bio-unichem 0.1.0

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"
+
+# Add dependencies to develop your gem here.
+# Include everything needed to run rake, tests, features, etc.
+group :development do
+  gem "shoulda", ">= 0"
+  gem "rdoc", "~> 3.12"
+  gem "bundler", "> 1.0.0"
+  gem "jeweler", "~> 1.8.4"
+  gem "bio", ">= 1.4.2"
+  gem "rdoc", "~> 3.12"
+end

data/LICENSE.txt

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+Copyright (c) 2013 Mitsuteru Nakao
+
+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-unichem
+
+[![Build Status](https://secure.travis-ci.org/nakao/bio-unichem.png)](http://travis-ci.org/nakao/bio-unichem)
+
+BioRuby plugin for [UniChem REST Web service](https://www.ebi.ac.uk/unichem/info/webservices).
+
+REST API address
+```ruby
+   Bio::UniChem::REST::UniChem_URI.src_compound_id("CHEMBL12", "1", "2")
+   #=> "http://www.ebi.ac.uk/unichem/rest/src_compound_id/CHEMBL12/1/2"
+   
+   Bio::UniChem::REST::UniChem_URI.mapping("4", "1")
+   #=> "http://www.ebi.ac.uk/unichem/rest/mapping/4/1"
+```
+
+Get Data 
+```ruby
+   client = Bio::UniChem::REST.new
+   result = client.src_compound_id("CHEMBL12", "1", "2")
+   p result 
+   #=> [{"src_compound_id"=>"DB00829"}]
+```
+
+Get Data using [Source ID by Short name](https://www.ebi.ac.uk/unichem/ucquery/listSources)
+```ruby
+   client = Bio::UniChem::REST.new
+   result = client.src_compound_id("CHEMBL12", 
+                                   Bio::UniChem::Sources['chembl'].src_id, 
+                                   Bio::UniChem::Sources['drugbank'].src_id)
+   p eresult 
+   #=> [{"src_compound_id"=>"DB00829"}]
+```
+
+Sources and Souece models [list of sources](https://www.ebi.ac.uk/unichem/ucquery/listSources)
+```ruby
+   chembl = Bio::UniChem::Sources['chembl']
+   chembl.src_id
+   #=> "1"
+   chembl.short_name
+   #=> "chembl"
+   chembl.full_name
+   #=> "ChEMBL"
+```
+
+The Ruby script bellow utilizes the Bio UniChem module
+```ruby
+   require 'bio-unichem'
+
+   ## --------------------------
+   ## create client ...
+   client = Bio::UniChem::REST.new
+
+   ## --------------------------
+   ## get the data ...
+   result = client.src_compound_id("CHEMBL12", Bio::UniChem::Sources["chembl"].src_id)
+   
+   ## --------------------------
+   ## print ...
+   p result   
+``` 
+
+
+
+Note: this software is under active development!
+
+## Installation
+
+```sh
+    gem install bio-unichem
+```
+
+## Usage
+
+```ruby
+    require 'bio-unichem'
+```
+
+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/nakao/bio-unichem
+
+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 [#bio-unichem](http://biogems.info/index.html)
+
+## Copyright
+
+Copyright (c) 2013 Mitsuteru Nakao. 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://docs.rubygems.org/read/chapter/20 for more options
+  gem.name = "bio-unichem"
+  gem.homepage = "http://github.com/nakao/bioruby-unichem"
+  gem.license = "MIT"
+  gem.summary = %Q{BioRuby plugin for UniChem REST Web service}
+  gem.description = %Q{BioRuby plugin for UniChem REST Web service}
+  gem.email = "mitsuteru.nakao@gmail.com"
+  gem.authors = ["Mitsuteru Nakao"]
+  # 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
+
+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-unichem #{version}"
+  rdoc.rdoc_files.include('README*')
+  rdoc.rdoc_files.include('lib/**/*.rb')
+end

data/VERSION

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+0.1.0

data/lib/bio-unichem.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-unichem/unichem.rb'
+

