oba-client 1.2.0 → 1.2.1

data/History.md

@@ -1,36 +1,40 @@
-# 1.0.0 / 2010-07-07
+## 1.2.1 / 2010-07-08
 
-* Initial release.
-* Does not yet parse statistics.
+* Link correctly (problem with using markdown-ed URL in README.md).
 
-## 1.0.1 / 2010-07-07
+## 1.2.0 / 2010-07-08
 
-* Oops, fix a symbol bug.
+* Parse statistics.
 
-## 1.0.2 / 2010-07-07
+## 1.1.1 / 2010-07-08
 
-* Oops, no release notes.
-	
-## 1.0.3 / 2010-07-07
+* Rake or Hoe bug workaround.
 
-* Add more tests.
+## 1.1.0 / 2010-07-08
+
+* Fully parse MGREP mappings.
+
+## 1.0.5 / 2010-07-08
+
+* Modify docs slightly.
 
 ## 1.0.4 / 2010-07-08
 
 * Add all possible parameter values for the Annotator.
 
-## 1.0.5 / 2010-07-08
+## 1.0.3 / 2010-07-07
 
-* Modify docs slightly.
+* Add more tests.
 
-## 1.1.0 / 2010-07-08
+## 1.0.2 / 2010-07-07
 
-* Fully parse MGREP mappings.
+* Oops, no release notes.
 
-## 1.1.1 / 2010-07-08
+## 1.0.1 / 2010-07-07
 
-* Rake or Hoe bug workaround.
+* Oops, fix a symbol bug.
 
-## 1.2.0 / 2010-07-08
+# 1.0.0 / 2010-07-07
 
-* Parse statistics.
+* Initial release.
+* Does not yet parse statistics.

data/README.md

@@ -1,12 +1,11 @@
 # oba-client
 
-* http://rubyforge.org/projects/oba-client
 * [RubyForge project](http://rubyforge.org/projects/oba-client "RubyForge project")
 
 ## 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
+See [the Annotator documentation](http://www.bioontology.org/wiki/index.php/Annotator_User_Guide "Documentation") for much more information.
 
 ## FEATURES:
 
@@ -23,8 +22,12 @@ See [the Annotator documentation](http://www.bioontology.org/wiki/index.php/Anno
 
 ## USAGE:
     
+    require "rubygems"
+    require "oba-client"
+    
     client = OBAClient.new
-    result = client.execute("some text string") # As XML.
+    # As XML.
+    result = client.execute("some text string") 
 
     client2 = OBAClient.new({:parse_xml => true})
     # Returns {:statistics  => {information about the annotation},
@@ -34,7 +37,7 @@ See [the Annotator documentation](http://www.bioontology.org/wiki/index.php/Anno
     client2.execute("this is the second query for this client!")
     
     # Or, parse some file you've already got lying about (pass as a string).
-    parsed = OBAClient::parse("<?xml ... ")
+    parsed = OBAClient::parse("<?xml version='1.0'>...</xml>")
 
 ## LICENSE:
  

data/Rakefile

@@ -5,6 +5,7 @@ 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"]

data/lib/oba_client.rb

@@ -5,7 +5,7 @@ require "net/http"
 require "uri"
 
 class OBAClient
-  VERSION = "1.2.0"
+  VERSION = "1.2.1"
 
   # A high HTTP read timeout, as the service sometimes takes awhile to respond.
   DEFAULT_TIMEOUT = 30
@@ -153,11 +153,11 @@ class OBAClient
     end
 
     doc.xpath(ONTOLOGY_BEANS_XPATH).each do |ontology|
-      parsed = {}
-      parsed[:localOntologyId]   = ontology.xpath("localOntologyId").text.to_i
-      parsed[:virtualOntologyId] = ontology.xpath("virtualOntologyId").text.to_i
-      parsed[:name]              = ontology.xpath("name").text
-      ontologies << parsed
+      ontologies << {
+        :localOntologyId   => ontology.xpath("localOntologyId").text.to_i,
+        :virtualOntologyId => ontology.xpath("virtualOntologyId").text.to_i,
+        :name              => ontology.xpath("name").text
+      }
     end
 
     {

data/test/test_oba_client.rb

@@ -69,4 +69,8 @@ class TestOBAClient < Test::Unit::TestCase
       assert parsed[:ontologies].is_a?(Array)
     end
   end
+  
+  def test_parse
+    parsed = OBAClient::parse("<?xml version='1.0'></xml>")
+  end
 end

metadata

@@ -1,13 +1,13 @@
 --- !ruby/object:Gem::Specification 
 name: oba-client
 version: !ruby/object:Gem::Version 
-  hash: 31
+  hash: 29
   prerelease: false
   segments: 
   - 1
   - 2
-  - 0
-  version: 1.2.0
+  - 1
+  version: 1.2.1
 platform: ruby
 authors: 
 - Rob Tirrell
@@ -68,7 +68,7 @@ dependencies:
   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
+  See [the Annotator documentation](http://www.bioontology.org/wiki/index.php/Annotator_User_Guide "Documentation") for much more information.
 email: 
 - rpt@stanford.edu
 executables: []