mimiweb 0.1.1 → 0.1.2

data/README.rdoc

@@ -6,37 +6,34 @@ http://portal.ncibi.org/gateway/
 
 http://mimi.ncibi.org/MimiWeb/main-page.jsp
 
-= Usage
+== Usage
 
-There are four methods on the Mimiweb Web Service. With this client you can access them as follows
+  require 'mimiweb'
 
-== Free text search
+  # Free text search
+  results = Mimiweb.search("pwp1")
 
-ruby-1.9.2-p290 :001 > results = Mimiweb.search("pwp1")
+  # GeneID search (Entrez)
+  results = Mimiweb.entrez(1436)
+  
+  # Or pass a type. Types are: compounds, interactions, reactions, nlp.
+  # Default = :interactions
 
-== GeneID search
+  results = Mimiweb.entrez(7389, :compounds)
 
-ruby-1.9.2-p290 :001 > results = Mimiweb.entrez(1436)
 
-or
+  # KEGG CompundID search
+  results = Mimiweb.kegg_compund("C00061")
 
-Pass a type as a second parameter
+  # KEGG ReactionID search
 
-:compounds
-:reactions
-:nlp
-:interactions # default
+  results = Mimiweb.kegg_reaction("R00548")
 
-ruby-1.9.2-p290 :001 > results = Mimiweb.entrez(1436, type)
 
+== To Do
 
-== KEGG CompundID search
-
-ruby-1.9.2-p290 :001 > results = Mimiweb.kegg_compund("C00061")
-
-== KEGG ReactionID search
-
-ruby-1.9.2-p290 :001 > results = Mimiweb.kegg_reaction("R00548")
+* Tests
+* Error handling
 
 == Contributing to mimiweb
  
@@ -51,4 +48,5 @@ ruby-1.9.2-p290 :001 > results = Mimiweb.kegg_reaction("R00548")
 == Copyright
 
 Copyright (c) 2011 Jose Irizarry. See LICENSE.txt for
-further details.
+further details.
+

data/VERSION

@@ -1 +1 @@
-0.1.1
+0.1.2

data/lib/mimiweb.rb

@@ -6,16 +6,16 @@ module Mimiweb
     include HTTParty 
     BASE_URL =  'http://mimi.ncibi.org/MimiWeb/fetch.jsp?'
     def search(term)
-      get_results(:search, term)
+      get_results(:search, term, type="")
     end
     def entrez(id, type="interactions")
       get_results(:geneid, id, type)
     end
     def kegg_compound(id)
-      results = get_results(:cid, id)
+      get_results(:cid, id, type="")
     end
     def kegg_reaction(id)
-      get_results(:rid, id)
+      get_results(:rid, id, type="")
     end
 
     private

data/mimiweb.gemspec

@@ -5,11 +5,11 @@
 
 Gem::Specification.new do |s|
   s.name = "mimiweb"
-  s.version = "0.1.1"
+  s.version = "0.1.2"
 
   s.required_rubygems_version = Gem::Requirement.new(">= 0") if s.respond_to? :required_rubygems_version=
   s.authors = ["Jose Irizarry"]
-  s.date = "2011-10-08"
+  s.date = "2011-10-11"
   s.description = "Access to MiMI and Metabolomics databases via a web service provided by NCIBI."
   s.email = "jose@mrkp.co"
   s.extra_rdoc_files = [

data/test/test_mimiweb.rb

@@ -1,4 +1,44 @@
 require 'helper'
 class TestMimiweb < Test::Unit::TestCase
+	def test_free_text_search
+		term = "pwp1"
+		results = Mimiweb.search(term)
+		assert_equal 'Array', results.class.to_s
+	end
 
+	def test_entrez_compounds_search
+		term = 7389
+		results = Mimiweb.entrez(term, :compounds)
+		assert_equal 'Array', results.class.to_s
+	end
+
+	def test_entrez_reactions_search
+		term = 1436
+		results = Mimiweb.entrez(term, :reactions)
+		assert_equal 'Hashie::Mash', results.class.to_s
+	end
+
+	def test_entrez_nlp_search
+		term = 4005
+		results = Mimiweb.entrez(term, :nlp)
+		assert_equal 'Array', results.class.to_s
+	end
+
+	def test_entrez_interactions_search
+		term = 1436
+		results = Mimiweb.entrez(term)
+		assert_equal 'Array', results.class.to_s
+	end
+
+	def test_kegg_compound_search
+		term = "C00061"
+		results = Mimiweb.kegg_compound(term)
+		assert_equal 'Hashie::Mash', results.class.to_s
+	end
+
+	def test_kegg_reactions_search
+		term = "R00548"
+		results = Mimiweb.kegg_reaction(term)
+		assert_equal 'Hashie::Mash', results.class.to_s
+	end
 end

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: mimiweb
 version: !ruby/object:Gem::Version
-  version: 0.1.1
+  version: 0.1.2
   prerelease: 
 platform: ruby
 authors:
@@ -9,11 +9,11 @@ authors:
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2011-10-08 00:00:00.000000000Z
+date: 2011-10-11 00:00:00.000000000Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: shoulda
-  requirement: &79493870 !ruby/object:Gem::Requirement
+  requirement: &81283900 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ! '>='
@@ -21,10 +21,10 @@ dependencies:
         version: '0'
   type: :development
   prerelease: false
-  version_requirements: *79493870
+  version_requirements: *81283900
 - !ruby/object:Gem::Dependency
   name: bundler
-  requirement: &79493550 !ruby/object:Gem::Requirement
+  requirement: &81283560 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ~>
@@ -32,10 +32,10 @@ dependencies:
         version: 1.0.0
   type: :development
   prerelease: false
-  version_requirements: *79493550
+  version_requirements: *81283560
 - !ruby/object:Gem::Dependency
   name: jeweler
-  requirement: &79493170 !ruby/object:Gem::Requirement
+  requirement: &81283310 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ~>
@@ -43,10 +43,10 @@ dependencies:
         version: 1.6.4
   type: :development
   prerelease: false
-  version_requirements: *79493170
+  version_requirements: *81283310
 - !ruby/object:Gem::Dependency
   name: rcov
-  requirement: &79492870 !ruby/object:Gem::Requirement
+  requirement: &81283010 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ! '>='
@@ -54,10 +54,10 @@ dependencies:
         version: '0'
   type: :development
   prerelease: false
-  version_requirements: *79492870
+  version_requirements: *81283010
 - !ruby/object:Gem::Dependency
   name: httparty
-  requirement: &79492560 !ruby/object:Gem::Requirement
+  requirement: &81282680 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ! '>='
@@ -65,10 +65,10 @@ dependencies:
         version: '0'
   type: :development
   prerelease: false
-  version_requirements: *79492560
+  version_requirements: *81282680
 - !ruby/object:Gem::Dependency
   name: hashie
-  requirement: &79492280 !ruby/object:Gem::Requirement
+  requirement: &81282380 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ! '>='
@@ -76,7 +76,7 @@ dependencies:
         version: '0'
   type: :development
   prerelease: false
-  version_requirements: *79492280
+  version_requirements: *81282380
 description: Access to MiMI and Metabolomics databases via a web service provided
   by NCIBI.
 email: jose@mrkp.co
@@ -112,7 +112,7 @@ required_ruby_version: !ruby/object:Gem::Requirement
       version: '0'
       segments:
       - 0
-      hash: -105208845
+      hash: 662934685
 required_rubygems_version: !ruby/object:Gem::Requirement
   none: false
   requirements: