bio-old-biofetch-emulator 0.0.0

checksums.yaml

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+---
+SHA1:
+  metadata.gz: 1acb392f7fea461ab1f0be3309f787a0bcc12cd7
+  data.tar.gz: 7ea00a53bcfb15ff82c7a868bfba893153b50476
+SHA512:
+  metadata.gz: b83d93062361505b405e173cc87a955ec946d3111273b278348f20d56ed275650e83f2c4eb7c3ef8f1f861572b06b9c75c82d3f0a8a5cfa8339cdf10999b6f60
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data/.document

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+lib/**/*.rb
+bin/*
+- 
+features/**/*.feature
+LICENSE.txt

data/.travis.yml

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+language: ruby
+rvm:
+  - 1.9.2
+  - 1.9.3
+  - jruby-19mode # JRuby in 1.9 mode
+
+# - rbx-19mode
+#  - 1.8.7
+#  - jruby-18mode # JRuby in 1.8 mode
+#  - rbx-18mode
+
+# uncomment this line if your project needs to run something other than `rake`:
+# script: bundle exec rspec spec

data/Gemfile

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+source "http://rubygems.org"
+# Add dependencies required to use your gem here.
+# Example:
+#   gem "activesupport", ">= 2.3.5"
+
+gem "bio", ">= 1.4.2"
+
+# Add dependencies to develop your gem here.
+# Include everything needed to run rake, tests, features, etc.
+group :development do
+  gem "rake"
+  gem "rdoc"
+  gem "jeweler"
+  gem "bundler", ">= 1.0.21"
+end

data/LICENSE.txt

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+Copyright (c) 2014 Naohisa Goto
+
+Permission is hereby granted, free of charge, to any person obtaining
+a copy of this software and associated documentation files (the
+"Software"), to deal in the Software without restriction, including
+without limitation the rights to use, copy, modify, merge, publish,
+distribute, sublicense, and/or sell copies of the Software, and to
+permit persons to whom the Software is furnished to do so, subject to
+the following conditions:
+
+The above copyright notice and this permission notice shall be
+included in all copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
+EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
+MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
+NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE
+LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION
+OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION
+WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.

data/README.md

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+# bio-old-biofetch-emulator
+
+[![Build Status](https://secure.travis-ci.org/ngoto/bioruby-old-biofetch-emulator.png)](http://travis-ci.org/ngoto/bioruby-old-biofetch-emulator)
+
+Full description goes here
+
+Note: this software is under active development!
+
+## Installation
+
+```sh
+gem install bio-old-biofetch-emulator
+```
+
+## Usage
+
+```ruby
+require 'bio-old-biofetch-emulator'
+```
+
+The API doc is online. For more code examples see the test files in
+the source tree.
+        
+## Project home page
+
+Information on the source tree, documentation, examples, issues and
+how to contribute, see
+
+  http://github.com/ngoto/bioruby-old-biofetch-emulator
+
+The BioRuby community is on IRC server: irc.freenode.org, channel: #bioruby.
+
+## Cite
+
+If you use this software, please cite one of
+  
+* [BioRuby: bioinformatics software for the Ruby programming language](http://dx.doi.org/10.1093/bioinformatics/btq475)
+* [Biogem: an effective tool-based approach for scaling up open source software development in bioinformatics](http://dx.doi.org/10.1093/bioinformatics/bts080)
+
+## Biogems.info
+
+This Biogem is published at (http://biogems.info/index.html#bio-old-biofetch-emulator)
+
+## Copyright
+
+Copyright (c) 2014 Naohisa Goto. See LICENSE.txt for further details.
+

