
+      def cdna_rep_h_invitational
+        @xml.elements['//CDNA_REP-H-INVITATIONAL'].text
+      end
+      def cdna_splicing_isoform_curation
+        @xml.elements['//CDNA_SPLICING-ISOFORM_CURATION'].text
+      end
+      def data_source_db_reference_protein_motif_id
+        @xml.elements['//DATA-SOURCE_DB-REFERENCE_PROTEIN-MOTIF-ID'].text
+      end
+      def data_source_identity
+        @xml.elements['//DATA-SOURCE_IDENTITY'].text.to_f
+      end
+      def data_source_coverage
+        @xml.elements['//DATA-SOURCE_COVERAGE'].text.to_f
+      end
+      def data_source_homologous_species
+        @xml.elements['//DATA-SOURCE_HOMOLOGOUS_SPECIES'].text
+      end
+      def data_source_similarity_category
+        @xml.elements['//DATA-SOURCE_SIMILARITY-CATEGORY'].text
+      end
+    end
+
+    # serv = Bio::Hinv::HitPubmedId.new
+    # serv.query("hit" => "HIT000053961")
+    # puts serv.result
+    class HitPubmedId
+      include Common
+
+      def initialize
+        @url = BASE_URI + "hit_pubmedid.php"
+      end
+
+      # <?xml version='1.0' encoding='UTF-8'?>
+      # <H-Inv>
+      #  <CDNA_DB-REFERENCE_PUBMED>7624364</CDNA_DB-REFERENCE_PUBMED>
+      #  <CDNA_DB-REFERENCE_PUBMED>11279095</CDNA_DB-REFERENCE_PUBMED>
+      #  <CDNA_DB-REFERENCE_PUBMED>15489334</CDNA_DB-REFERENCE_PUBMED>
+      # </H-Inv>
+      def result
+        list = []
+        @xml.elements.each('//CDNA_DB-REFERENCE_PUBMED') do |e|
+          list << e.text.to_i
+        end
+        return list
+      end
+    end
+
+    # serv = Bio::Hinv::HitXML.new
+    # serv.query("hit" => "HIT000000001")
+    # puts serv.result
+    class HitXML
+      include Common
+
+      def initialize
+        @url = BASE_URI + "hit_xml.php"
+      end
+
+      # <?xml version="1.0" standalone="yes" ?>
+      # <H-Inv>
+      #  <cDNAXML>
+      #  <CLUSTER-ID>HIX0021591</CLUSTER-ID>
+      #  <CLUSTER-ID-VERSION>HIX0021591.11</CLUSTER-ID-VERSION>
+      #  <H-INVITATIONAL-ID>HIT000000001</H-INVITATIONAL-ID>
+      #    :
+      #    </PROBE-MAPPING>
+      #   </EXPRESSION>
+      #  </cDNAXML>
+      # </H-Inv>
+      def result
+        @result
+      end
+    end
+
+    # serv = Bio::Hinv::Hix2hit.new
+    # serv.query("hix" => "HIX0000004")
+    # puts serv.result
+    class Hix2hit
+      include Common
+
+      def initialize
+        @url = BASE_URI + "hix2hit.php"
+      end
+
+      # <?xml version='1.0' encoding='UTF-8'?>
+      # <H-Inv>
+      #  <H-INVITATIONAL-ID>HIT000012846</H-INVITATIONAL-ID>
+      #  <H-INVITATIONAL-ID>HIT000022124</H-INVITATIONAL-ID>
+      #  <H-INVITATIONAL-ID>HIT000007722</H-INVITATIONAL-ID>
+      #    :
+      #  <H-INVITATIONAL-ID>HIT000262478</H-INVITATIONAL-ID>
+      # </H-Inv>
+      def result
+        list = []
+        @xml.elements.each('//H-INVITATIONAL-ID') do |e|
+          list << e.text
+        end
+        return list
+      end
+    end
+
+    # serv = Bio::Hinv::HixCnt.new
+    # serv.query
+    # puts serv.result
+    class HixCnt
+      include Common
+
+      def initialize
+        @url = BASE_URI + "hix_cnt.php"
+      end
+
+      # <?xml version='1.0' encoding='UTF-8'?>
+      # <H-Inv>
+      #  <LOCUS_CNT>36073</LOCUS_CNT>
+      # </H-Inv>
+      def result
