oba-client 2.0.3 → 2.1.0

data/.gitignore

@@ -0,0 +1,6 @@
+doc
+pkg
+.yardoc
+.buildpath
+.project
+

data/History.md

@@ -1,3 +1,6 @@
+## 2.0.4 / 2010-07-17
+No notes were provided for this release.
+
 ## 2.0.3 / 2010-07-17
 Quick fix in docs.
 

data/README.md

@@ -1,10 +1,10 @@
 # oba-client
 
-* [RubyForge project](http://rubyforge.org/projects/oba-client "RubyForge project")
+* [GitHub](github.com/rtirrell/oba-client_ruby)
 
 ## DESCRIPTION:
 
-A client for accessing the NCBO's Open Biomedical Annotator service.
+A client for accessing the NCBO's Open Biomedical Annotator web service.
 See [the Annotator documentation](http://www.bioontology.org/wiki/index.php/Annotator_User_Guide "Documentation") for much more information.
 
 ## FEATURES:

data/Rakefile

@@ -1,17 +1,71 @@
 require "rubygems"
-require "hoe"
+require File.dirname(__FILE__) + "/lib/oba-client.rb"
+#require "hoe"
 
-Hoe.plugin :yard
+#Hoe.plugin :yard
 
-Hoe.spec "oba-client" do
-  self.developer "Rob Tirrell", "rpt@stanford.edu"
-  self.url             = "http://rubyforge.org/projects/oba-client"
-    
-  self.yard_title      = "OBAClient Documentation"
-  self.yard_options    = ["--default-return", "void"]
-  self.yard_markup     = "markdown"
-  self.remote_yard_dir = ""
+#Hoe.spec "oba-client" do
+#  self.developer "Rob Tirrell", "rpt@stanford.edu"
+#  self.url             = "http://rubyforge.org/projects/oba-client"
+#    
+#  self.yard_title      = "OBAClient Documentation"
+#  self.yard_options    = ["--default-return", "void"]
+#  self.yard_markup     = "markdown"
+#  self.remote_yard_dir = ""
+#
+#  self.rubyforge_name = "oba-client"
+#end
 
-  self.rubyforge_name = "oba-client"
+require "rubygems"
+require "rake"
+
+begin
+  require "jeweler"
+  Jeweler::Tasks.new do |gem|
+    gem.name = "oba-client"
+    gem.summary = "A client for the Open Biomedical Annotator."
+    gem.description = "See above."
+    gem.email = "rpt@stanford.edu"
+    gem.homepage = "http://github.com/rtirrell/oba-client"
+    gem.authors = ["Rob Tirrell"]
+    gem.add_development_dependency "thoughtbot-shoulda", ">= 0"
+    gem.add_development_dependency "yard", ">= 0"
+    # gem is a Gem::Specification... see http://www.rubygems.org/read/chapter/20 for additional settings
+  end
+  Jeweler::GemcutterTasks.new
+rescue LoadError
+  puts "Jeweler (or a dependency) not available. Install it with: gem install jeweler"
 end
 
+require "rake/testtask"
+Rake::TestTask.new(:test) do |test|
+  test.libs << "lib" << "test"
+  test.pattern = "test/**/test_*.rb"
+  test.verbose = true
+end
+
+begin
+  require "rcov/rcovtask"
+  Rcov::RcovTask.new do |test|
+    test.libs << "test"
+    test.pattern = "test/**/test_*.rb"
+    test.verbose = true
+  end
+rescue LoadError
+  task :rcov do
+    abort "RCov is not available. In order to run rcov, you must: sudo gem install spicycode-rcov"
+  end
+end
+
+task :test => :check_dependencies
+
+task :default => :test
+
+begin
+  require "yard"
+  YARD::Rake::YardocTask.new
+rescue LoadError
+  task :yardoc do
+    abort "YARD is not available. In order to run yardoc, you must: sudo gem install yard"
+  end
+end

data/VERSION

@@ -0,0 +1 @@
+2.1.0

data/lib/oba-client.rb

@@ -9,7 +9,7 @@ require "uri"
 # things we do: get text, and parse it. We can do both independently or 
 # serially.
 class OBAClient
-  VERSION = "2.0.3"
+  VERSION = "2.0.4"
 