data/README.rdoc

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+= bio-old-biofetch-emulator
+
+{<img
+src="https://secure.travis-ci.org/ngoto/bioruby-old-biofetch-emulator.png"
+/>}[http://travis-ci.org/#!/ngoto/bioruby-old-biofetch-emulator]
+
+Full description goes here
+
+Note: this software is under active development!
+
+== Installation
+
+        gem install bio-old-biofetch-emulator
+
+== Usage
+
+== Developers
+
+To use the library 
+
+        require 'bio-old-biofetch-emulator'
+
+The API doc is online. For more code examples see also the test files in
+the source tree.
+        
+== Project home page
+
+Information on the source tree, documentation, issues and how to contribute, see
+
+  http://github.com/ngoto/bioruby-old-biofetch-emulator
+
+The BioRuby community is on IRC server: irc.freenode.org, channel: #bioruby.
+
+== Cite
+
+  If you use this software, please cite one of
+ 
+* [BioRuby: bioinformatics software for the Ruby programming language](http://dx.doi.org/10.1093/bioinformatics/btq475)
+* [Biogem: an effective tool-based approach for scaling up open source software development in bioinformatics](http://dx.doi.org/10.1093/bioinformatics/bts080)
+
+== Biogems.info
+
+This Biogem is published at http://biogems.info/index.html#bio-old-biofetch-emulator
+
+== Copyright
+
+Copyright (c) 2014 Naohisa Goto. See LICENSE.txt for further details.
+

data/Rakefile

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+# encoding: utf-8
+
+require 'rubygems'
+require 'bundler'
+begin
+  Bundler.setup(:default, :development)
+rescue Bundler::BundlerError => e
+  $stderr.puts e.message
+  $stderr.puts "Run `bundle install` to install missing gems"
+  exit e.status_code
+end
+require 'rake'
+
+require 'jeweler'
+Jeweler::Tasks.new do |gem|
+  # gem is a Gem::Specification... see http://guides.rubygems.org/specification-reference/ for more options
+  gem.name = "bio-old-biofetch-emulator"
+  gem.homepage = "http://github.com/ngoto/bioruby-old-biofetch-emulator"
+  gem.license = "MIT"
+  gem.summary = %Q{Emulates as if old BioRuby BioFetch alives}
+  gem.description = %Q{Emulator that emulates Bio::Fetch object in BioRuby as if old BioRuby BioFetch server were still alive. It overrides methods and objects in Bio::Fetch, and if the old BioRuby BioFetch server's URL is given, it intercepts all requests and converts them into existing web services such as TogoWS, KEGG REST API, NCBI E-Utilities, and GenomeNet(genome.jp).}
+  gem.email = "ng@bioruby.org"
+  gem.authors = ["Naohisa Goto"]
+  # dependencies defined in Gemfile
+end
+Jeweler::RubygemsDotOrgTasks.new
+
+require 'rake/testtask'
+Rake::TestTask.new(:test) do |test|
+  test.libs << 'lib' << 'test'
+  test.pattern = 'test/**/test_*.rb'
+  test.verbose = true
+end
+
+desc "Code coverage detail"
+task :simplecov do
+  ENV['COVERAGE'] = "true"
+  Rake::Task['test'].execute
+end
+
+task :default => :test
+
+require 'rdoc/task'
+Rake::RDocTask.new do |rdoc|
+  version = File.exist?('VERSION') ? File.read('VERSION') : ""
+
+  rdoc.rdoc_dir = 'rdoc'
+  rdoc.title = "bio-old-biofetch-emulator #{version}"
+  rdoc.rdoc_files.include('README*')
+  rdoc.rdoc_files.include('lib/**/*.rb')
+end

data/VERSION

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+0.0.0

data/lib/bio-old-biofetch-emulator.rb

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+# Please require your code below, respecting the naming conventions in the
+# bioruby directory tree.
+#
+# For example, say you have a plugin named bio-plugin, the only uncommented
+# line in this file would be 
+#
+#   require 'bio/bio-plugin/plugin'
+#
+# In this file only require other files. Avoid other source code.
+
+require 'bio-old-biofetch-emulator/emulator.rb'
+

