sylfy 0.0.2 → 0.1.0

data/lib/sylfy/utils/reactionkey.rb

@@ -0,0 +1,197 @@
+# 
+# UniSysDB library in Ruby
+# Copyright (C) 2012
+#
+# @author Natapol Pornputtapong <natapol@chalmers.se>
+#
+
+require 'sylfy/utils/keyhash'
+
+class Array
+	def include_all?(array = [])
+		result = true
+		self_array = {}
+		self.each {|e| self_array[e.split(/;/)[0]] = e.split(/;/)[1] ? e.split(/;/)[1].to_f : 1.0}
+		
+		array.each do |item|
+			if !self_array.has_key?(item.split(/;/)[0])
+				result = false
+			else 
+				result = false if self_array[item] != item.split(/;/)[1].to_f
+			end
+		end
+		
+		return result
+	end
+	
+	def _key_version?
+		array = self.flatten.uniq
+		return array.length == 1 ? array[0] : "X"
+	end
+	
+	def _key_cal_charge
+		charge = [0, 0]
+		self[0].each {|e| charge[0] += e.ord - 78}
+		self[1].each {|e| charge[1] += e.ord - 78}
+		return charge[0] == charge[1] ? "B" : "X"
+	end
+	
+	def _key_cal_coef
+		sum = 0
+		self.flatten.each {|e| sum += e}
+		return sum.floor >= 26 ? "Z" : (sum.floor + 64).chr
+	end
+	
+	def _key_include?(str)
+		result = false
+		self.each {|e| result = true if e.split(/;/)[0] == str.split(/;/)[0]}
+		return result
+	end
+end
+
+module Sylfy
+	
+	module Utils
+        
+        #COFACTORS = [
+        #    ["FAD-FADH2", ["VWWQXMAJTJZDQX-UYBVJOGSSA-N"], ["YPZRHBJKEMOYQH-UYBVJOGSSA-N"], "B"],
+        #    ["FMN-FMNH2", ["FVTCRASFADXXNN-SCRDCRAPSA-N"], ["YTNIXZGTHTVJBW-SCRDCRAPSA-N"], "C"],
+        #    ["NAD-NADH", ["BAWFJGJZGIEFAR-NNYOXOHSSA-O"], ["BOPGDPNILDQYTO-NNYOXOHSSA-N"], "D"],
+        #    ["NADP-NADPH", ["XJLXINKUBYWONI-NNYOXOHSSA-O"], ["ACFIXJIJDZMPPO-NNYOXOHSSA-N"], "E"]
+        #]
+        
+        COFACTORS = []
+        
+        PORTERS = []
+        
+        
+		def self.reactionkey(leftin, rightin, direction = nil)
+			
+            #key[:first].push(item[0][0..13])
+            #key[:second].push(item[0][15..22])
+            #key[:flag].push(item[0][23])
+            #key[:ver].push(item[0][24])
+            #key[:indicator].push(item[0][26])
+            #
+			#AAAAAAAAAAAAAA-BBBBBBBBFV-P
+			#AAAAAAAAAAAAAA is the first hash block.
+			#It is a 14-character hash encoding the basic (Mobile-H) InChI layer, that is, molecular skeleton (connectivity).
+			#BBBBBBBB is the second hash block.
+			#It is an 8-character hash of the remaining layers (except for the "/p" segment, which accounts for added or removed protons and is not hashed at all; instead, the number of protons is indicated at the end of the InChIKey). In all cases, this block encodes stereochemistry and isotopic substitution information, associated with molecular connectivity expressed by the first block. In case of Non-standard InChI, it also encodes information on the exact position of tautomeric hydrogens (if any), as well as on the related stereo/isotopic data.
+			#F is a flag which indicates the kind of InChIKey.
+			#It is 'S' for Standard InChIKey (produced out of Standard InChI) and 'N' for Non-standard.
+			#V is an InChI version character.
+			#It is 'A' for version 1 ( 'B' is reserved for version 2, etc. ).
+			#P is a [de]protonation indicator.
+			#
+            #
+            # input InChIKey;coef
+            
+            version = "A"
+            
+			reverse_sign = {'<=' => '=>', '=>' => '<=', '<=>' => '<=>', '<?>' => '<?>'}
+			sign_symbol = {'<=' => 'B', '=>' => 'F', '<=>' => 'R', '<?>' => 'U'}
+			
+            both = []
+            
+            if direction && sign_symbol.keys.include?(direction) && leftin && rightin && !leftin.empty? && !rightin.empty? && leftin != rightin
+				
+				left = leftin.dup
+				right = rightin.dup
+				
+				cofactor_symbol = "A"
+				
+				COFACTORS.each do |cofactor|