   ##
   # A high HTTP read timeout, as the service sometimes takes awhile to respond.
@@ -50,10 +50,13 @@ class OBAClient
   # Instantiate the class with a set of reused options. Options used by the
   # method are:
   #
-  #   * [String] uri: the URI of the annotator service (default: {DEFAULT_URI}).
-  #   * [Fixnum] timeout: the length of the read timeout (default: {DEFAULT_TIMEOUT}).
-  #   * [Boolean] parse_xml: whether to parse the received text (default: false).
-  #   * [Array<String>] ontologies: a pseudo-parameter which will set both
+  #   * {String} **uri**: the URI of the annotator service (default: 
+  #     {DEFAULT_URI}).
+  #   * {Fixnum} **timeout**: the length of the read timeout (default: 
+  #     {DEFAULT_TIMEOUT}).
+  #   * {Boolean} **parse_xml**: whether to parse the received text (default: 
+  #     false).
+  #   * {Array}<{String}> **ontologies**: a pseudo-parameter which sets both
   #      ontologiesToExpand and ontologiesToKeepInResult.
   # @param [Hash<String, String>] options Parameters for the annotation.
   def initialize(options = {})
@@ -83,7 +86,8 @@ class OBAClient
     end
 
     if !@options.include?(:email)
-      puts "TIP: as a courtesy, consider including your email in the request (:email => 'a@b.com')"
+      puts "TIP: as a courtesy, consider including your email in the " + 
+           "request (:email => 'a@b.com')"
     end
   end
 
@@ -187,9 +191,11 @@ class OBAClient
   }
 
   ##
-  # Parse a context - an annotation, or a mapping/mgrep context bean.
+  # Parse a context: an annotation, or a mapping/mgrep context bean.
+  #
   # @param [Nokgiri::XML::Node] context The root node of the context.
-  # @return Hash<Symbol, Object> The parsed context.
+  #
+  # @return [Hash<Symbol, Object>] The parsed context.
   def self.parse_context(context)
     # Annotations (annotationBeans) do not have a class, so we'll refer to them
     # as annotationContextBeans. context_class will be one of the types in
@@ -206,9 +212,11 @@ class OBAClient
   end
 
   ##
-  # Parse a concept - a toplevel annotation concept, or an annotation's
+  # Parse a concept: a toplevel annotation concept, or an annotation's
   # mapping concept.
+  #
   # @param [Nokogiri::XML::Node] concept The root node of the concept.
+  #
   # @return [Hash<Symbol, Object>] The parsed concept.
   def self.parse_concept(concept)
     Hash[CONCEPT_ATTRIBUTES.map do |k, v| 
@@ -222,9 +230,11 @@ class OBAClient
   # statistics (annotations by mapping type, etc., as a Hash), an Array of
   # each annotation (as a Hash), and an Array of ontologies used (also as
   # a Hash).
-  # @param [String] xml The XMl we'll be parsing.
+  #
+  # @param [String] xml The XML we'll be parsing.
+  #
   # @return [Hash<Symbol, Object>] A Hash representation of the XML, as
-  #   described above.
+  #   described in the README.
   def self.parse(xml)
     puts "WARNING: text is empty!" if (xml.gsub(/\n/, "") == "")
     doc = Nokogiri::XML.parse(xml)
@@ -257,7 +267,9 @@ class OBAClient
   ##
   # A little helper: convert a string true/false or 1/0 value to boolean.
   # AFAIK, there's no better way to do this.
+  #
   # @param [String] value The value to convert.
+  #
   # @return [true, false]
   def self.to_b(value)
     case value

