rx_nav 0.1.0

checksums.yaml

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+---
+SHA1:
+  metadata.gz: cb4e475d76c23889b8562311f14a44dfbd8b2922
+  data.tar.gz: e522d9a590ca890ca3b2f1aa0f89ad3eeba55e9f
+SHA512:
+  metadata.gz: 796b5de96b725a354f1c2d8e223abb8f4095696908b15109fa08ae58da44da2a18e4ad365f752f0e6906b9400b88f0e88311dd790ac789bdd9fa7296bd4fc711
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data/.gitignore

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+*.gem
+*.rbc
+.bundle
+.config
+.yardoc
+Gemfile.lock
+InstalledFiles
+_yardoc
+coverage
+doc/
+lib/bundler/man
+pkg
+rdoc
+spec/reports
+test/tmp
+test/version_tmp
+tmp

data/Gemfile

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+source 'https://rubygems.org'
+
+# Specify your gem's dependencies in rx_nav.gemspec
+gemspec

data/LICENSE.txt

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+Copyright (c) 2013 Jonathan Bender
+
+MIT License
+
+Permission is hereby granted, free of charge, to any person obtaining
+a copy of this software and associated documentation files (the
+"Software"), to deal in the Software without restriction, including
+without limitation the rights to use, copy, modify, merge, publish,
+distribute, sublicense, and/or sell copies of the Software, and to
+permit persons to whom the Software is furnished to do so, subject to
+the following conditions:
+
+The above copyright notice and this permission notice shall be
+included in all copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
+EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
+MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
+NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE
+LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION
+OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION
+WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.

data/README.md

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+# RxNav
+
+TODO: Write a gem description
+
+## Installation
+
+Add this line to your application's Gemfile:
+
+    gem 'rx_nav'
+
+And then execute:
+
+    $ bundle
+
+Or install it yourself as:
+
+    $ gem install rx_nav
+
+## Usage
+
+TODO: Write usage instructions here
+
+## Contributing
+
+1. Fork it
+2. Create your feature branch (`git checkout -b my-new-feature`)
+3. Commit your changes (`git commit -am 'Add some feature'`)
+4. Push to the branch (`git push origin my-new-feature`)
+5. Create new Pull Request

data/Rakefile

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+require "bundler/gem_tasks"

data/lib/rx_nav.rb

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+require 'net/http'
+require 'nori'
+require 'nokogiri'
+require 'ostruct'
+
+# Core of the API responses
+require 'rx_nav/concept'
+require 'rx_nav/interaction'
+
+# Individual APIs
+require 'rx_nav/ndfrt'
+require 'rx_nav/rx_norm'
+require 'rx_nav/rx_terms'
+
+module RxNav
+
+  def self.nori
+    Nori.new(convert_tags_to: -> tag { tag.snakecase.to_sym })
+  end
+
+  def self.make_request query
+    encoded_query = URI.encode(query)
+    request = URI.parse('http://rxnav.nlm.nih.gov/REST' + encoded_query)
+    return RxNav.nori.parse(Net::HTTP.get request)
+  end
+
+end

data/lib/rx_nav/concept.rb

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+require 'ostruct'
+
+module RxNav
+  class Concept < OpenStruct
+
+    def name
+      name = self.concept_name
+      name ? name.capitalize : nil
+    end
+
+    def kind
+      kind = self.concept_kind
+      kind ? titleize_kind(self.concept_kind) : nil
+    end
+
+    def to_s
+      display_name || full_name || full_generic_name || name
+    end
+
+    def get_terms_info
+      if self.rxcui.nil?
+        if self.nui.nil?
+          raise "This concept doesn't have a nui or rxcui"
+        else
+          rxcui = RxNav::RxNorm.find_rxcui_by_id('nui', self.nui)
+        end
+      end
+      rxcui = rxcui ? rxcui : self.rxcui
+      rxcui ? merge_concept(RxNav::RxTerms.get_info(rxcui)) : self
+    end
+
+    def get_ndfrt_info
+      if self.nui.nil?
+        if self.rxcui.nil?
+          raise "This concept doesn't have a nui or rxcui"
+        else
+          concept = RxNav::NDFRT.find_by_id('rxcui', self.rxcui)
+        end
+      end
+      nui = concept ? concept.nui : self.nui
+      nui ? merge_concept(RxNav::NDFRT.get_info(nui)) : self
+    end
+
+    private
+
+    def titleize_kind str
+      str.split("_")[0...-1].map(&:capitalize).join(" ") if str.is_a? String
+    end
+
+    def merge_concept concept
+      return self if concept.attributes.nil?
+      concept.attributes.each do |k,v|
+        self.k = v if self.k.nil?
+      end
+    end
+
+  end
+end