+        @xml.elements['//LOCUS_CNT'].text.to_i
+      end
+    end
+
+    # serv = Bio::Hinv::HixRepresent.new
+    # serv.query("hix" => "HIX0000001")
+    # puts serv.result
+    # puts serv.rep_h_invitational_id
+    # puts serv.rep_accession_no
+    class HixRepresent
+      include Common
+
+      def initialize
+        @url = BASE_URI + "hix_represent.php"
+      end
+
+      # <?xml version='1.0' encoding='UTF-8'?>
+      # <H-Inv>
+      #  <LOCUS>
+      #   <CLUSTER-ID>HIX0000001</CLUSTER-ID>
+      #   <REP-H-INVITATIONAL-ID>HIT000022181</REP-H-INVITATIONAL-ID>
+      #   <REP-ACCESSION-NO>AK097327</REP-ACCESSION-NO>
+      #  </LOCUS>
+      # </H-Inv>
+      def result
+        @xml.elements['//REP-H-INVITATIONAL-ID'].text
+      end
+      alias :rep_h_invitational_id :result
+
+      def rep_accession_no
+        @xml.elements['//REP-ACCESSION-NO'].text
+      end
+    end
+
+    # example at "http://www.jbirc.aist.go.jp/hinv/hws/doc/index_jp.html"
+    # is for hit_xml.php (not for hix_xml.php)
+    class HixXML
+    end
+
+    # serv = Bio::Hinv::KeywordSearch.new
+    # serv.query("query" => "HIT00002218*", "start" => 1, "end" => 100)
+    # puts serv.result
+    # puts serv.size
+    # puts serv.start
+    # puts serv.end
+    class KeywordSearch
+      include Common
+
+      def initialize
+        @url = BASE_URI + "keyword_search.php"
+      end
+
+      def query(hash = {})
+        default = {
+          "start" => 1,
+          "end" => 100
+        }
+        options = default.update(hash)
+        super(options)
+      end
+
+      # <?xml version='1.0' encoding='UTF-8'?>
+      # <HINVDB_SEARCH>
+      #  <QUERY>HIT00002218*</QUERY>
+      #  <SIZE>8</SIZE>
+      #  <START>1</START>
+      #  <END>8</END>
+      #  <H-INVITATIONAL-ID>HIT000022180</H-INVITATIONAL-ID>
+      #  <H-INVITATIONAL-ID>HIT000022181</H-INVITATIONAL-ID>
+      #  <H-INVITATIONAL-ID>HIT000022183</H-INVITATIONAL-ID>
+      #  <H-INVITATIONAL-ID>HIT000022184</H-INVITATIONAL-ID>
+      #  <H-INVITATIONAL-ID>HIT000022185</H-INVITATIONAL-ID>
+      #  <H-INVITATIONAL-ID>HIT000022186</H-INVITATIONAL-ID>
+      #  <H-INVITATIONAL-ID>HIT000022188</H-INVITATIONAL-ID>
+      #  <H-INVITATIONAL-ID>HIT000022189</H-INVITATIONAL-ID>
+      # </HINVDB_SEARCH>
+      def result
+        list = []
+        @xml.elements.each('//H-INVITATIONAL-ID') do |e|
+          list << e.text
+        end
+        return list
+      end
+
+      def size
+        @xml.elements['//SIZE'].text.to_i
+      end
+      def start
+        @xml.elements['//START'].text.to_i
+      end
+      def end
+        @xml.elements['//END'].text.to_i
+      end
+    end
+
+    # serv = Bio::Hinv::IdSearch.new
+    # serv.query("query" => "HIT00002218*", "id_type" => "H-INVITATIONAL-ID", "start" => 1, "end" => 100)
+    # puts serv.result
+    # puts serv.size
+    # puts serv.start
+    # puts serv.end
+    class IdSearch < KeywordSearch
+      def initialize
+        @url = BASE_URI + "id_search.php"
+      end
+
+      def query(hash = {})
+        default = {
+          "id_type" => "H-INVITATIONAL-ID",
+          "start" => 1,
+          "end" => 100
+        }
+        options = default.update(hash)
+        super(options)
+      end
+    end
+
+  end
+end
+