data/lib/bio-old-biofetch-emulator/emulator.rb

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+
+require 'bio'
+require 'cgi'
+
+module Bio
+
+  module OldBioFetchEmulator
+
+    URL = "http://bioruby.org/cgi-bin/biofetch.rb".freeze
+
+    MAX_ID_NUM = 50
+
+    class Client < Bio::Fetch
+
+      # https://web.archive.org/web/20070803003306/http://www.genome.jp/about_genomenet/service.html
+      # https://web.archive.org/web/20110525080429/http://www.genome.jp/dbget/
+
+      # https://web.archive.org/web/20070306215757/http://bioruby.org/cgi-bin/biofetch.rb?info=dbs
+      # aa aax bl cpd dgenes dr ec eg emb embu epd est exp
+      # gb gbu genes gl gn gp gpu gss htgs ko ld lit mim nt
+      # og path pd pdb pdoc pf pir pmd pr prf ps rn rp rs
+      # rsaa rsnt sp str sts tr vg
+
+      Databases = {
+        # fetching via Bio::PubMed (NCBI E-Utilities)
+        "pubmed"  => [ :PubMed, true ],
+
+        # fetching via TogoWS REST API
+        "genbank"    => [ :TogoWS, "ncbi-nucleotide" ],
+        "gb"         => "genbank",
+
+        "genpept"    => [ :TogoWS, "ncbi-protein" ],
+        "gp"         => "genpept",
+
+        "refseq"     => [ :TogoWS, "ncbi-nucleotide", "ncbi-protein" ],
+        "rs"         => "refseq",
+        "refnuc"     => [ :TogoWS, "ncbi-nucleotide" ], 
+        "rsnt"       => "refnuc",
+        "refpep"     => [ :TogoWS, "ncbi-protein" ],
+        "rsaa"       => "refpep",
+
+        "embl"       => [ :TogoWS, "ebi-ena" ],
+        "emb"        => "embl",
+
+        "uniprot"    => [ :TogoWS, true ],
+        "up"         => "uniprot",
+        "swissprot"  => "uniprot",
+        "sp"         => "uniprot",
+        "trembl"     => "uniprot",
+        "tr"         => "uniprot",
+
+        "pdb"        => [ :TogoWS, true ],
+
+        #"genes"      => [ :TogoWS, "kegg-genes" ],
+
+        # fetching via KEGG REST API
+        "pathway"    => [ :KEGG, true ],
+        "path"       => "pathway",
+        "brite"      => [ :KEGG, true ],
+        "br"         => "brite",
+        "module"     => [ :KEGG, true ],
+        "md"         => "module",
+        "orthology"  => [ :KEGG, true ],
+        "ko"         => "orthology",
+        "genome"     => [ :KEGG, true ],
+        "genomes"    => [ :KEGG, true ],
+        "gn"         => "genomes",
+        "genes"      => [ :KEGG, true ],
+        "ligand"     => [ :KEGG, true ],
+        "compound"   => [ :KEGG, true ],
+        "cpd"        => "compound",
+        "glycan"     => [ :KEGG, true ],
+        "gl"         => "glycan",
+        "reaction"   => [ :KEGG, true ],
+        "rn"         => "reaction",
+        "rpair"      => [ :KEGG, true ],
+        "rp"         => "rpair",
+        "rclass"     => [ :KEGG, true ],
+        "rc"         => "rclass",
+        "enzyme"     => [ :KEGG, true ],
+        "ec"         => "enzyme",
+        "disease"    => [ :KEGG, true ],
+        "ds"         => "disease",
+        "drug"       => [ :KEGG, true ],
+        "dr"         => "drug",
+        "dgroup"     => [ :KEGG, true ],
+        "dg"         => "dgroup",
+        "environ"    => [ :KEGG, true ],
+        "ev"         => "environ",
+
+        "expression" => [ nil ], #[ :KEGG, true ],
+        "ex"         => "expression",
+        "exp"        => "expression",
+
+        "dgenes"     => [ :KEGG, true ],
+        "egenes"     => [ :KEGG, true ],
+        "eg"         => "egenes",
+        "mgenes"     => [ nil ], #[ :KEGG, true ],
+        "mgenome"    => [ nil ], #[ :KEGG, true ],
+        "mgnm"       => "mgenome",
+
+        "vgenome"    => [ :KEGG, true ],
+        "vgnm"       => "vgenome",
+        "vgenes"     => [ :KEGG, true ],
+        "vg"         => "vgenes",
+
+        # fetching from GenemeNet
+        "aaindex"  => [ :DBGET, true ],
+        "aax"      => "aaindex",
+        "aaindex1" => [ :DBGET, true ],
+        "aax1"     => "aaindex1",
+        "aaindex2" => [ :DBGET, true ],
+        "aax2"     => "aaindex2",
+        "aaindex3" => [ :DBGET, true ],
+        "aax3"     => "aaindex3",
+
+        # formerly can be get from GenomeNet but not available now
+        "prf"        => [ nil ], #[ :DBGET, true ],
+        "litdb"      => [ nil ], #[ :DBGET, true ],
+        "lit"        => [ nil ], #"litdb",
