oba-client 1.1.1 → 1.2.0

data/History.md

@@ -29,4 +29,8 @@
 
 ## 1.1.1 / 2010-07-08
 
-* Rake or Hoe bug workaround.
+* Rake or Hoe bug workaround.
+
+## 1.2.0 / 2010-07-08
+
+* Parse statistics.

data/README.md

@@ -31,6 +31,10 @@ See [the Annotator documentation](http://www.bioontology.org/wiki/index.php/Anno
     #          :annotations => [Array of annotations of text],
     #          :ontologies  => [Array of ontologies used]}
     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 ... ")
 
 ## LICENSE:
  

data/lib/oba_client.rb

@@ -5,7 +5,7 @@ require "net/http"
 require "uri"
 
 class OBAClient
-  VERSION = "1.1.1"
+  VERSION = "1.2.0"
 
   # A high HTTP read timeout, as the service sometimes takes awhile to respond.
   DEFAULT_TIMEOUT = 30
@@ -37,6 +37,10 @@ class OBAClient
     :withDefaultStopWords,
     :withSynonyms,
   ]
+  
+  STATISTICS_BEANS_XPATH = "/success/data/annotatorResultBean/statistics/statisticsBean"
+  ANNOTATION_BEANS_XPATH = "/success/data/annotatorResultBean/annotations/annotationBean"
+  ONTOLOGY_BEANS_XPATH =   "/success/data/annotatorResultBean/ontologies/ontologyUsedBean"
 
   # Instantiate the class with a set of reused options. Options used by the
   # method are:
@@ -115,7 +119,11 @@ class OBAClient
     ontologies  = []
     doc = Nokogiri::XML.parse(xml)
 
-    doc.xpath("//annotationBean").each do |ann|
+    doc.xpath(STATISTICS_BEANS_XPATH).each do |sb|
+      statistics[sb.xpath("mapping").text] = sb.xpath("nbAnnotation").text.to_i
+    end
+  
+    doc.xpath(ANNOTATION_BEANS_XPATH).each do |ann|
       parsed = {
         :score           => ann.xpath("score").text.to_i,
         :id              => ann.xpath("concept/id").text.to_i,
@@ -144,7 +152,7 @@ class OBAClient
       annotations << parsed
     end
 
-    doc.xpath("//ontologyUsedBean").each do |ontology|
+    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

data/test/test_oba_client.rb

@@ -67,7 +67,6 @@ class TestOBAClient < Test::Unit::TestCase
       assert parsed[:statistics].is_a?(Hash)
       assert parsed[:annotations].is_a?(Array)
       assert parsed[:ontologies].is_a?(Array)
-      p parsed[:annotations].first
     end
   end
 end

metadata

@@ -1,13 +1,13 @@
 --- !ruby/object:Gem::Specification 
 name: oba-client
 version: !ruby/object:Gem::Version 
-  hash: 17
+  hash: 31
   prerelease: false
   segments: 
   - 1
-  - 1
-  - 1
-  version: 1.1.1
+  - 2
+  - 0
+  version: 1.2.0
 platform: ruby
 authors: 
 - Rob Tirrell