+					if left.include_all?(cofactor[1]) && right.include_all?(cofactor[2])
+						left.delete_if {|x| cofactor[1].include?(x.split(/;/)[0]) }
+						right.delete_if {|x| cofactor[2].include?(x.split(/;/)[0]) }
+						cofactor_symbol = cofactor[3]
+					elsif left.include_all?(cofactor[2]) && right.include_all?(cofactor[1])
+						left.delete_if {|x| cofactor[2].include?(x.split(/;/)[0]) }
+						right.delete_if {|x| cofactor[1].include?(x.split(/;/)[0]) }
+						cofactor_symbol = cofactor[3]
+					end
+				end
+				
+				if (left.sort <=> right.sort) < 0
+					dsign = sign_symbol[direction]
+					both = [left.sort, right.sort]
+				else
+					dsign = sign_symbol[reverse_sign[direction]]
+					both = [right.sort, left.sort]
+				end
+				
+			elsif leftin != rightin && ((leftin && !leftin.empty?) || (rightin && rightin.empty?))
+				left = leftin ? leftin.dup : []
+				right = rightin ? rightin.dup : []
+				
+				cofactor_symbol = "Z"
+				
+				PORTERS.each do |cofactor|
+					if left.include_all?(cofactor[1]) && right.include_all?(cofactor[2])
+						left.delete_if {|x| cofactor[1]._key_include?(x) }
+						right.delete_if {|x| cofactor[2]._key_include?(x) }
+						cofactor_symbol = cofactor[3]
+					elsif left.include_all?(cofactor[2]) && right.include_all?(cofactor[1])
+						left.delete_if {|x| cofactor[2]._key_include?(x) }
+						right.delete_if {|x| cofactor[1]._key_include?(x) }
+						cofactor_symbol = cofactor[3]
+					end
+				end
+				
+				if (left.sort <=> right.sort) < 0
+					dsign = "A"
+					both = [left.sort, right.sort]
+				else
+					dsign = "Z"
+					both = [right.sort, left.sort]
+				end
+			else
+				return nil
+            end
+            
+            
+            code = {:first => [], :second => [], :flag => [], :ver => [], :charge => [], :coef => []}
+            both.each do |side|
+				part = {:first => [], :second => [], :flag => [], :ver => [], :charge => [], :coef => []}
+				side.each do |item|
+					part[:first].push(item[0..13])
+					part[:second].push(item[15..22])
+					part[:flag].push(item[23])
+					part[:ver].push(item[24])
+					part[:charge].push(item[26])
+					part[:coef].push(item.split(/;/)[1] ? item.split(/;/)[1].to_f : 1.0)
+				end
+				
+				part.each_pair do |k, v|
+					code[k].push([:first, :second].include?(k) ? v.join('+') : v)
+				end
+			end
+			
+			# construct code string
+			codeString = {}
+			codeString[:A] = Sylfy::Utils::Keyhash.key(code[:first].join('/'))
+			codeString[:B] = Sylfy::Utils::Keyhash.key(code[:second].join('/'), false)
+			codeString[:v] = code[:ver]._key_version?
+			codeString[:F] = codeString[:version] != "X" ? code[:flag]._key_version? : "X"
+			codeString[:H] = code[:charge]._key_cal_charge
+			codeString[:E] = code[:coef]._key_cal_coef
+			codeString[:CC] = "#{["A", "Z"].include?(dsign) ? "Z" : "A"}#{cofactor_symbol}"
+				
+			# construct key AAAAAAAAAAAAAA-BBBBBBBBFvV-HE-CC-D
+            # A calculate from list of First part of InChIKey
+            # B calculate from list of Second part of InChIKey
+            # F Flag S for standard X for not
+            # E sum of co-efficient
+            # H charge B for balance and X for not
+            # C indicate cofactor code
+            # v indicate version of InChIKey
+            # V indicate version of this key function
+            # D indicate direction
+			# return "#{codeString[:A]}-#{codeString[:B]}#{codeString[:F]}#{codeString[:v]}#{version}-#{codeString[:H]}#{codeString[:E]}-#{codeString[:CC]}-#{dsign}"
+			return "#{codeString[:A]}-#{codeString[:B]}#{codeString[:F]}#{codeString[:v]}#{version}-#{codeString[:H]}#{codeString[:E]}-#{dsign}"
+        end
+		
+	end
+end
+