+
+        "pdbstr"  => [ nil ], # Protein sequence generated from PDB (GenomeNet)
+
+        "aa"      => [ nil ], # nr-aa ???
+        #"aax" # AAindex (KEGG)
+        "bl"      => [ nil ], # Blocks (http://blocks.fhcrc.org/)
+        #"cpd" # KEGG Compound
+        #"dgenes" # KEGG DGenes
+        #"dr" # KEGG Drug
+        #"ec" # KEGG Enzyme
+        #"eg" # KEGG EGenes
+        #"emb" # EMBL
+        "embu"    => [ nil ], # EMBL UniGene ???
+        "epd"     => [ nil ], # The Eukaryotic Promoter Database
+        "est"     => [ nil ], # NCBI EST ???
+        #"gb" # GenBank
+        "gbu"     => [ nil ], # NCBI UniGene ???
+        #"genes" # KEGG Genes
+        #"gl" # KEGG Glycan
+        #"gn" # KEGG Genomes
+        #"gp" # GenPept ???
+        "gpu"     => [ nil ], # ???
+        "gss"     => [ nil ], # NCBI GSS ???
+        "htgs"    => [ nil ], # NCBI HTGS ???
+        #"ko" # KEGG Orthology
+        "ld"      => [ nil ], # ???
+        #"lit" # PRF LitDB
+        "mim"     => [ nil ], # ???
+        "nt"      => [ nil ], # nr-nt ???
+        "og"      => [ nil ], # ???
+        #"path" # KEGG Pathway
+        "pd"      => [ nil ], # prodom
+        #"pdb" # PDB
+        "pdoc"    => [ nil ], # Prosite literature (GenomeNet)
+        "pf"      => [ nil ], # Pfam
+        "pir"     => [ nil ], # pir
+        "pmd"     => [ nil ], # Protein mutants (DDBJ) (GenomeNet)
+        "pr"      => [ nil ], # prints
+        #"prf" # PRF (Protein Research Foundation)
+        "ps"      => [ nil ], # prosite
+        #"rn" # KEGG Reaction
+        #"rp" # KEGG RPair
+        #"rs" # NCBI RefSeq
+        #"rsaa" # NCBI RefSeq Amino Acide
+        #"rsnt" # NCBI RefSeq NucleoTide
+        #"sp" # SwissProt
+        "str"     => [ nil ], # ???
+        "sts"     => [ nil ], # NCBI STS ???
+        #"tr" # TrEMBL
+        #"vg" # KEGG VGenes
+      }
+
+      def initialize(url = URL)
+        super
+      end
+
+      def fetch(db, id, style = 'raw', format = nil)
+        _fetch(:fetch, db, id, style, format)
+      end
+
+      def databases
+        Databases.collect do |key, val|
+          while val && val.is_a?(String)
+            val = Databases[val]
+          end
+          if val && val.is_a?(Array) && val[0] then
+            key
+          else
+            nil
+          end
+        end.compact
+      end
+
+      def formats(database = @database)
+        if database
+          [ "default" ]
+        end
+      end
+
+      def maxids
+        MAX_ID_NUM
+      end
+
+      private
+      def _fetch(cmd, db, id, style, format)
+        db_orig = db
+        db = db.to_s.downcase
+        while a = Databases[db]
+          case a
+          when Array
+            break
+          when String
+            db = a
+          else
+            break
+          end
+        end
+
+        if !a and /[a-z]{3}/ =~ db then
+          remote = :KEGG
+          dbs = [ 'genes' ]
+          id_prefix = db
+        elsif a.is_a?(Array) then
+          remote = a[0]
+          dbs = a[1..-1]
+          dbs.collect! { |x| x == true ? db : x }
+        end
+        
+        if !remote then
+          return "ERROR 1 Unknown database [#{db_orig.inspect}]"
+        end
+        
+        ids = id.strip.split(/(?:\s*\,\s*|\s+)/)
+        if ids.size > MAX_ID_NUM then
+          return "ERROR 5 Too many IDs [#{ids.size}]. Max [#{MAX_ID_NUM}] allowed."
+        end
+        if id_prefix then
+          ids.collect! { |x| "#{id_prefix}:#{x.strip}" }
+        end
+
+        case cmd
+        when :fetch
+          ret = case remote
+                when :TogoWS
+                  _fetch_togows(cmd, dbs, ids)
+                when :KEGG
+                  _fetch_kegg(cmd, dbs, ids)
+                when :DBGET
+                  _fetch_dbget(cmd, dbs, ids)
+                when :PubMed
+                  _fetch_pubmed(cmd, dbs, ids)
+                else
+            raise "Bug: unknown remote site #{remote.inspect}"
+          end
+        end
+        ret
+      end
+
+      def _fetch_pubmed(cmd, dbs, ids)
+        a = Bio::PubMed.efetch(ids)
+        if a && a.size > 0 then
+          a.join("\n\n") + "\n"
+        else
+          "Error 4 ID not found [#{ids.inspect}]"
