oba-client 2.0.0 → 2.0.1

data/History.md

@@ -1,4 +1,8 @@
-## 2.0.0 / 2010-07-08
+## 2.0.1 / 2010-07-08
+
+Rubyforge doesn't allow "_", so we have "oba-client", not "oba_client".
+
+# 2.0.0 / 2010-07-08
 
 * Parse XML entirely. See README for more information on the return value.
 

data/Manifest.txt

@@ -3,5 +3,5 @@ History.md
 Manifest.txt
 README.md
 Rakefile
-lib/oba_client.rb
+lib/oba-client.rb
 test/test_oba_client.rb

data/README.md

@@ -46,34 +46,33 @@ See [the Annotator documentation](http://www.bioontology.org/wiki/index.php/Anno
       :synonyms        => ["body cell"],
       :definitions     => ["a cell", "some other definition"],
     	
-    	:semanticTypes => [
-    		{:id => 230820, :semanticType => "T043", :description => "desc"},
-    		"etc..."
-    	]
+      :semanticTypes => [
+        {:id => 230820, :semanticType => "T043", :description => "desc"},
+        "etc..."
+      ]
     	
-    	:context => {
-    		:contextName   => "MAPPING",
-    		:isDirect      => false,
-    		:from          => 10,
-    		:to            => 20,
-    		:mappedConcept => {
-    			"has" => "the same information as other annotations, minus score"
-    	  }
-    	}
+      :context => {
+        :contextName   => "MAPPING",
+        :isDirect      => false,
+        :from          => 10,
+        :to            => 20,
+        :mappedConcept => {
+          "has" => "the same information as other annotations, minus score"
+        }
+      }
     	
       :mappingType => "Automatic"
     }, "more annotations..."]
     	
     :ontologies => [{
-    	:localOntologyId   => 40404,
-    	:name	             => "Ontology Name",
-    	:virtualOntologyId => 1042
+      :localOntologyId   => 40404,
+      :name              => "Ontology Name",
+      :virtualOntologyId => 1042
     }, "more ontologies..."]
     	
     client2.execute("another text string, maybe longer this time.")
     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 version='1.0'>...</xml>")
 

data/lib/{oba_client.rb → oba-client.rb}

@@ -5,7 +5,7 @@ require "net/http"
 require "uri"
 
 class OBAClient
-  VERSION = "2.0.0"
+  VERSION = "2.0.1"
 
   # A high HTTP read timeout, as the service sometimes takes awhile to respond.
   DEFAULT_TIMEOUT = 30
@@ -117,8 +117,9 @@ class OBAClient
     end
   end
 
-  # Attributes for mapping concepts (annotation concepts add one, 
-  # @see ANNOTATION_CONCEPT_ATTRIBUTES.
+  # Attributes for mapping concepts (annotation concepts add one additional
+  # attribute.
+  # @see ANNOTATION_CONCEPT_ATTRIBUTES
   CONCEPT_ATTRIBUTES = {
     :id              => lambda {|c| c.xpath("id").text.to_i},
     :localConceptId  => lambda {|c| c.xpath("localConceptId").text},
@@ -149,7 +150,7 @@ class OBAClient
     :mappingType => lambda {|c| c.xpath("mappingType").text}
   )
 
-  #  # Toplevel attributes for annotation contexts.
+  #  Toplevel attributes for annotation contexts.
   ANNOTATION_CONTEXT_ATTRIBUTES = {
     :score   => lambda {|c| c.xpath("score").text.to_i},
     :concept => lambda {|c| parse_concept(c.xpath("concept").first)},
@@ -164,7 +165,7 @@ class OBAClient
     :to              => lambda {|c| c.xpath("to").text.to_i},
   }
 
-  #  # Toplevel attributes for mapping contexts.
+  # Toplevel attributes for mapping contexts.
   MAPPED_CONTEXT_ATTRIBUTES = CONTEXT_ATTRIBUTES.merge(
     :mappedConcept => lambda {|c| parse_concept(c.xpath("mappedConcept").first)}
   )
@@ -227,6 +228,7 @@ class OBAClient
   # @return [Hash<Symbol, Object>] A Hash representation of the XML, as
   #   described above.
   def self.parse(xml)
+    puts "WARNING: text is empty!" if (xml.gsub(/\n/, "") == "")
     doc = Nokogiri::XML.parse(xml)
 
     statistics = Hash[doc.xpath(STATISTICS_BEANS_XPATH).map do |sb|

data/test/test_oba_client.rb

@@ -1,6 +1,5 @@
 require "test/unit"
-require "oba_client"
-require "pp"
+require "oba-client"
 
 TEST_TEXTS = [
   "Mexico,, Disease Thing \o\r\m\n\t\v\l\rzebrafish !!! cancer of the thorax. large intestine thorax",

metadata

@@ -1,13 +1,13 @@
 --- !ruby/object:Gem::Specification 
 name: oba-client
 version: !ruby/object:Gem::Version 
-  hash: 15
+  hash: 13
   prerelease: false
   segments: 
   - 2
   - 0
-  - 0
-  version: 2.0.0
+  - 1
+  version: 2.0.1
 platform: ruby
 authors: 
 - Rob Tirrell
@@ -84,7 +84,7 @@ files:
 - Manifest.txt
 - README.md
 - Rakefile
-- lib/oba_client.rb
+- lib/oba-client.rb
 - test/test_oba_client.rb
 has_rdoc: yard
 homepage: http://rubyforge.org/projects/oba-client