data/lib/rx_nav/interaction.rb

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+require 'ostruct'
+
+module RxNav
+  class Interaction < OpenStruct
+
+    def initialize interaction_hash
+      concepts = interaction_hash[:group_concepts][:concept]
+
+      @drugs    = extract_drugs concepts
+      @nui      = extract_interaction_id concepts
+      @severity = interaction_hash[:severity]
+    end
+
+    private
+
+    def extract_drugs concepts
+      concepts.select { |c| c[:concept_kind] != 'DRUG_INTERACTION_KIND' }.map{ |c| RxNav::Concept.new(c) }
+    end
+
+    def extract_interaction_id concepts
+      concepts.select { |c| c[:concept_kind] == 'DRUG_INTERACTION_KIND' }.first[:concept_nui]
+    end
+
+  end
+end

data/lib/rx_nav/ndfrt.rb

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+module RxNav
+  class NDFRT
+    class << self
+      def api_version
+        get_response_hash("/version")[:version][:version_name].to_s
+      end
+
+      def possible_options_for type
+        get_options type.to_s.downcase
+      end
+
+      def possible_associations
+        get_options "association"
+      end
+
+      def possible_types
+        get_options "type"
+      end
+
+      def possible_kinds
+        get_options("kind").map { |k| k.split('_')[0...-1].join('_').downcase }
+      end
+
+      def possible_properties
+        get_options "property"
+      end
+
+      def possible_roles
+        get_options "role"
+      end
+
+      def find_by hash
+        return find_by_id(hash[:type], hash[:id]) if hash.has_key? :id
+        return find_by_name(hash[:name], hash[:kind]) if hash.has_key? :name
+      end
+
+      def find_by_id type, id
+        type  = type.upcase
+        id    = id.to_s
+        query = "/idType=#{type}&idString=#{id}"
+        return get_concepts query
+      end
+
+      def find_by_name name, kind = nil
+        query = "/search?conceptName=#{name}"
+        unless kind.nil?
+          kind = kind.upcase + '_KIND'
+          query += "&kindName=#{kind}"
+        end
+        return get_concepts query
+      end
+
+      def find_interacting_drugs nui, scope = 3
+        query = "/interaction/nui=#{nui}&scope=#{scope}"
+        response = get_response_hash query
+        data = response[:group_interactions][:interactions][:group_interacting_drugs][:interacting_drug]
+        data = [data] unless data.is_a? Array
+        return data.map { |i| RxNav::Concept.new i[:concept] }
+      end
+
+      def find_interactions_between nuis, scope = 3
+        query = "/interaction?nuis=#{nuis.join('+')}&scope=#{scope}"
+        data = get_response_hash query
+        return data[:full_interaction_group][:full_interaction].map do |fi|
+          RxNav::Interaction.new fi[:interaction_triple_group][:interaction_triple]
+        end
+      end
+
+      def get_info nui, concept = nil
+        raise "Nui cannot be nil" if nui.nil?
+        query = "/allInfo/#{nui}"
+        data = get_response_hash(query)[:full_concept]
+        return RxNav::Concept.new(data)
+      end
+
+      def all_records_by_kind kind
+        kind = kind.upcase + "_KIND"
+        query = "/allconcepts?kind=#{kind}"
+        data = get_response_hash(query)[:group_concepts][:concept]
+        return data.map { |c| RxNav::Concept.new c }
+      end
+  
+      private
+
+      def get_response_hash query
+        RxNav.make_request('/Ndfrt' + query)[:ndfrtdata]
+      end
+
+      def get_options type
+        data = get_response_hash "/#{type}List"
+        return data["#{type}_list".to_sym]["#{type}_name".to_sym].map { |a| a.to_s }
+      end
+
+      def get_concepts query
+        data = get_response_hash(query)[:group_concepts]
+        if data && data[:concept]
+          data = [data] unless data.is_a?(Array)
+          return data.map { |c| RxNav::Concept.new(c) }
+        else
+          return nil
+        end
+      end
+
+    end
+
+    self.singleton_class.send(:alias_method, :version, :api_version)
+
+    self.singleton_class.send(:alias_method, :available_options_for, :possible_options_for)
+
+    self.singleton_class.send(:alias_method, :all_concepts_by_kind, :all_records_by_kind)
+
+  end
+end