data/lib/bio-unichem/model.rb

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+module Bio
+  class UniChem
+    
+    # Bio::UniChem::Source
+    #
+    # hash = {'src_id' => '1, 'short_name' => ... }
+    # chembl = Bio::UniChem::Source.new(hash)
+    # chembl.src_id
+    # #=> "1"
+    # chembl.short_name
+    # #=> "chembl"
+    # chembl.full_name
+    # #=> "ChEMBL"
+    #
+    class Source      
+      attr_reader :src_id
+      attr_reader :short_name
+      attr_reader :full_name
+      attr_reader :description
+      attr_reader :process_of_data_acquisition
+      
+      
+      # Bio::UniChem::Source.new(hash)
+      def initialize(hash = nil)
+        @src_id      = hash["src_id"]
+        @short_name  = hash["short_name"]
+        @full_name   = hash["full_name"]
+        @description = hash["description"]
+        @process_of_data_acquisition = hash["process_of_data_acquisition"]
+      end
+      
+    end
+    
+    # Bio::UniChem::Sources
+    #
+    # Usage
+    #  aSource = Bio::UniChem::Sources["chembl"]
+    #  aSource = Bio::UniChem::Sources["1"]
+    #  aSource.src_id     
+    #  #=> "1"
+    #  aSource.short_name 
+    #  #=> "chembl"
+    #  aSource.full_name  
+    #  #=> "ChEMBL"
+    #        
+    class Sources
+      
+      # 2013-02-09 at https://www.ebi.ac.uk/unichem/ucquery/listSources
+      # src_id  
+      # Short name  
+      # Full name 
+      # Description 
+      # Process of Data Acquisition
+      data = %q|
+        1
+        chembl
+        ChEMBL
+        A database of bioactive drug-like small molecules and associated bioactivities abstracted from the scientific literature
+        Standard InChIs and Keys provided on ftp site for each release.
+        //
+        2
+        drugbank
+        DrugBank
+        A database that combines drug (i.e. chemical, pharmacological and pharmaceutical) data with drug target (i.e. sequence, structure, and pathway) information.
+        Standard InChIs and Keys provided within sd file on ftp site for each release.
+        //
+        3
+        pdb
+        PDBe (Protein Data Bank Europe)
+        The European resource for the collection, organisation and dissemination of data on biological macromolecular structures, including structures of small molecule ligands for proteins.
+        Standard InChIs and Keys provided by direct querying of Oracle DB.
+        //
+        4
+        iuphar
+        International Union of Basic and Clinical Pharmacology  A resource for representing the interests of pharmacologists around the world. DB contains structures of small molecule ligands of pharmacological significance.
+        Standard InChIs and Keys provided by email on request.
+        //
+        5
+        pubchem_dotf
+        PubChem ('Drugs of the Future' subset)  A subset of the PubChem DB: from the original depositor 'drugs of the future' (Prous).
+        Mol files for SIDs downloaded manually, via PubChem interface, and Standard InChIs and Keys generated by InChI software. SIDs used as identifiers.
+        //
+        6
+        kegg_ligand
+        KEGG (Kyoto Encyclopedia of Genes and Genomes) Ligand
+        KEGG LIGAND is a composite DB consisting of COMPOUND, GLYCAN, REACTION, RPAIR, RCLASS, and ENZYME DBs, whose entries are identified by C, G, R, RP, RC, and EC numbers, respectively.
+        Mol files were downloaded manually prior to this download becoming private. Standard InChIs and Keys generated by InChI software.
+        //
+        7
+        chebi
+        ChEBI (Chemical Entities of Biological Interest).
+        ChEBI is a freely available dictionary of molecular entities focused on 'small' chemical compounds
+        Std InChis (but no keys) provided on ftp site. Keys generated by UniChem. Only 'three star' compounds downloaded
+        //
+        8
+        nih_ncc
+        NIH Clinical Collection
+        Collections of plated arrays of small molecules that have a history of use in human clinical trials. Assembled by the National Institutes of Health (NIH) through the Molecular Libraries Roadmap Initiative
+        Mol files downloaded manually and Standard InChIs and Keys generated by InChI software
+        //
+        9
+        zinc
+        ZINC
+        A free database of commercially-available compounds for virtual screening, provided by the Shoichet Laboratory in the Department of Pharmaceutical Chemistry at the University of California, San Francisco (UCSF). [Irwin and Shoichet, J. Chem. Inf. Model. 2005;45(1):177-82]
+        SD file ('Standard', 'All Purchasable' of ~17.8 million) downloaded from source and InChis generated by UniChem
+        //
+        10
+        emolecules
+        eMolecules
+        A free chemical structure search engine containing millions of public domain structures. Pricing, availabilities, and vendor information requires an eMolecules Plus subscription.
+        Downloaded as an SD file from source, Converted to InChI and INChIKeys by UniChem
+        //
+        11
+        ibm
+        IBM strategic IP insight platform and the National Institutes of Health
+        A massive, searchable database of chemical and pharmaceutical data, extracted from millions of patents and scientific literature. Identifiers in UniChem are IBM compound identifiers.
+        SMILES download available. Converted to InChi by PPP in house.
+        //
+        12
+        atlas
+        Gene Expression Atlas
+        The Gene Expression Atlas is a semantically enriched database of meta-analysis based summary statistics over a curated subset of ArrayExpress Archive, servicing queries for condition-specific gene expression patterns as well as broader exploratory searches for biologically interesting genes/samples.
+        Currently extracted from compound names.
+        //
+        13
+        patents
+        IBM strategic IP insight platform and the National Institutes of Health.
+        Data, provided by IBM-NIH, was originally extracted from patents from three publishing bodies (US, EPO and WIPO) with publication dates through (including) 2000-12-31. For UniChem, these data were parsed to include only whole molecules present in either the title or claims fields. Further filters included removal of: 1. All molecules mapping to > 10,000 patents, 2. Non-organic molecules, 3. Small molecules (mw <90, number of atoms < 7). In addition, for structures mapping to >100 patents, only 100 randomly selected patents were selected. Identifiers in UniChem are patent number identifiers
+        SMILES download available. Converted to InChi in house. Patent Ids used for Ids instead of cpd_ids. Data set filtered to remove compounds not appearing in the title or claims sections of the patent, and to remove very frequently occurring compounds
+    |
+      delimiter = "/\/\//"
+      Data = data.strip.split(delimiter).map do |record|
+        t = record.strip.split("\n").map {|line| line.strip }
+        Bio::UniChem::Source.new({"src_id" => t[0],  
+                              "short_name" => t[1],  
+                               "full_name" => t[2], 
+                             "description" => t[3], 
+             "process_of_data_acquisition" => t[4]})
+      end
+      
+      # Bio::UniChem::Sources.find_by_src_id(src_id) #=> aSource
+      def self.find_by_src_id(src_id)
+        Data.find {|x| x.src_id == src_id.to_s }
+      end
+      
+      # Bio::UniChem::Sources.find_by_short_name(short_name) #=> aSource
+      def self.find_by_short_name(short_name)
+        Data.find {|x| x.short_name == short_name }
+      end
+      
+      # Bio::UniChem::Sources[arg] #=> aSource
+      # arg : src_id, short_name 
+      def self.[](arg)
+        case arg
+        when /^\d$/
+          self.find_by_src_id(arg)
+        else
+          self.find_by_short_name(arg)
+        end
+      end
+    end
+
+  end
+  
+end