data/lib/sylfy/version.rb

@@ -8,5 +8,5 @@
 #
 
 module Sylfy
-    VERSION = "0.0.2"
+    VERSION = "0.1.0"
 end

data/sylfy.gemspec

@@ -5,7 +5,7 @@ require "sylfy/version"
 Gem::Specification.new do |s|
     s.name          = 'sylfy'
     s.version       = Sylfy::VERSION
-    s.date          = '2010-04-28'
+    s.date          = '2014-07-03'
     s.platform      = Gem::Platform::RUBY
     
     s.summary       = "Provides some useful functions for systems biology field."
@@ -16,24 +16,20 @@ Gem::Specification.new do |s|
     s.homepage      = 'http://rubygems.org/gems/sylfy'
     s.license       = 'GPL'
     
-#    s.rubyforge_project = "neography"
+#    s.rubyforge_project = ""
     
     s.files         = `git ls-files`.split("\n")
     s.test_files    = `git ls-files -- {test,spec,features}/*`.split("\n")
     s.executables   = `git ls-files -- bin/*`.split("\n").map{ |f| File.basename(f) }
     s.require_paths = ["lib"]
     
-    s.add_dependency "gsl", ">= 1.15.3"
-    s.add_dependency "bio", ">= 1.4.3.0001"
+    s.add_dependency "rb-gsl", "~> 1.16"
+    s.add_dependency "bio", "~> 1.4"
+    s.add_dependency "savon", "~> 2.0"
+    s.add_dependency "statsample", "~> 1.0"
+    s.add_dependency "rubabel", "~> 0.4"
     
-#    s.add_development_dependency "rspec", ">= 2.11"
-#    s.add_development_dependency "net-http-spy", "0.2.1"
-#    s.add_development_dependency "rake", ">= 0.8.7"
-#    s.add_development_dependency "coveralls"
-#    s.add_dependency "httpclient", ">= 2.3.3"
-#    s.add_dependency "rake", ">= 0.8.7"
-#    s.add_dependency "json", ">= 1.7.7"
-#    s.add_dependency "os", ">= 0.9.6"
-#    s.add_dependency "rubyzip", ">= 0.9.7"
-#    s.add_dependency "multi_json", ">= 1.3.2"
-end
+#    s.add_development_dependency "rspec", "~> 2.11"
+#    s.add_dependency "httpclient", "~> 2.3.3"
+
+end