data/lib/rx_nav/rx_norm.rb

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+module RxNav
+  class RxNorm
+    class << self
+      def search_by_name name, max_results = 20, option = 0
+        query = "/approximateTerm?term=#{name}&maxEntries=#{max_results}"
+        # The API spec includes an option parameter, but doesn't specify options
+        # other than the default
+        # query += "&option=#{option}" if option
+        data = get_response_hash(query)[:approximate_group][:candidate]
+        data = [data] if (data && !data.is_a?(Array))
+        return data.nil? ? nil : data.map { |c| RxNav::Concept.new(c) }
+      end
+
+      def find_rxcui_by_id type, id
+        type  = type.upcase
+        id    = id.to_s
+        query = "/rxcui?idtype=#{type}&id=#{id}"
+        return extract_rxcui query
+      end
+
+      def find_rxcui_by_name name
+        query = "/rxcui?name=#{name}"
+        return extract_rxcui query
+      end
+
+      def properties id
+        query = "/rxcui/#{id}/properties"
+        return OpenStruct.new get_response_hash(query)[:properties]
+      end
+
+      def quantity id
+        query = "/rxcui/#{id}/quantity"
+        return OpenStruct.new get_response_hash(query)[:quantity_group]
+      end
+
+      def strength id
+        query = "/rxcui/#{id}/strength"
+        return OpenStruct.new get_response_hash(query)[:strength_group]
+      end
+
+      def complete_info id
+        result = self.properties(id)
+        result.strength = self.strength(id).strength
+        result.quantity = self.quantity(id).quantity
+        return result
+      end
+
+      private
+
+      def get_response_hash query
+        RxNav.make_request(query)[:rxnormdata]
+      end
+      
+      def extract_rxcui query
+        data = get_response_hash(query)
+        if data[:id_group]
+          data = [data] unless data.is_a?(Array)
+          return data.map { |c| c[:rxnorm_id] }
+        else
+          return nil
+        end
+      end
+
+    end
+  end
+end

data/lib/rx_nav/rx_terms.rb

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+module RxNav
+  class RxTerms
+    class << self
+      def all_concepts
+        query = "/allconcepts"
+        data = get_response_hash(query)[:min_concept_group]
+        return data.map{ |c| RxNav::Concept.new(c) }
+      end
+
+      def all_info id
+        query = "/rxcui/#{id}/allinfo"
+        data = get_response_hash(query)[:rxterms_properties]
+        return RxNav::Concept.new(data)
+      end
+
+      private
+
+      def get_response_hash query
+        RxNav.make_request('/RxTerms' + query)[:rxtermsdata]
+      end
+    end
+    
+    self.singleton_class.send(:alias_method, :get_info, :all_info)
+
+  end
+end

data/lib/rx_nav/version.rb

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+module RxNav
+  VERSION = "0.1.0"
+end