data/lib/bio-unichem/unichem.rb

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+require 'bio'
+require 'open-uri'
+require 'json'
+
+module Bio
+  
+class UniChem
+  
+
+  # UniChem REST Web service API Client.
+  #
+  #  # URI
+  #  Bio::UniChem::REST::UniChem_URI
+  #
+  class REST
+
+    HOST_NAME = "www.ebi.ac.uk"
+    API_ROOT = "unichem/rest"
+    BASE_URL = "https://" + HOST_NAME + "/" + API_ROOT
+
+    # Generate URIs for UniChem REST Web service
+    # Bio::UniChem::REST::UniChem_URI
+    module UniChem_URI
+
+      def self.address(path)
+        "#{BASE_URL}/#{path}"
+      end
+
+      # Example:  http://www.ebi.ac.uk/unichem/rest/src_compound_id/CHEMBL12/1
+      # Example:  http://www.ebi.ac.uk/unichem/rest/src_compound_id/CHEMBL12/1/2
+      def self.src_compound_id(src_compound_id, src_id, to_src_id = nil)
+        path = [src_compound_id, src_id, to_src_id].compact.join("/")
+        address("src_compound_id/#{path}")
+      end
+
+      # Example:  http://www.ebi.ac.uk/unichem/rest/src_compound_id_all/CHEMBL12/1
+      # Example:  http://www.ebi.ac.uk/unichem/rest/src_compound_id_all/CHEMBL12/1/2
+      def self.src_compound_id_all(src_compound_id, src_id, to_src_id = nil)
+        path = [src_compound_id, src_id, to_src_id].compact.join("/")
+        address("src_compound_id_all/#{path}")
+      end
+
+      # Example:  http://www.ebi.ac.uk/unichem/rest/mapping/4/1
+      def self.mapping(src_id, to_src_id)
+        address("mapping/#{src_id}/#{to_src_id}")
+      end
+
+      # Example:  http://www.ebi.ac.uk/unichem/rest/inchikey/AAOVKJBEBIDNHE-UHFFFAOYSA-N
+      def self.inchikey(inchikey)
+        address("inchikey/#{inchikey}")
+      end
+
+      # Example:  http://www.ebi.ac.uk/unichem/rest/inchikey_all/AAOVKJBEBIDNHE-UHFFFAOYSA-N
+      def self.inchikey_all(inchikey)
+        address("inchikey_all/#{inchikey}")
+      end
+ 
+      # Example:  http://www.ebi.ac.uk/unichem/rest/src_ids/
+      def self.src_ids
+        address("src_ids/")
+      end
+
+      # Example:  http://www.ebi.ac.uk/unichem/rest/sources/1
+      def self.sources(src_id)
+        address("sources/#{src_id}")
+      end
+
+      # Example:  http://www.ebi.ac.uk/unichem/rest/structure/CHEMBL12/1
+      def self.structure(src_compound_id, src_id)
+        address("structure/#{src_compound_id}/#{src_id}")
+      end
+
+      # Example:  http://www.ebi.ac.uk/unichem/rest/structure_all/CHEMBL12/1
+      def self.structure_all(src_compound_id, src_id)
+        address("structure_all/#{src_compound_id}/#{src_id}")
+      end
+
+      # Example:  http://www.ebi.ac.uk/unichem/rest/src_compound_id_url/CHEMBL12/1/2
+      def self.src_compound_id_url(src_compound_id, src_id, to_src_id)
+        address("src_compound_id_url/#{src_compound_id}/#{src_id}/#{to_src_id}")
+      end
+
+      # Example:  http://www.ebi.ac.uk/unichem/rest/src_compound_id_all_obsolete/DB07699/2
+      # Example:  http://www.ebi.ac.uk/unichem/rest/src_compound_id_all_obsolete/DB07699/2/1
+      def self.src_compound_id_all_obsolete(src_compound_id, src_id, to_src_id = nil)
+        path = [src_compound_id, src_id, to_src_id].compact.join("/")
+        address("src_compound_id_all_obsolete/#{path}")
+      end
+
+      # Example:  http://www.ebi.ac.uk/unichem/rest/verbose_inchikey/HAUGRYOERYOXHX-UHFFFAOYSA-N
+      def self.verbose_inchikey(inchikey)
+        address("verbose_inchikey/#{inchikey}")
+      end
+
+    end
+    
+
+    # Bio::UniChem::REST.new 
+    def initialize
+      @header = {
+        'User-Agent' => "Bio::UniChem, BioRuby/#{Bio::BIORUBY_VERSION_ID}"
+      }
+      @debug = false
+      @status = ""
+    end
+    
+    #
+    def get(uri)
+      res = open(uri, @header)
+      @status = res.status
+      return JSON(res.read)
+    end
+    private :get
+    
+    #
+    def src_compound_id(src_compound_id, src_id, to_src_id = nil)
+      get(Bio::UniChem::REST::UniChem_URI.src_compound_id(src_compound_id, src_id, to_src_id))
+    end
+    
+    def src_compound_id_all(src_compound_id, src_id, to_src_id = nil)
+      get(Bio::UniChem::REST::UniChem_URI.src_compound_id_all(src_compound_id, src_id, to_src_id))
+    end
+    
+    def mapping(src_id, to_src_id)
+      get(Bio::UniChem::REST::UniChem_URI.mapping(src_id, to_src_id))
+    end
+
+    def inchikey(inchikey)
+      get(Bio::UniChem::REST::UniChem_URI.inchikey(inchikey))
+    end
+
+    def inchikey_all(inchikey)
+      get(Bio::UniChem::REST::UniChem_URI. inchikey_all(inchikey))
+    end
+
+    def src_ids
+      get(Bio::UniChem::REST::UniChem_URI.src_ids)
+    end
+
+    def sources(src_id)
+      get(Bio::UniChem::REST::UniChem_URI.sources(src_id))
+    end
+
+    def structure(src_compound_id, src_id)
+      get(Bio::UniChem::REST::UniChem_URI.structure(src_compound_id, src_id))
+    end
+
+    def structure_all(src_compound_id, src_id)
+      get(Bio::UniChem::REST::UniChem_URI.structure_all(src_compound_id, src_id))
+    end
+
+    def src_compound_id_url(src_compound_id, src_id, to_src_id)
+      get(Bio::UniChem::REST::UniChem_URI.src_compound_id_url(src_compound_id, src_id, to_src_id))
+    end
+
+    def src_compound_id_all_obsolete(src_compound_id, src_id, to_src_id = nil)
+      get(Bio::UniChem::REST::UniChem_URI.src_compound_id_all_obsolete(src_compound_id, src_id, to_src_id = nil))
+    end
+
+    def verbose_inchikey(inchikey)
+      get(Bio::UniChem::REST::UniChem_URI.verbose_inchikey(inchikey))
+    end
+    
+  end
+  
+end
+
+end

data/test/helper.rb

@@ -0,0 +1,18 @@
+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-unichem'
+
+class Test::Unit::TestCase
+end