data/oba-client.gemspec

@@ -0,0 +1,53 @@
+# Generated by jeweler
+# DO NOT EDIT THIS FILE DIRECTLY
+# Instead, edit Jeweler::Tasks in Rakefile, and run the gemspec command
+# -*- encoding: utf-8 -*-
+
+Gem::Specification.new do |s|
+  s.name = %q{oba-client}
+  s.version = "2.1.0"
+
+  s.required_rubygems_version = Gem::Requirement.new(">= 0") if s.respond_to? :required_rubygems_version=
+  s.authors = ["Rob Tirrell"]
+  s.date = %q{2010-07-26}
+  s.description = %q{See above.}
+  s.email = %q{rpt@stanford.edu}
+  s.extra_rdoc_files = [
+    "README.md"
+  ]
+  s.files = [
+    ".gitignore",
+     "History.md",
+     "README.md",
+     "Rakefile",
+     "VERSION",
+     "lib/oba-client.rb",
+     "oba-client.gemspec",
+     "test/test_oba_client.rb"
+  ]
+  s.homepage = %q{http://github.com/rtirrell/oba-client}
+  s.rdoc_options = ["--charset=UTF-8"]
+  s.require_paths = ["lib"]
+  s.rubygems_version = %q{1.3.7}
+  s.summary = %q{A client for the Open Biomedical Annotator.}
+  s.test_files = [
+    "test/test_oba_client.rb"
+  ]
+
+  if s.respond_to? :specification_version then
+    current_version = Gem::Specification::CURRENT_SPECIFICATION_VERSION
+    s.specification_version = 3
+
+    if Gem::Version.new(Gem::VERSION) >= Gem::Version.new('1.2.0') then
+      s.add_development_dependency(%q<thoughtbot-shoulda>, [">= 0"])
+      s.add_development_dependency(%q<yard>, [">= 0"])
+    else
+      s.add_dependency(%q<thoughtbot-shoulda>, [">= 0"])
+      s.add_dependency(%q<yard>, [">= 0"])
+    end
+  else
+    s.add_dependency(%q<thoughtbot-shoulda>, [">= 0"])
+    s.add_dependency(%q<yard>, [">= 0"])
+  end
+end
+

data/test/test_oba_client.rb

@@ -3,10 +3,10 @@ require "oba-client"
 
 TEST_TEXTS = [
   "Mexico,, Disease Thing \o\r\m\n\t\v\l\rzebrafish !!! cancer of the thorax. large intestine thorax",
-#  %Q{LOROE aonuhaso unseu anoeuhs aeuhsaonuh asoneuhason uaosenuh aosenuhaose
-#  aoneuhasonuhaoenuh anoeuhasn euhasoneu haosneuhaosenuhaoesunahoeusnaoeuteeano
-#  aot tt t t t t t t tae \n!!@)$@(#)%@#!)@# asoeuaohsenutahoeusaheou
-#  }
+  %Q{LOROE aonuhaso unseu anoeuhs aeuhsaonuh asoneuhason uaosenuh aosenuhaose
+  aoneuhasonuhaoenuh anoeuhasn euhasoneu haosneuhaosenuhaoesunahoeusnaoeuteeano
+  aot tt t t t t t t tae \n!!@)$@(#)%@\#!)@# asoeuaohsenutahoeusaheou
+  }
 ]
 
 class TestOBAClient < Test::Unit::TestCase

metadata

@@ -1,13 +1,13 @@
 --- !ruby/object:Gem::Specification 
 name: oba-client
 version: !ruby/object:Gem::Version 
-  hash: 9
+  hash: 11
   prerelease: false
   segments: 
   - 2
+  - 1
   - 0
-  - 3
-  version: 2.0.3
+  version: 2.1.0
 platform: ruby
 authors: 
 - Rob Tirrell
@@ -15,90 +15,61 @@ autorequire:
 bindir: bin
 cert_chain: []
 