+        end
+      end
+
+      def _fetch_togows(cmd, dbs, ids)
+        all = []
+        ids.each do |id|
+          ret = nil
+          dbs.each do |db|
+            url = "http://togows.org/entry/#{CGI.escape(db)}/#{CGI.escape(id)}"
+            begin
+              ret = Bio::Command.read_uri(url)
+            rescue OpenURI::HTTPError
+              ret = nil
+            end
+            if ret && /\AError/ !~ ret && ret.strip.size > 0 then
+              break
+            else
+              ret = nil
+            end
+          end
+          all.push ret if ret
+        end
+        if all.empty?
+          return "Error 4 ID not found [#{ids.inspect}]"
+        else
+          return all.join("")
+        end
+      end
+      
+      def _fetch_kegg(cmd, dbs, ids)
+        all = []
+        ids.each do |id|
+          ret = nil
+          dbs.each do |db|
+            if db == "genes" then
+              url = "http://rest.kegg.jp/get/#{CGI.escape(id)}"
+            else
+              url = "http://rest.kegg.jp/get/#{CGI.escape(db)}:#{CGI.escape(id)}"
+            end
+            begin
+              ret = Bio::Command.read_uri(url)
+            rescue OpenURI::HTTPError
+              ret = nil
+            end
+            if ret && ret.strip.size > 0 then
+              break
+            else
+              ret = nil
+            end
+          end
+          all.push ret if ret
+        end
+        if all.empty?
+          return "Error 4 ID not found [#{ids.inspect}]"
+        else
+          return all.join("")
+        end
+      end
+
+      def _fetch_dbget(cmd, dbs, ids)
+        all = []
+        ids.each do |id|
+          ret = nil
+          dbs.each do |db|
+            url = "http://www.genome.jp/dbget-bin/www_bget?#{CGI.escape(db)}:#{CGI.escape(id)}"
+            begin
+              ret = Bio::Command.read_uri(url)
+            rescue OpenURI::HTTPError
+              ret = nil
+            end
+            if ret then
+              ret = _scrape_dbget(ret)
+              break if ret
+            end
+            ret = nil
+          end
+          all.push ret if ret
+        end
+        if all.empty?
+          return "Error 4 ID not found [#{ids.inspect}]"
+        else
+          return all.join("")
+        end
+      end
+
+      def _scrape_dbget(orig_str)
+        a = orig_str.split(/^\s*\<\!\-\- bget\:result \-\-\>$\s*/)
+        if a[1] then
+          str = a[1]
+          str.sub!(/\A\s*\<pre\>$\s*/, "")
+          str.sub!(/^\s*\<\/pre\>.*/m, "")
+          str.gsub!(/\<[^\>]+\>/, "")
+          return str
+        end
+        nil
+      end
+
+    end #class Client
+
+    module Query
+      # Shortcut for using BioRuby's BioFetch server. You can fetch an entry
+      # without creating an instance of BioFetch server. This method uses the
+      # default dbfetch server, which is http://bioruby.org/cgi-bin/biofetch.rb
+      #
+      # Example:
+      #   puts Bio::Fetch.query('refseq','NM_123456')
+      #
+      # ---
+      # *Arguments*:
+      # * _database_: name of database to query (see Bio::Fetch#databases to get list of supported databases)
+      # * _id_: single ID or ID list separated by commas or white space
+      # * _style_: [raw|html] (default = 'raw')
+      # * _format_: name of output format (see Bio::Fetch#formats)
+      def query(*args)
+        Client.new.fetch(*args)
+      end
+    end #module Query
+
+    DONT_OVERRIDE = ::Bio::Fetch.const_defined?(:EBI) ?
+    [ Client, ::Bio::Fetch::EBI ] : [ Client ]
+
+    class << ::Bio::Fetch
+
+      alias_method :new_without_old_biofetch_emulator, :new
+
+      def new_with_old_biofetch_emulator(*arg)
+        tmp = self.ancestors
+        if (tmp - DONT_OVERRIDE).size == tmp.size then
+          $stderr.puts self
+          case arg.size
+          when 0
+            return Client.new
+          when 1
+            case arg[0]
+            when URL
+              return Client.new(*arg)
+            end
+          end
+        end
+        new_without_old_biofetch_emulator(*arg)
+      end
+
+      alias_method :new, :new_with_old_biofetch_emulator
+
+      include Query
+
+    end #class << Bio::Fetch
+
+  end #module OldBioFetchEmulator
+
+end #module Bio