data/test/test.sh

@@ -0,0 +1,7 @@
+#!/bin/sh
+
+# testing script for Jnekins task
+# test/test.sh test_bio-unichem-model.rb
+
+cd /Users/mitsuteru/Applications/biogems/bioruby-unichem/
+/opt/local/bin/ruby1.9 -I lib -I test test/${1}

data/test/test_bio-unichem-model.rb

@@ -0,0 +1,75 @@
+require 'helper'
+require 'bio-unichem/model.rb'
+
+class TestBioUniChemModelSource < Test::Unit::TestCase
+  def setup
+    record = {
+      'src_id' => "1",
+      "short_name" => "chembl",
+      "description" => "A database of bioactive drug-like small molecules and associated bioactivities abstracted from the scientific literature",
+      "full_name" => "ChEMBL",
+      "process_of_data_acquisition" => "Standard InChIs and Keys provided on ftp site for each release.",
+    }
+    @obj = Bio::UniChem::Source.new(record)
+  end
+
+
+  def test_src_id
+    assert_equal(@obj.src_id, "1")
+  end  
+
+  def test_short_name
+    assert_equal(@obj.short_name, "chembl")
+  end  
+  
+  def test_description
+    assert_equal(@obj.description, "A database of bioactive drug-like small molecules and associated bioactivities abstracted from the scientific literature")
+  end
+  
+  def test_full_name
+    assert_equal(@obj.full_name, "ChEMBL")
+  end
+  
+  def test_process_of_data_acquisition
+    assert_equal(@obj.process_of_data_acquisition, "Standard InChIs and Keys provided on ftp site for each release.")
+  end
+
+end
+
+
+
+
+class TestBioUniChemModelSources < Test::Unit::TestCase
+  def setup
+  	@o = Bio::UniChem::Sources.new
+  end
+
+  def test_new
+  	assert_equal(@o.class, Bio::UniChem::Sources)
+  end
+
+  def test_find_by_src_id
+    assert_equal(Bio::UniChem::Sources.find_by_src_id("1").class, Bio::UniChem::Source) 
+  end
+
+  def test_find_by_src_id_integer
+    assert_equal(Bio::UniChem::Sources.find_by_src_id(1).class, Bio::UniChem::Source) 
+  end
+
+  
+  def test_find_by_short_name
+    assert_equal(Bio::UniChem::Sources.find_by_short_name("chembl").class, Bio::UniChem::Source) 
+    assert_equal(Bio::UniChem::Sources.find_by_short_name("chembl").src_id, "1") 
+  end
+
+  def test_a_short_name
+    assert_equal(Bio::UniChem::Sources["chembl"].class, Bio::UniChem::Source) 
+    assert_equal(Bio::UniChem::Sources["chembl"].src_id, "1") 
+  end
+
+  def test_a_src_id
+    assert_equal(Bio::UniChem::Sources["1"].class, Bio::UniChem::Source) 
+    assert_equal(Bio::UniChem::Sources["1"].short_name, "chembl") 
+  end
+  
+end