data/test/test_kegg_rest.rb

@@ -0,0 +1,58 @@
+require "./lib/sylfy.rb"
+require "test/unit"
+
+
+class TestKEGGREST < Test::Unit::TestCase
+    
+    def test_list
+        assert_nothing_thrown("pathway") {Sylfy::Service::KEGGREST::list("pathway")}
+        assert_nothing_thrown("pathway/hsa") {Sylfy::Service::KEGGREST::list("pathway/hsa")}
+        assert_nothing_thrown("organism") {Sylfy::Service::KEGGREST::list("organism")}
+        assert_nothing_thrown("hsa") {Sylfy::Service::KEGGREST::list("hsa")}
+        assert_nothing_thrown("T01001") {Sylfy::Service::KEGGREST::list("T01001")}
+        assert_nothing_thrown("hsa:10458+ece:Z5100") {Sylfy::Service::KEGGREST::list("hsa:10458+ece:Z5100")}
+        assert_nothing_thrown("cpd:C01290+gl:G00092") {Sylfy::Service::KEGGREST::list("cpd:C01290+gl:G00092")}
+        assert_nothing_thrown("C01290+G00092") {Sylfy::Service::KEGGREST::list("C01290+G00092")}
+    end
+    
+    def test_find
+        assert_nothing_thrown("") {Sylfy::Service::KEGGREST::find("genes", "shiga+toxin")}
+        assert_nothing_thrown("") {Sylfy::Service::KEGGREST::find("genes", '"shiga toxin"')}
+        assert_nothing_thrown("") {Sylfy::Service::KEGGREST::find("compound", "C7H10O5", "formula")}
+        assert_nothing_thrown("") {Sylfy::Service::KEGGREST::find("compound", "O5C7", "formula")}
+        assert_nothing_thrown("") {Sylfy::Service::KEGGREST::find("compound", "174.05", "exact_mass")}
+        assert_nothing_thrown("") {Sylfy::Service::KEGGREST::find("compound", "300-310", "mol_weight")}
+    end
+    
+    def test_get
+        assert_nothing_thrown("cpd:C01290+gl:G00092	") {Sylfy::Service::KEGGREST::get("cpd:C01290+gl:G00092")}
+        assert_nothing_thrown("C01290+G00092") {Sylfy::Service::KEGGREST::get("C01290+G00092")}
+        assert_nothing_thrown("hsa:10458+ece:Z5100") {Sylfy::Service::KEGGREST::get("hsa:10458+ece:Z5100")}
+        assert_nothing_thrown("hsa:10458+ece:Z5100/aaseq") {Sylfy::Service::KEGGREST::get("hsa:10458+ece:Z5100", "aaseq")}
+        assert_nothing_thrown("hsa05130/kgml") {Sylfy::Service::KEGGREST::get("hsa05130", "kgml")}
+    end
+
+    def test_conv
+        assert_nothing_thrown("eco/ncbi-geneid") {Sylfy::Service::KEGGREST::conv("eco", "ncbi-geneid")}
+        assert_nothing_thrown("ncbi-geneid/eco") {Sylfy::Service::KEGGREST::conv("ncbi-geneid", "eco")}
+        assert_nothing_thrown("ncbi-gi/hsa:10458+ece:Z5100") {Sylfy::Service::KEGGREST::conv("ncbi-gi", "hsa:10458+ece:Z5100")}
+        assert_nothing_thrown("genes/ncbi-gi:3113320") {Sylfy::Service::KEGGREST::conv("genes", "ncbi-gi:3113320")}
+    end
+    
+    def test_link
+        assert_nothing_thrown("pathway/hsa") {Sylfy::Service::KEGGREST::link("pathway", "hsa")}
+        assert_nothing_thrown("hsa/pathway") {Sylfy::Service::KEGGREST::link("hsa", "pathway")}
+        assert_nothing_thrown("pathway/hsa:10458+ece:Z5100") {Sylfy::Service::KEGGREST::link("pathway", "hsa:10458+ece:Z5100")}
+        assert_nothing_thrown("genes/K00500") {Sylfy::Service::KEGGREST::link("genes", "K00500")}
+        assert_nothing_thrown("genes/hsa00010") {Sylfy::Service::KEGGREST::link("genes", "hsa00010")}
+        assert_nothing_thrown("hsa/hsa00010") {Sylfy::Service::KEGGREST::link("hsa", "hsa00010")}
+        assert_nothing_thrown("ko/map00010") {Sylfy::Service::KEGGREST::link("ko", "map00010")}
+        assert_nothing_thrown("ko/ko00010") {Sylfy::Service::KEGGREST::link("ko", "ko00010")}
+        assert_nothing_thrown("rn/map00010") {Sylfy::Service::KEGGREST::link("rn", "map00010")}
+        assert_nothing_thrown("rn/rn00010") {Sylfy::Service::KEGGREST::link("rn", "rn00010")}
+        assert_nothing_thrown("ec/map00010") {Sylfy::Service::KEGGREST::link("ec", "map00010")}
+        assert_nothing_thrown("ec/ec00010") {Sylfy::Service::KEGGREST::link("ec", "ec00010")}
+        assert_nothing_thrown("cpd/map00010") {Sylfy::Service::KEGGREST::link("cpd", "map00010")}
+    end
+    
+end