data/test/helper.rb

@@ -0,0 +1,35 @@
+#
+#require 'simplecov'
+#
+#module SimpleCov::Configuration
+#  def clean_filters
+#    @filters = []
+#  end
+#end
+#
+#SimpleCov.configure do
+#  clean_filters
+#  load_adapter 'test_frameworks'
+#end
+#
+#ENV["COVERAGE"] && SimpleCov.start do
+#  add_filter "/.rvm/"
+#end
+require 'rubygems'
+#require 'bundler'
+#begin
+#  Bundler.setup(:default, :development)
+#rescue Bundler::BundlerError => e
+#  $stderr.puts e.message
+#  $stderr.puts "Run `bundle install` to install missing gems"
+#  exit e.status_code
+#end
+require 'test/unit'
+#require 'shoulda'
+
+$LOAD_PATH.unshift(File.join(File.dirname(__FILE__), '..', 'lib'))
+$LOAD_PATH.unshift(File.dirname(__FILE__))
+require 'bio-old-biofetch-emulator'
+
+class Test::Unit::TestCase
+end

data/test/test_bio-old-biofetch-emulator.rb

@@ -0,0 +1,96 @@
+require 'helper'
+
+module FuncTestBioOldBiofetchEmulator
+
+  module CommonTestMethods
+
+    def fetch_and_check_ids(db, ids, regexp)
+      tmp_ids = ids.dup
+      str = @bf.fetch(db, ids.join(","))
+      str.scan(regexp) do |x|
+        assert_equal(tmp_ids.shift.to_s, $1)
+      end
+      assert(tmp_ids.empty?)
+
+      str2 = @bf.fetch(db, ids.join(" "))
+      assert_equal(str, str2)
+    end
+    private :fetch_and_check_ids
+
+    def test_fetch_pubmed
+      db = "pubmed"
+      ids = [ 20739307, 22332238 ]
+      regexp = /^PMID- +(\d+)/
+      fetch_and_check_ids(db, ids, regexp)
+    end
+
+    def test_fetch_refseq
+      db = "rs"
+      ids = [ "NM_123456", "NP_198907" ]
+      regexp = /^ACCESSION +([\_A-Z0-9]+)/
+      fetch_and_check_ids(db, ids, regexp)
+    end
+
+    def test_fetch_kegg_genes
+      db = "hal"
+      ids = [ "VNG1467G", "VNG6476G", "VNG2243G" ]
+      regexp = /^ENTRY +([A-Z0-9]+)/
+      fetch_and_check_ids(db, ids, regexp)
+    end
+
+    def test_fetch_aaindex
+      db = "aax"
+      ids = [ "PRAM900102", "DAYM780301" ] # (aaindex1, aaindex2)
+      regexp = /^H +([A-Z0-9]+)$/
+      fetch_and_check_ids(db, ids, regexp)
+    end
+
+    def test_class
+      assert_instance_of(Bio::OldBioFetchEmulator::Client, @bf)
+      assert_equal(Bio::OldBioFetchEmulator::Client, @bf.class)
+    end
+  end #module CommonTestMethods
+
+  class TestClient < Test::Unit::TestCase
+    include CommonTestMethods
+
+    def setup
+      Bio::NCBI.default_email ||= "staff@bioruby.org"
+      @bf = Bio::OldBioFetchEmulator::Client.new
+    end
+  end #class TestClient
+
+  class TestBioFetch < Test::Unit::TestCase
+    include CommonTestMethods
+
+    def setup
+      Bio::NCBI.default_email ||= "staff@bioruby.org"
+      @bf = Bio::Fetch.new
+    end
+
+  end #class TestClient
+
+  class TestBioFetchWithURL < Test::Unit::TestCase
+    include CommonTestMethods
+
+    def setup
+      Bio::NCBI.default_email ||= "staff@bioruby.org"
+      @bf = Bio::Fetch.new("http://bioruby.org/cgi-bin/biofetch.rb")
+    end
+
+  end #class TestClient
+
+  class TestBioFetchWithOtherURL < Test::Unit::TestCase
+    def setup
+      Bio::NCBI.default_email ||= "staff@bioruby.org"
+      @bf = Bio::Fetch.new("http://www.ebi.ac.uk/Tools/dbfetch/dbfetch")
+    end
+
+    def test_class
+      assert_instance_of(Bio::Fetch, @bf)
+      assert_equal(Bio::Fetch, @bf.class)
+    end
+  end #class TestClient
+
+end #module FuncTestBioOldBiofetchEmulator
+