data/test/test_bio-unichem-rest-client.rb

@@ -0,0 +1,169 @@
+require 'helper'
+require 'bio-unichem/unichem.rb'
+
+class TestBioUniChemRESTClient < Test::Unit::TestCase
+  def setup
+    @obj = Bio::UniChem::REST.new
+  end
+  
+  def test_src_compound_id_2
+    res = @obj.src_compound_id("CHEMBL12", "1") 
+    assert_equal(res.class, Array)
+    assert_equal(res.first.class, Hash)
+  end
+
+  def test_src_compound_id_2_src_id
+    res = @obj.src_compound_id("CHEMBL12", "1") 
+    assert_equal(res.class, Array)
+    assert_equal(res.first.class, Hash)
+  end
+
+  def test_src_compound_id_3
+    res = @obj.src_compound_id("CHEMBL12", "1", "2") 
+    assert_equal(res.class, Array)
+    assert_equal(res.first.class, Hash)
+    assert_equal(res.first["src_compound_id"], "DB00829")
+  end
+
+  def test_src_compound_id_3_src_id
+    res = @obj.src_compound_id("CHEMBL12", "1", "2") 
+    assert_equal(res.class, Array)
+    assert_equal(res.first.class, Hash)
+    assert_equal(res.first["src_compound_id"], "DB00829")
+  end
+
+  def test_src_compound_id_all_2
+    res = @obj.src_compound_id_all("CHEMBL12", "1")
+    t = res.find {|x| x['src_id'] == "1" }
+    assert_equal(res.class, Array)
+    assert_equal(t.class, Hash)
+    assert_equal(t["assignment"], "1")
+    assert_equal(t["src_id"], "1")
+    assert_equal(t["src_compound_id"], "CHEMBL12")
+  end
+
+  def test_src_compound_id_all_3
+    res = @obj.src_compound_id_all("CHEMBL12", "1", "2")
+    t = res.find {|x| x['src_compound_id'] == "DB00829" }    
+    assert_equal(res.class, Array)
+    assert_equal(t.class, Hash)
+    assert_equal(t["assignment"], "1")
+    assert_equal(t["src_compound_id"], "DB00829")
+  end
+
+  def test_mapping
+    res = @obj.mapping("4", "1")
+    t = res.find {|x| x['1'] == "CHEMBL247132" }
+    assert_equal(res.class, Array)
+    assert_equal(t.class, Hash)
+    assert_equal(t["1"], "CHEMBL247132")
+    assert_equal(t["4"], "1592")
+  end
+
+  def test_mapping_src_id
+    res = @obj.mapping("4", "1")
+    t = res.find {|x| x['1'] == "CHEMBL247132" }
+    assert_equal(res.class, Array)
+    assert_equal(t.class, Hash)
+    assert_equal(t["1"], "CHEMBL247132")
+    assert_equal(t["4"], "1592")
+  end
+  
+  def test_inchikey
+    res = @obj.inchikey("AAOVKJBEBIDNHE-UHFFFAOYSA-N")
+    t = res.find {|x| x['src_id'] == "1" }
+    assert_equal(res.class, Array)
+    assert_equal(t.class, Hash)
+    assert_equal(t["src_id"], "1")
+    assert_equal(t["src_compound_id"], "CHEMBL12")
+  end
+  
+  def test_inchikey_all
+    res = @obj.inchikey_all("AAOVKJBEBIDNHE-UHFFFAOYSA-N")
+    t = res.find {|x| x['src_id'] == "1" }
+    assert_equal(res.class, Array)
+    assert_equal(t.class, Hash)
+    assert_equal(t["assignment"], "1")
+    assert_equal(t["src_id"], "1")
+    assert_equal(t["src_compound_id"], "CHEMBL12")
+  end
+  
+  def test_src_ids
+    res = @obj.src_ids
+    assert_equal(res.class, Array)
+    assert_equal(res.first.class, Hash)