-date: 2010-07-16 00:00:00 -07:00
+date: 2010-07-26 00:00:00 -07:00
 default_executable: 
 dependencies: 
 - !ruby/object:Gem::Dependency 
-  name: rubyforge
+  name: thoughtbot-shoulda
   prerelease: false
   requirement: &id001 !ruby/object:Gem::Requirement 
     none: false
     requirements: 
     - - ">="
       - !ruby/object:Gem::Version 
-        hash: 7
+        hash: 3
         segments: 
-        - 2
         - 0
-        - 4
-        version: 2.0.4
+        version: "0"
   type: :development
   version_requirements: *id001
 - !ruby/object:Gem::Dependency 
-  name: hoe-yard
+  name: yard
   prerelease: false
   requirement: &id002 !ruby/object:Gem::Requirement 
     none: false
     requirements: 
     - - ">="
       - !ruby/object:Gem::Version 
-        hash: 31
+        hash: 3
         segments: 
         - 0
-        - 1
-        - 2
-        version: 0.1.2
+        version: "0"
   type: :development
   version_requirements: *id002
-- !ruby/object:Gem::Dependency 
-  name: hoe
-  prerelease: false
-  requirement: &id003 !ruby/object:Gem::Requirement 
-    none: false
-    requirements: 
-    - - ">="
-      - !ruby/object:Gem::Version 
-        hash: 21
-        segments: 
-        - 2
-        - 6
-        - 1
-        version: 2.6.1
-  type: :development
-  version_requirements: *id003
-description: |-
-  A client for accessing the NCBO's Open Biomedical Annotator service.
-  See [the Annotator documentation](http://www.bioontology.org/wiki/index.php/Annotator_User_Guide "Documentation") for much more information.
-email: 
-- rpt@stanford.edu
+description: See above.
+email: rpt@stanford.edu
 executables: []
 
 extensions: []
 
 extra_rdoc_files: 
-- Manifest.txt
-- History.md
+- README.md
 files: 
-- .autotest
+- .gitignore
 - History.md
-- Manifest.txt
 - README.md
 - Rakefile
+- VERSION
 - lib/oba-client.rb
+- oba-client.gemspec
 - test/test_oba_client.rb
-has_rdoc: yard
-homepage: http://rubyforge.org/projects/oba-client
+has_rdoc: true
+homepage: http://github.com/rtirrell/oba-client
 licenses: []
 
 post_install_message: 
 rdoc_options: 
-- --default-return
-- void
-- --title
-- OBAClient Documentation
-- --markup
-- markdown
-- --quiet
+- --charset=UTF-8
 require_paths: 
 - lib
 required_ruby_version: !ruby/object:Gem::Requirement 
@@ -121,10 +92,10 @@ required_rubygems_version: !ruby/object:Gem::Requirement
       version: "0"
 requirements: []
 
-rubyforge_project: oba-client
+rubyforge_project: 
 rubygems_version: 1.3.7
 signing_key: 
 specification_version: 3
-summary: A client for accessing the NCBO's Open Biomedical Annotator service
+summary: A client for the Open Biomedical Annotator.
 test_files: 
 - test/test_oba_client.rb

data/.autotest

@@ -1,23 +0,0 @@
-# -*- ruby -*-
-
-require 'autotest/restart'
-
-# Autotest.add_hook :initialize do |at|
-#   at.extra_files << "../some/external/dependency.rb"
-#
-#   at.libs << ":../some/external"
-#
-#   at.add_exception 'vendor'
-#
-#   at.add_mapping(/dependency.rb/) do |f, _|
-#     at.files_matching(/test_.*rb$/)
-#   end
-#
-#   %w(TestA TestB).each do |klass|
-#     at.extra_class_map[klass] = "test/test_misc.rb"
-#   end
-# end
-
-# Autotest.add_hook :run_command do |at|
-#   system "rake build"
-# end

data/Manifest.txt

@@ -1,7 +0,0 @@
-.autotest
-History.md
-Manifest.txt
-README.md
-Rakefile
-lib/oba-client.rb
-test/test_oba_client.rb