metadata

@@ -0,0 +1,132 @@
+--- !ruby/object:Gem::Specification
+name: bio-old-biofetch-emulator
+version: !ruby/object:Gem::Version
+  version: 0.0.0
+platform: ruby
+authors:
+- Naohisa Goto
+autorequire: 
+bindir: bin
+cert_chain: []
+date: 2014-11-13 00:00:00.000000000 Z
+dependencies:
+- !ruby/object:Gem::Dependency
+  name: bio
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: 1.4.2
+  type: :runtime
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: 1.4.2
+- !ruby/object:Gem::Dependency
+  name: rake
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: '0'
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: '0'
+- !ruby/object:Gem::Dependency
+  name: rdoc
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: '0'
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: '0'
+- !ruby/object:Gem::Dependency
+  name: jeweler
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: '0'
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: '0'
+- !ruby/object:Gem::Dependency
+  name: bundler
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: 1.0.21
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: 1.0.21
+description: Emulator that emulates Bio::Fetch object in BioRuby as if old BioRuby
+  BioFetch server were still alive. It overrides methods and objects in Bio::Fetch,
+  and if the old BioRuby BioFetch server's URL is given, it intercepts all requests
+  and converts them into existing web services such as TogoWS, KEGG REST API, NCBI
+  E-Utilities, and GenomeNet(genome.jp).
+email: ng@bioruby.org
+executables: []
+extensions: []
+extra_rdoc_files:
+- LICENSE.txt
+- README.md
+- README.rdoc
+files:
+- ".document"
+- ".travis.yml"
+- Gemfile
+- LICENSE.txt
+- README.md
+- README.rdoc
+- Rakefile
+- VERSION
+- lib/bio-old-biofetch-emulator.rb
+- lib/bio-old-biofetch-emulator/emulator.rb
+- test/helper.rb
+- test/test_bio-old-biofetch-emulator.rb
+homepage: http://github.com/ngoto/bioruby-old-biofetch-emulator
+licenses:
+- MIT
+metadata: {}
+post_install_message: 
+rdoc_options: []
+require_paths:
+- lib
+required_ruby_version: !ruby/object:Gem::Requirement
+  requirements:
+  - - ">="
+    - !ruby/object:Gem::Version
+      version: '0'
+required_rubygems_version: !ruby/object:Gem::Requirement
+  requirements:
+  - - ">="
+    - !ruby/object:Gem::Version
+      version: '0'
+requirements: []
+rubyforge_project: 
+rubygems_version: 2.2.2
+signing_key: 
+specification_version: 4
+summary: Emulates as if old BioRuby BioFetch alives
+test_files: []