data/rx_nav.gemspec

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+# coding: utf-8
+lib = File.expand_path('../lib', __FILE__)
+$LOAD_PATH.unshift(lib) unless $LOAD_PATH.include?(lib)
+require 'rx_nav/version'
+
+Gem::Specification.new do |spec|
+  spec.name          = 'rx_nav'
+  spec.version       = RxNav::VERSION
+  spec.authors       = ['Jonathan Bender']
+  spec.email         = ['jlbender@gmail.com']
+  spec.description   = 'Ruby wrappers for the RxNav RESTful APIs'
+  spec.summary       = 'Ruby-based way of interacting with the RxNav APIs (http://rxnav.nlm.nih.gov/APIsOverview.html)'
+  spec.homepage      = 'https://github.com/jbender/rx_nav_ruby'
+  spec.license       = 'MIT'
+
+  spec.files         = `git ls-files`.split($/)
+  spec.executables   = spec.files.grep(%r{^bin/}) { |f| File.basename(f) }
+  spec.test_files    = spec.files.grep(%r{^(test|spec|features)/})
+  spec.require_paths = ['lib']
+
+  spec.add_dependency 'httparty'
+  spec.add_dependency 'nori'
+  spec.add_dependency 'nokogiri'
+
+  spec.add_development_dependency 'bundler', '~> 1.3'
+  spec.add_development_dependency 'rake'
+end

metadata

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+--- !ruby/object:Gem::Specification
+name: rx_nav
+version: !ruby/object:Gem::Version
+  version: 0.1.0
+platform: ruby
+authors:
+- Jonathan Bender
+autorequire: 
+bindir: bin
+cert_chain: []
+date: 2013-11-15 00:00:00.000000000 Z
+dependencies:
+- !ruby/object:Gem::Dependency
+  name: httparty
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - '>='
+      - !ruby/object:Gem::Version
+        version: '0'
+  type: :runtime
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - '>='
+      - !ruby/object:Gem::Version
+        version: '0'
+- !ruby/object:Gem::Dependency
+  name: nori
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - '>='
+      - !ruby/object:Gem::Version
+        version: '0'
+  type: :runtime
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - '>='
+      - !ruby/object:Gem::Version
+        version: '0'
+- !ruby/object:Gem::Dependency
+  name: nokogiri
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - '>='
+      - !ruby/object:Gem::Version
+        version: '0'
+  type: :runtime
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - '>='
+      - !ruby/object:Gem::Version
+        version: '0'
+- !ruby/object:Gem::Dependency
+  name: bundler
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - ~>
+      - !ruby/object:Gem::Version
+        version: '1.3'
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - ~>
+      - !ruby/object:Gem::Version
+        version: '1.3'
+- !ruby/object:Gem::Dependency
+  name: rake
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - '>='
+      - !ruby/object:Gem::Version
+        version: '0'
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - '>='
+      - !ruby/object:Gem::Version
+        version: '0'
+description: Ruby wrappers for the RxNav RESTful APIs
+email:
+- jlbender@gmail.com
+executables: []
+extensions: []
+extra_rdoc_files: []
+files:
+- .gitignore
+- Gemfile
+- LICENSE.txt
+- README.md
+- Rakefile
+- lib/rx_nav.rb
+- lib/rx_nav/concept.rb
+- lib/rx_nav/interaction.rb
+- lib/rx_nav/ndfrt.rb
+- lib/rx_nav/rx_norm.rb
+- lib/rx_nav/rx_terms.rb
+- lib/rx_nav/version.rb
+- rx_nav.gemspec
+homepage: https://github.com/jbender/rx_nav_ruby
+licenses:
+- MIT
+metadata: {}
+post_install_message: 
+rdoc_options: []
+require_paths:
+- lib
+required_ruby_version: !ruby/object:Gem::Requirement
+  requirements:
+  - - '>='
+    - !ruby/object:Gem::Version
+      version: '0'
+required_rubygems_version: !ruby/object:Gem::Requirement
+  requirements:
+  - - '>='
+    - !ruby/object:Gem::Version
+      version: '0'
+requirements: []
+rubyforge_project: 
+rubygems_version: 2.1.10
+signing_key: 
+specification_version: 4
+summary: Ruby-based way of interacting with the RxNav APIs (http://rxnav.nlm.nih.gov/APIsOverview.html)
+test_files: []