oba-client 1.0.1 → 1.0.2

data/Manifest.txt

@@ -1,8 +1,7 @@
 .autotest
 History.txt
 Manifest.txt
-README.txt
+README.md
 Rakefile
-bin/oba_client
 lib/oba_client.rb
 test/test_oba_client.rb

data/README.md

@@ -0,0 +1,54 @@
+# oba-client
+
+* http://rubyforge.org/projects/oba-client
+
+## DESCRIPTION:
+
+A client for accessing the NCBO's Open Biomedical Annotator service.
+
+## FEATURES:
+
+* Many
+
+## REQUIREMENTS:
+
+* None
+
+## INSTALL:
+
+    sudo gem install oba-client
+    gem install --user-install oba-client
+
+## USAGE:
+    
+    client = OBAClient.new
+    result = client.execute("some text string") # As XML.
+
+    client2 = OBAClient.new({:parse_xml => true})
+    # Returns {:statistics  => {information about the annotation},
+    #          :annotations => [Array of annotations of text],
+    #          :ontologies  => [Array of ontologies used]}
+    client2.execute("another text string, maybe longer this time.")
+
+## LICENSE:
+ 
+Copyright (c) 2010 Rob Tirrell
+
+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/Rakefile

@@ -4,8 +4,11 @@ require "hoe"
 Hoe.plugin :yard
 
 Hoe.spec "oba-client" do
-  developer("Rob Tirrell", "rpt@stanford.edu")
-  self.yard_options = ["--default-return", "void", "--readme", "README.txt"]
+  self.developer "Rob Tirrell", "rpt@stanford.edu"
+  self.yard_options = ["--default-return", "void"]
+  self.yard_markup = "markdown"
+  self.remote_yard_dir = ""
+
   self.rubyforge_name = "oba-client"
 end
 

data/lib/oba_client.rb

@@ -5,7 +5,7 @@ require "net/http"
 require "uri"
 
 class OBAClient
-  VERSION = "1.0.1"
+  VERSION = "1.0.2"
 
   # A high HTTP read timeout, as the service sometimes takes awhile to respond.
   DEFAULT_TIMEOUT = 30
@@ -31,10 +31,12 @@ class OBAClient
     :email
   ]
 
-  # Annotate a blob of text. Method options 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).
+  # 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).
   # @param [Hash<String, String>] options Parameters for the annotation.
   def initialize(options = {})
     @uri         = URI.parse(options.delete(:uri) || DEFAULT_URI)
@@ -122,8 +124,8 @@ class OBAClient
 
     doc.xpath("//ontologyUsedBean").each do |ontology|
       parsed = {}
-      parsed[:localOntologyId]   = ontology.xpath("localOntologyId").text
-      parsed[:virtualOntologyId] = ontology.xpath("virtualOntologyId").text
+      parsed[:localOntologyId]   = ontology.xpath("localOntologyId").text.to_i
+      parsed[:virtualOntologyId] = ontology.xpath("virtualOntologyId").text.to_i
       parsed[:name]              = ontology.xpath("name").text
       ontologies << parsed
     end

data/test/test_oba_client.rb

@@ -2,9 +2,7 @@ require "test/unit"
 require "oba_client"
 
 TEST_TEXTS = [
-   "hello I am a monkeyfish with a benign neoplastic....\t\n\\n",
-  "zebrafish echo delta tango TURN <?xml MY VOLUME UP cancer of the thorax.",
-  "zebrafish DROP TABLE !!! TURN MY VOLUME UP cancer of the thorax.",
+  "Mexico,, Disease Thing \o\r\m\n\t\v\l\rzebrafish !!! cancer of the 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
@@ -53,9 +51,7 @@ class TestOBAClient < Test::Unit::TestCase
         :parse_xml => true
       )
       parsed = ann.execute(text)
-      assert parsed[:statistics].is_a?(Array)
-      assert parsed[:annotations].is_a?(Array)
-      assert parsed[:ontologies].is_a?(Array)
+      assert (parsed[:ontologies].all? {|o| o[:localOntologyId] == 42812})
     end
   end
   

metadata

@@ -1,13 +1,13 @@
 --- !ruby/object:Gem::Specification 
 name: oba-client
 version: !ruby/object:Gem::Version 
-  hash: 21
+  hash: 19
   prerelease: false
   segments: 
   - 1
   - 0
-  - 1
-  version: 1.0.1
+  - 2
+  version: 1.0.2
 platform: ruby
 authors: 
 - Rob Tirrell
@@ -66,38 +66,36 @@ dependencies:
         version: 2.6.1
   type: :development
   version_requirements: *id003
-description: FIX (describe your package)
+description: A client for accessing the NCBO's Open Biomedical Annotator service.
 email: 
 - rpt@stanford.edu
-executables: 
-- oba_client
+executables: []
+
 extensions: []
 
 extra_rdoc_files: 
 - History.txt
 - Manifest.txt
-- README.txt
 files: 
 - .autotest
 - History.txt
 - Manifest.txt
-- README.txt
+- README.md
 - Rakefile
-- bin/oba_client
 - lib/oba_client.rb
 - test/test_oba_client.rb
 has_rdoc: yard
-homepage: http://rubyforge.org/oba-client
+homepage: http://rubyforge.org/projects/oba-client
 licenses: []
 
 post_install_message: 
 rdoc_options: 
 - --default-return
 - void
-- --readme
-- README.txt
 - --title
 - ObaClient Documentation
+- --markup
+- markdown
 - --quiet
 require_paths: 
 - lib
@@ -125,6 +123,6 @@ rubyforge_project: oba-client
 rubygems_version: 1.3.7
 signing_key: 
 specification_version: 3
-summary: FIX (describe your package)
+summary: A client for accessing the NCBO's Open Biomedical Annotator service.
 test_files: 
 - test/test_oba_client.rb

data/README.txt

@@ -1,57 +0,0 @@
-= oba_client
-
-* http://rubyforge.org/oba-client
-
-== DESCRIPTION:
-
-FIX (describe your package)
-
-== FEATURES/PROBLEMS:
-
-* FIX (list of features or problems)
-
-== SYNOPSIS:
-
-  FIX (code sample of usage)
-
-== REQUIREMENTS:
-
-* None
-
-== INSTALL:
-
-* FIX (sudo gem install, anything else)
-
-== DEVELOPERS:
-
-After checking out the source, run:
-
-  $ rake newb
-
-This task will install any missing dependencies, run the tests/specs,
-and generate the RDoc.
-
-== LICENSE:
-
-(The MIT License)
-
-Copyright (c) 2010 FIX
-
-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/bin/oba_client

@@ -1,3 +0,0 @@
-#!/usr/bin/env ruby
-
-abort "you need to write me"