data/test/test_reactionkey.rb

@@ -0,0 +1,37 @@
+require "./lib/sylfy.rb"
+require "test/unit"
+
+class TestReactionKey < Test::Unit::TestCase
+    def test_reactionkey
+        a = ['MEFKEPWMEQBLKI-AIRLBKTGSA-O', 'QAIPRVGONGVQAS-DUXPYHPUSA-M;2.0']
+        b = ['ZJUKTBDSGOFHSH-WFMPWKQPSA-N', 'KSEBMYQBYZTDHS-HWKANZROSA-M', 'GPRLSGONYQIRFK-UHFFFAOYSA-N']
+        
+        c = ['MEFKEPWMEQBLKI-AIRLBKTGSA-O', 'QAIPRVGONGVQAS-DUXPYHPUSA-M;2.0', "VWWQXMAJTJZDQX-UYBVJOGSSA-N"]
+        d = ['ZJUKTBDSGOFHSH-WFMPWKQPSA-N', 'KSEBMYQBYZTDHS-HWKANZROSA-M', 'GPRLSGONYQIRFK-UHFFFAOYSA-N', "YPZRHBJKEMOYQH-UYBVJOGSSA-N"]
+        
+        assert_equal(Sylfy::Utils::reactionkey(b, a, "<="), Sylfy::Utils::reactionkey(a, b, "=>"))
+        assert_equal(Sylfy::Utils::reactionkey(b, a, "<=>"), Sylfy::Utils::reactionkey(a, b, "<=>"))
+        assert_equal(Sylfy::Utils::reactionkey(b, a, "<?>"), Sylfy::Utils::reactionkey(a, b, "<?>"))
+        
+        assert_equal("#{Sylfy::Utils::reactionkey(a, b, "<=")[0..-2]}B", Sylfy::Utils::reactionkey(a, b, "=>"))
+        assert_equal("#{Sylfy::Utils::reactionkey(a, b, "<=")[0..-2]}F", Sylfy::Utils::reactionkey(a, b, "<="))
+        assert_equal("#{Sylfy::Utils::reactionkey(a, b, "<=")[0..-2]}R", Sylfy::Utils::reactionkey(a, b, "<=>"))
+        assert_equal("#{Sylfy::Utils::reactionkey(a, b, "<=")[0..-2]}U", Sylfy::Utils::reactionkey(a, b, "<?>"))
+        
+        assert_equal(Sylfy::Utils::reactionkey(d, c, "<="), Sylfy::Utils::reactionkey(c, d, "=>"))
+        assert_equal(Sylfy::Utils::reactionkey(d, c, "<=>"), Sylfy::Utils::reactionkey(c, d, "<=>"))
+        assert_equal(Sylfy::Utils::reactionkey(d, c, "<?>"), Sylfy::Utils::reactionkey(c, d, "<?>"))
+        assert_equal("#{Sylfy::Utils::reactionkey(c, d, "<=")[0..-2]}B", Sylfy::Utils::reactionkey(c, d, "=>"))
+        assert_equal("#{Sylfy::Utils::reactionkey(c, d, "<=")[0..-2]}F", Sylfy::Utils::reactionkey(c, d, "<="))
+        assert_equal("#{Sylfy::Utils::reactionkey(c, d, "<=")[0..-2]}R", Sylfy::Utils::reactionkey(c, d, "<=>"))
+        assert_equal("#{Sylfy::Utils::reactionkey(c, d, "<=")[0..-2]}U", Sylfy::Utils::reactionkey(c, d, "<?>"))
+        
+        assert_not_equal(Sylfy::Utils::reactionkey(a, d, "<?>"), Sylfy::Utils::reactionkey(c, d, "<?>"))
+        assert_not_equal(Sylfy::Utils::reactionkey(c, b, "<?>"), Sylfy::Utils::reactionkey(c, d, "<?>"))
+        
+        assert_equal(Sylfy::Utils::reactionkey(b.shuffle, a.shuffle, "=>"), Sylfy::Utils::reactionkey(b, a, "=>"))
+        
+        #assert_equal("RBBGYPGMOGQICO-ANDFYIIK-PRHFFSIG-AB-A-B", Sylfy::Utils::reactionkey(c, d, "=>"))
+        #assert_equal("RBBGYPGMOGQICO-ANDFYIIK-PRHFFSIG-AA-A-B", Sylfy::Utils::reactionkey(a, b, "=>"))
+    end
+end