+    assert_equal(res.first["src_id"], "1")
+  end
+  
+  def test_sources
+    res = @obj.sources("1")
+    assert_equal(res.class, Array)
+    assert_equal(res.first.class, Hash)
+    assert_equal(res.first["src_id"], "1")
+  end
+  
+  def test_structure
+    res = @obj.structure("CHEMBL12", "1")
+    t = res.find {|x| x['standardinchikey'] == "AAOVKJBEBIDNHE-UHFFFAOYSA-N" }
+    assert_equal(res.class, Array)
+    assert_equal(t.class, Hash)
+    assert_equal(t["standardinchikey"], "AAOVKJBEBIDNHE-UHFFFAOYSA-N")
+    assert_equal(t["standardinchi"], 
+      "InChI=1S/C16H13ClN2O/c1-19-14-8-7-12(17)9-13(14)16(18-10-15(19)20)11-5-3-2-4-6-11/h2-9H,10H2,1H3")
+  end
+  
+  def test_structure_all
+    res = @obj.structure_all("CHEMBL12", "1")
+    assert_equal(res.class, Array)
+    assert_equal(res.first.class, Hash)
+    assert_equal(res.first["assignment"], "1")
+    assert_equal(res.first["standardinchikey"], "AAOVKJBEBIDNHE-UHFFFAOYSA-N")
+    assert_equal(res.first["standardinchi"], 
+      "InChI=1S/C16H13ClN2O/c1-19-14-8-7-12(17)9-13(14)16(18-10-15(19)20)11-5-3-2-4-6-11/h2-9H,10H2,1H3")
+  end
+  
+  def test_src_compound_id_url
+    res = @obj.src_compound_id_url("CHEMBL12", "1", "2")
+    assert_equal(res.class, Array)
+    assert_equal(res.first.class, Hash)
+    assert_equal(res.first["url"], "http://www.drugbank.ca/drugs/DB00829")
+  end
+  
+  def test_src_compound_id_all_obsolete_2
+    res = @obj.src_compound_id_all_obsolete("DB07699", "2")
+    t = res.find {|x| x['src_id'] == "1" }
+    assert_equal(res.class, Array)
+    assert_equal(t.class, Hash)
+    assert_equal(t["assignment"], "1")
+    assert_equal(t["src_id"], "1")
+    assert_equal(t["UCI"], "304698")
+    assert_equal(t["src_compound_id"], "CHEMBL12")
+  end
+  
+  def test_src_compound_id_all_obsolete_3
+    res = @obj.src_compound_id_all_obsolete("DB07699", "2", "1")
+    t = res.find {|x| x['src_id'] == "1" }
+    assert_equal(res.class, Array)
+    assert_equal(t.class, Hash)
+    assert_equal(t["assignment"], "1")
+    assert_equal(t["src_id"], "1")
+    assert_equal(t["UCI"], "304698")
+    assert_equal(t["src_compound_id"], "CHEMBL12")
+  end
+  
+  def test_verbose_inchikey
+    res = @obj.verbose_inchikey("HAUGRYOERYOXHX-UHFFFAOYSA-N")
+    t = res.find {|x| x['name'] == "chembl" }
+    assert_equal(res.class, Array)
+    assert_equal(res.first.class, Hash)
+    assert_equal(res.first["name"], "chembl")
+    assert_equal(res.first["description"], "A database of bioactive drug-like small molecules and associated bioactivities abstracted from the scientific literature")
+    assert_equal(res.first["name_long"], "ChEMBL")
+    assert_equal(res.first["src_compound_id"], ["CHEMBL68500"])
+    assert_equal(res.first["base_id_url"], "https://www.ebi.ac.uk/chembldb/compound/inspect/")
+    assert_equal(res.first["src_id"], "1")
+    assert_equal(res.first["base_id_url_available"], "1")
+    assert_equal(res.first["src_url"], "https://www.ebi.ac.uk/chembl/")
+  end
+  
+end

