ncbo_annotator 1.0.1 → 1.0.3

data/lib/ncbo_annotator/parser.rb

@@ -20,7 +20,6 @@ module NCBO
       def initialize(results)
         @root = "/success/data/annotatorResultBean"
         @results = parse_xml(results)
-        @result = AnnotatorResult.new
       end
       
       def self.parse_results(results)
@@ -28,6 +27,8 @@ module NCBO
       end
       
       def parse_results
+        @result = AnnotatorResult.new
+        p @results
         @result.id = @results.find_first(@root + "/resultID").content
         @result.statistics = parse_statistics
         @result.annotations = parse_annotations
@@ -35,6 +36,28 @@ module NCBO
         @result
       end
       
+      def self.parse_included_ontologies(ontologies)
+        new(ontologies).parse_included_ontologies
+      end
+        
+      def parse_included_ontologies
+        @root = "/success/data/list"
+        ontologies = parse_ontologies("ontologyBean")
+        ontologies
+      end
+
+      private
+      
+      def parse_ontologies(ontology_location = "ontologies/ontologyUsedBean")
+        ontologies = []
+        @results.find(@root + "/#{ontology_location}").each do |ontology|
+          ont = {}
+          ontology.children.each {|child| ont[child.name.to_sym] = safe_to_i(child.content)}
+          ontologies << ont
+        end
+        ontologies
+      end
+      
       def parse_statistics
         statistics = {}
         @results.find(@root + "/statistics/statisticsBean").each do |statistic|
@@ -55,18 +78,6 @@ module NCBO
         annotations
       end
       
-      def parse_ontologies
-        ontologies = []
-        @results.find(@root + "/ontologies/ontologyUsedBean").each do |ontology|
-          ont = {}
-          ontology.children.each {|child| ont[child.name.to_sym] = safe_to_i(child.content)}
-          ontologies << ont
-        end
-        ontologies
-      end
-      
-      private
-      
       def parse_concept(annotation, concept_location = "concept")
         a = {}
         annotation.find("#{concept_location}/*").each {|child| a[child.name.to_sym] = safe_to_i(child.content) if !child.first.nil? && !child.first.children?}

data/lib/ncbo_annotator.rb

@@ -2,6 +2,7 @@ require 'rubygems'
 require 'net/http'
 require 'xml'
 require 'uri'
+require 'open-uri'
 require 'ncbo_annotator/parser'
 
 module NCBO
@@ -10,7 +11,7 @@ module NCBO
     def initialize(args = {})
       @options = {}
   
-      @options[:annotator_location] = "http://rest.bioontology.org/obs/annotator"
+      @options[:annotator_location] = "http://rest.bioontology.org/obs"
       @options[:filterNumber] = true
       @options[:isStopWordsCaseSensitive] = false
       @options[:isVirtualOntologyId] = true
@@ -28,6 +29,8 @@ module NCBO
       @options[:withSynonyms] = true
     
       @options.merge!(args)
+      
+      @ontologies = nil
     
       raise ArgumentError, ":apikey is required, you can obtain one at http://bioportal.bioontology.org/accounts/new" if @options[:apikey].nil?
     end
@@ -43,18 +46,31 @@ module NCBO
       
       raise ArgumentError, ":textToAnnotate must be included" if @options[:textToAnnotate].nil?
       
-      result_xml = post
+      result_xml = annotate_post
       Parser::Annotator.parse_results(result_xml)
     end
     
+    def self.ontologies(options)
+      new(options).ontologies
+    end
+    
+    def ontologies
+      if @ontologies.nil?
+        ontologies_xml = open("#{@options[:annotator_location]}/ontologies?apikey=#{@options[:apikey]}").read
+        @ontologies = Parser::Annotator.parse_included_ontologies(ontologies_xml)
+      else
+        @ontologies
+      end
+    end
+    
     def options
       @options
     end
 
     private
 
-    def post
-      url = @options[:annotator_location]
+    def annotate_post
+      url = @options[:annotator_location] + "/annotator"
       options = @options.clone
       options.each do |k,v|
         if v.kind_of?(Array)
@@ -65,4 +81,4 @@ module NCBO
       return res.body
     end
   end # end Annotator class
-end # end NCBO module
+end # end NCBO module

metadata

@@ -1,13 +1,13 @@
 --- !ruby/object:Gem::Specification 
 name: ncbo_annotator
 version: !ruby/object:Gem::Version 
-  hash: 21
+  hash: 17
   prerelease: 
   segments: 
   - 1
   - 0
-  - 1
-  version: 1.0.1
+  - 3
+  version: 1.0.3
 platform: ruby
 authors: 
 - Paul R Alexander