metadata

@@ -1,43 +1,85 @@
 --- !ruby/object:Gem::Specification
 name: sylfy
 version: !ruby/object:Gem::Version
-  version: 0.0.2
+  version: 0.1.0
 platform: ruby
 authors:
 - Natapol Pornputtapong
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2010-04-28 00:00:00.000000000 Z
+date: 2014-07-03 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
-  name: gsl
+  name: rb-gsl
   requirement: !ruby/object:Gem::Requirement
     requirements:
-    - - '>='
+    - - ~>
       - !ruby/object:Gem::Version
-        version: 1.15.3
+        version: '1.16'
   type: :runtime
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
-    - - '>='
+    - - ~>
       - !ruby/object:Gem::Version
-        version: 1.15.3
+        version: '1.16'
 - !ruby/object:Gem::Dependency
   name: bio
   requirement: !ruby/object:Gem::Requirement
     requirements:
-    - - '>='
+    - - ~>
       - !ruby/object:Gem::Version
-        version: 1.4.3.0001
+        version: '1.4'
   type: :runtime
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
-    - - '>='
+    - - ~>
       - !ruby/object:Gem::Version
-        version: 1.4.3.0001
+        version: '1.4'
+- !ruby/object:Gem::Dependency
+  name: savon
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - ~>
+      - !ruby/object:Gem::Version
+        version: '2.0'
+  type: :runtime
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - ~>
+      - !ruby/object:Gem::Version
+        version: '2.0'
+- !ruby/object:Gem::Dependency
+  name: statsample
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - ~>
+      - !ruby/object:Gem::Version
+        version: '1.0'
+  type: :runtime
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - ~>
+      - !ruby/object:Gem::Version
+        version: '1.0'
+- !ruby/object:Gem::Dependency
+  name: rubabel
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - ~>
+      - !ruby/object:Gem::Version
+        version: '0.4'
+  type: :runtime
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - ~>
+      - !ruby/object:Gem::Version
+        version: '0.4'
 description: Systems Biology Library for Ruby
 email: natapol.por@gmail.com
 executables: []
@@ -45,16 +87,44 @@ extensions: []
 extra_rdoc_files: []
 files:
 - README.md
+- Rakefile
 - lib/sylfy.rb
-- lib/sylfy/math.rb
+- lib/sylfy/add.rb
+- lib/sylfy/add/bio_kegg_kgml.rb
+- lib/sylfy/datamodel.rb
+- lib/sylfy/feature.rb
+- lib/sylfy/mathf.rb
+- lib/sylfy/pattern.rb
+- lib/sylfy/service.rb
+- lib/sylfy/service/biocycrest.rb
+- lib/sylfy/service/cactusncirest.rb
+- lib/sylfy/service/cbioportal.rb
+- lib/sylfy/service/chembl.rb
+- lib/sylfy/service/ebisoap.rb
+- lib/sylfy/service/ensemblrest.rb
+- lib/sylfy/service/ensemblrest/archive.rb
+- lib/sylfy/service/ensemblrest/comparative.rb
+- lib/sylfy/service/ensemblrest/xrefs.rb
+- lib/sylfy/service/hgncrest.rb
 - lib/sylfy/service/keggrest.rb
 - lib/sylfy/service/keggrest/conv.rb
 - lib/sylfy/service/keggrest/find.rb
+- lib/sylfy/service/keggrest/get.rb
 - lib/sylfy/service/keggrest/link.rb
 - lib/sylfy/service/keggrest/list.rb
-- lib/sylfy/service/keggrest/restKegg_get.rb
+- lib/sylfy/service/lipidmaprest.rb
+- lib/sylfy/service/pubchem.rb
+- lib/sylfy/service/pubchemrest.rb
+- lib/sylfy/service/rest.rb
+- lib/sylfy/service/soapwsdl.rb
+- lib/sylfy/service/unichemrest.rb
+- lib/sylfy/utils.rb
+- lib/sylfy/utils/keyhash.rb
+- lib/sylfy/utils/reactionkey.rb
 - lib/sylfy/version.rb
 - sylfy.gemspec
+- test/test_kegg_rest.rb
+- test/test_reactionkey.rb
 homepage: http://rubygems.org/gems/sylfy
 licenses:
 - GPL
@@ -75,8 +145,10 @@ required_rubygems_version: !ruby/object:Gem::Requirement
       version: '0'
 requirements: []
 rubyforge_project: 
-rubygems_version: 2.0.3
+rubygems_version: 2.0.14.1
 signing_key: 
 specification_version: 4
 summary: Provides some useful functions for systems biology field.
-test_files: []
+test_files:
+- test/test_kegg_rest.rb
+- test/test_reactionkey.rb