data/test/test_bio-unichem-rest-uri.rb

@@ -0,0 +1,99 @@
+require 'helper'
+require 'bio-unichem/unichem.rb'
+
+class TestBioUniChemURI < Test::Unit::TestCase
+  def setup
+    @obj = Bio::UniChem::REST::UniChem_URI
+  end
+  
+  def test_src_compound_id_2
+    assert_equal(
+      @obj.src_compound_id("CHEMBL12", "1"), 
+      "https://www.ebi.ac.uk/unichem/rest/src_compound_id/CHEMBL12/1")
+  end
+
+  def test_src_compound_id_3
+    assert_equal(
+      @obj.src_compound_id("CHEMBL12", "1", "2"), 
+      "https://www.ebi.ac.uk/unichem/rest/src_compound_id/CHEMBL12/1/2")
+  end
+
+  def test_src_compound_id_all_2
+    assert_equal(
+      @obj.src_compound_id_all("CHEMBL12", "1"),
+      "https://www.ebi.ac.uk/unichem/rest/src_compound_id_all/CHEMBL12/1")
+  end
+
+  def test_src_compound_id_all_3
+    assert_equal(
+      @obj.src_compound_id_all("CHEMBL12", "1", "2"), 
+      "https://www.ebi.ac.uk/unichem/rest/src_compound_id_all/CHEMBL12/1/2")
+  end
+
+  def test_mapping
+    assert_equal(
+      @obj.mapping("4", "1"), 
+      "https://www.ebi.ac.uk/unichem/rest/mapping/4/1")
+  end
+  
+  def test_inchikey
+    assert_equal(
+      @obj.inchikey("AAOVKJBEBIDNHE-UHFFFAOYSA-N"),
+      "https://www.ebi.ac.uk/unichem/rest/inchikey/AAOVKJBEBIDNHE-UHFFFAOYSA-N")
+  end
+  
+  def test_inchikey_all
+    assert_equal(
+      @obj.inchikey_all("AAOVKJBEBIDNHE-UHFFFAOYSA-N"),
+      "https://www.ebi.ac.uk/unichem/rest/inchikey_all/AAOVKJBEBIDNHE-UHFFFAOYSA-N")
+  end
+  
+  def test_src_ids
+    assert_equal(
+      @obj.src_ids,
+      "https://www.ebi.ac.uk/unichem/rest/src_ids/")      
+  end
+  
+  def test_sources
+    assert_equal(
+      @obj.sources("1"),
+      "https://www.ebi.ac.uk/unichem/rest/sources/1")      
+  end
+  
+  def test_structure
+    assert_equal(
+      @obj.structure("CHEMBL12", "1"),
+      "https://www.ebi.ac.uk/unichem/rest/structure/CHEMBL12/1")    
+  end
+  
+  def test_structure_all
+    assert_equal(
+      @obj.structure_all("CHEMBL12", "1"),
+      "https://www.ebi.ac.uk/unichem/rest/structure_all/CHEMBL12/1")      
+  end
+  
+  def test_src_compound_id_url
+    assert_equal(
+      @obj.src_compound_id_url("CHEMBL12", "1", "2"),
+      "https://www.ebi.ac.uk/unichem/rest/src_compound_id_url/CHEMBL12/1/2")      
+  end
+  
+  def test_src_compound_id_all_obsolete_2
+    assert_equal(
+      @obj.src_compound_id_all_obsolete("DB07699", "2"),
+      "https://www.ebi.ac.uk/unichem/rest/src_compound_id_all_obsolete/DB07699/2")
+  end
+  
+  def test_src_compound_id_all_obsolete_3
+    assert_equal(
+      @obj.src_compound_id_all_obsolete("DB07699", "2", "1"),
+      "https://www.ebi.ac.uk/unichem/rest/src_compound_id_all_obsolete/DB07699/2/1")      
+  end
+  
+  def test_verbose_inchikey
+    assert_equal(
+      @obj.verbose_inchikey("HAUGRYOERYOXHX-UHFFFAOYSA-N"),
+      "https://www.ebi.ac.uk/unichem/rest/verbose_inchikey/HAUGRYOERYOXHX-UHFFFAOYSA-N")      
+  end
+  
+end

