ncbo_resource_index_client 1.4 → 1.5.0

checksums.yaml

@@ -0,0 +1,7 @@
+---
+SHA1:
+  metadata.gz: d577d2cbd404bd5442cd4f84f0e58c136b4b07b5
+  data.tar.gz: 9b8db209cf08a747a664cf5f3375e86195f327a3
+SHA512:
+  metadata.gz: 174c8362112943484444bec3988b77de763a08e8abfcccf6bab0aa05ba81af30c53a48ba8d7bbfed1306fc91448344680979b3d3673787a993262c257299f5ca
+  data.tar.gz: 95a149959c6cc5da1e2c683b9a43882d83f261dcb4dbc74f4a520541baa63cd61fc82c946a60c3f43f335abb033cc3b89646bd02624e5d43cc9b67f6070bb9e8

data/lib/ncbo_resource_index.rb

@@ -3,8 +3,8 @@ require 'xml'
 require 'uri'
 require 'open-uri'
 require 'cgi'
-require 'ncbo_resource_index/parser'
-require 'ncbo_resource_index/data'
+require_relative 'ncbo_resource_index/parser'
+require_relative 'ncbo_resource_index/data'
 
 
 module NCBO
@@ -130,6 +130,27 @@ module NCBO
       end
       primary_annotations
     end
+    
+    def self.element(element_id, resource_id, options = {})
+      new(options).element(element_id, resource_id)
+    end
+    
+    def element(element_id, resource_id)
+      @options.merge!(options) unless options.empty?
+      
+      raise ArugmentError, "element_id must be provided" if element_id.nil?
+      raise ArugmentError, "resource_id must be provided" if resource_id.nil?
+
+      result_url = [
+        "#{@options[:resource_index_location]}",
+        "elementDetails/#{resource_id}",
+        "?elementid=#{element_id}",
+        "&apikey=#{@options[:apikey]}"
+      ].join("")
+      
+      result_xml = open(result_url).read
+      Parser::ResourceIndex.parse_element_results(result_xml)
+    end
 
     def self.ranked_elements(concepts, options = {})
       new(options).ranked_elements(concepts)

data/lib/ncbo_resource_index/data.rb

@@ -12,6 +12,11 @@ module NCBO
     class RankedElements
       attr_accessor :concepts, :resources
     end
+    
+    class Element
+      attr_accessor :id, :resource, :text, :weights, :ontoIds
+      alias :localElementId :id
+    end
 
   end
 end

data/lib/ncbo_resource_index/parser.rb

@@ -51,13 +51,12 @@ module NCBO
       end
       
       def parse_results(options = {})
-        resource ||= options[:resource]
         annotation_location ||= options[:annotation_location]
         
         results = []
         @results.find("/success/data/list/*").each do |result|
           resource_annotations = NCBO::ResourceIndex::Annotations.new
-          resource_annotations.resource = resource ||= result.find_first("resourceId").content
+          resource_annotations.resource = result.find_first("resourceId").content
 
           # Check to see if parameters are enabled that will change how we process the output
           with_context = result.find_first("withContext").content.eql?("true") rescue false
@@ -118,7 +117,22 @@ module NCBO
         end
         concepts
       end
-
+      
+      def self.parse_element_results(results)
+        new(results).parse_element_results
+      end
+      
+      def parse_element_results
+        element = parse_element(@results.find_first("/success/data"), "obs.obr.populate.Element")
+        new_element = NCBO::ResourceIndex::Element.new
+        new_element.id = element[:localElementId]
+        new_element.weights = element[:weights]
+        new_element.ontoIds = element[:ontoIds]
+        new_element.text = element[:text]
+        new_element.resource = element[:text].first[0].split("_")[0]
+        new_element
+      end
+        
       def self.parse_element_annotations(results)
         new(results).parse_element_annotations
       end
@@ -209,18 +223,18 @@ module NCBO
         a
       end
       
-      def parse_element(annotation)
+      def parse_element(annotation, element_location = "element")
         a = {}
-        a[:localElementId] = annotation.find_first("element/localElementId").content unless annotation.find_first("element/localElementId").nil?
+        a[:localElementId] = annotation.find_first("#{element_location}/localElementId").content unless annotation.find_first("#{element_location}/localElementId").nil?
         # element text
         a[:text] = {}
-        annotation.find("element/elementStructure/contexts/*").each {|context| a[:text][context.children[0].content] = context.children[1].content}
+        annotation.find("#{element_location}/elementStructure/contexts/*").each {|context| a[:text][context.children[0].content] = context.children[1].content}
         # element weights
         a[:weights] = []
-        annotation.find("element/elementStructure/weights/*").each {|weight| a[:weights] << {:name => weight.children[0].content, :weight => weight.children[1].content.to_f} }
+        annotation.find("#{element_location}/elementStructure/weights/*").each {|weight| a[:weights] << {:name => weight.children[0].content, :weight => weight.children[1].content.to_f} }
         # which element portions are associated with an ontology
         a[:ontoIds] = {}
-        annotation.find("element/elementStructure/ontoIds/*").each {|ont_id| a[:ontoIds][ont_id.children[0].content] = ont_id.children[1].content.to_i}
+        annotation.find("#{element_location}/elementStructure/ontoIds/*").each {|ont_id| a[:ontoIds][ont_id.children[0].content] = ont_id.children[1].content.to_i}
         return a
       end
     end

metadata

@@ -1,8 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: ncbo_resource_index_client
 version: !ruby/object:Gem::Version
-  prerelease: 
-  version: '1.4'
+  version: 1.5.0
 platform: ruby
 authors:
 - Paul R Alexander
@@ -13,16 +12,14 @@ date: 2013-04-02 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: libxml-ruby
-  type: :runtime
   requirement: !ruby/object:Gem::Requirement
-    none: false
     requirements:
     - - ~>
       - !ruby/object:Gem::Version
         version: 2.2.0
+  type: :runtime
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
-    none: false
     requirements:
     - - ~>
       - !ruby/object:Gem::Version
@@ -46,27 +43,26 @@ files:
 - lib/ncbo_resource_index.rb
 homepage: http://github.com/ncbo/resource_index_ruby_client
 licenses: []
+metadata: {}
 post_install_message: 
 rdoc_options: []
 require_paths:
 - lib
 required_ruby_version: !ruby/object:Gem::Requirement
-  none: false
   requirements:
-  - - ! '>='
+  - - '>='
     - !ruby/object:Gem::Version
       version: '0'
 required_rubygems_version: !ruby/object:Gem::Requirement
-  none: false
   requirements:
-  - - ! '>='
+  - - '>='
     - !ruby/object:Gem::Version
       version: '0'
 requirements: []
 rubyforge_project: 
-rubygems_version: 1.8.23
+rubygems_version: 2.0.0
 signing_key: 
-specification_version: 3
+specification_version: 4
 summary: The NCBO Resource Index Gem is a Ruby client for NCBO's Resource Index Web
   service
 test_files: []