data/test/test_bio-unichem.rb

@@ -0,0 +1,5 @@
+require 'helper'
+require 'bio-unichem/unichem.rb'
+
+class TestBioUnichem < Test::Unit::TestCase
+end

metadata

@@ -0,0 +1,162 @@
+--- !ruby/object:Gem::Specification
+name: bio-unichem
+version: !ruby/object:Gem::Version
+  version: 0.1.0
+  prerelease: 
+platform: ruby
+authors:
+- Mitsuteru Nakao
+autorequire: 
+bindir: bin
+cert_chain: []
+date: 2013-02-09 00:00:00.000000000 Z
+dependencies:
+- !ruby/object:Gem::Dependency
+  name: shoulda
+  requirement: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ! '>='
+      - !ruby/object:Gem::Version
+        version: '0'
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ! '>='
+      - !ruby/object:Gem::Version
+        version: '0'
+- !ruby/object:Gem::Dependency
+  name: rdoc
+  requirement: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ~>
+      - !ruby/object:Gem::Version
+        version: '3.12'
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ~>
+      - !ruby/object:Gem::Version
+        version: '3.12'
+- !ruby/object:Gem::Dependency
+  name: bundler
+  requirement: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ! '>'
+      - !ruby/object:Gem::Version
+        version: 1.0.0
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ! '>'
+      - !ruby/object:Gem::Version
+        version: 1.0.0
+- !ruby/object:Gem::Dependency
+  name: jeweler
+  requirement: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ~>
+      - !ruby/object:Gem::Version
+        version: 1.8.4
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ~>
+      - !ruby/object:Gem::Version
+        version: 1.8.4
+- !ruby/object:Gem::Dependency
+  name: bio
+  requirement: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ! '>='
+      - !ruby/object:Gem::Version
+        version: 1.4.2
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ! '>='
+      - !ruby/object:Gem::Version
+        version: 1.4.2
+- !ruby/object:Gem::Dependency
+  name: rdoc
+  requirement: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ~>
+      - !ruby/object:Gem::Version
+        version: '3.12'
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ~>
+      - !ruby/object:Gem::Version
+        version: '3.12'
+description: BioRuby plugin for UniChem REST Web service
+email: mitsuteru.nakao@gmail.com
+executables: []
+extensions: []
+extra_rdoc_files:
+- LICENSE.txt
+- README.md
+files:
+- .document
+- .travis.yml
+- Gemfile
+- LICENSE.txt
+- README.md
+- Rakefile
+- VERSION
+- lib/bio-unichem.rb
+- lib/bio-unichem/model.rb
+- lib/bio-unichem/unichem.rb
+- test/helper.rb
+- test/test.sh
+- test/test_bio-unichem-model.rb
+- test/test_bio-unichem-rest-client.rb
+- test/test_bio-unichem-rest-uri.rb
+- test/test_bio-unichem.rb
+homepage: http://github.com/nakao/bioruby-unichem
+licenses:
+- MIT
+post_install_message: 
+rdoc_options: []
+require_paths:
+- lib
+required_ruby_version: !ruby/object:Gem::Requirement
+  none: false
+  requirements:
+  - - ! '>='
+    - !ruby/object:Gem::Version
+      version: '0'
+      segments:
+      - 0
+      hash: -2975473207476778755
+required_rubygems_version: !ruby/object:Gem::Requirement
+  none: false
+  requirements:
+  - - ! '>='
+    - !ruby/object:Gem::Version
+      version: '0'
+requirements: []
+rubyforge_project: 
+rubygems_version: 1.8.23
+signing_key: 
+specification_version: 3
+summary: BioRuby plugin for UniChem REST Web service
+test_files: []