rx_nav 0.1.3 → 0.2.0

checksums.yaml

@@ -1,7 +1,7 @@
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data/Gemfile

@@ -2,3 +2,9 @@ source 'https://rubygems.org'
 
 # Specify your gem's dependencies in rx_nav.gemspec
 gemspec
+
+gem "codeclimate-test-reporter", group: :test, require: nil
+
+group :development do
+  gem 'guard-rspec', require: false
+end

data/Guardfile

@@ -0,0 +1,16 @@
+clearing :on
+
+guard :rspec, cmd: "bundle exec rspec" do
+  require "guard/rspec/dsl"
+  dsl = Guard::RSpec::Dsl.new(self)
+
+  # RSpec files
+  rspec = dsl.rspec
+  watch(rspec.spec_helper) { rspec.spec_dir }
+  watch(rspec.spec_support) { rspec.spec_dir }
+  watch(rspec.spec_files)
+
+  # Ruby files
+  ruby = dsl.ruby
+  dsl.watch_spec_files_for(ruby.lib_files)
+end

data/README.md

@@ -1,6 +1,8 @@
 # RxNav
 
-[![Gem Version](https://badge.fury.io/rb/rx_nav.png)](http://badge.fury.io/rb/rx_nav) [![Code Climate](https://codeclimate.com/github/jbender/rx_nav_ruby.png)](https://codeclimate.com/github/jbender/rx_nav_ruby)
+[![Gem Version](http://img.shields.io/gem/v/rx_nav.svg?style=flat-square)](https://rubygems.org/gems/rx_nav) [![Dependency Status](http://img.shields.io/gemnasium/jbender/rx_nav_ruby.svg?style=flat-square)](https://gemnasium.com/jbender/rx_nav_ruby)
+ [![Code Climate](http://img.shields.io/codeclimate/github/jbender/rx_nav_ruby.svg?style=flat-square)](https://codeclimate.com/github/jbender/rx_nav_ruby) [![Test Coverage](https://img.shields.io/codeclimate/coverage/github/jbender/rx_nav_ruby.svg?style=flat-square)](https://codeclimate.com/github/jbender/rx_nav_ruby)
+ [ ![Codeship Status for jbender/rx_nav_ruby](https://img.shields.io/codeship/e1dd97e0-8d48-0132-a9a4-5691319bff63.svg?style=flat-square)](https://codeship.com/projects/60640)
 
 This gem makes it easier to work with the RxNav REST APIs, as enumerated on [this page](http://rxnav.nlm.nih.gov/APIsOverview.html).
 
@@ -22,7 +24,41 @@ Or install it yourself as:
 
 ## Usage
 
-TODO: Write usage instructions here
+Each service has it's own class, which have the class methods enumerated below. When appropriate, these methods will return `Concept`s, which are further queryable to retrieve more information about a specific drug. **Question marks indicate optional parameters.**
+
+Please note that according to the [NLM Terms of Service](http://rxnav.nlm.nih.gov/TermOfService.html), you can will only be able to make **20 requests/second/IP**, so keep that in mind when implementing this project.
+
+### [NDF-RT (Class named NDFRT)](https://github.com/jbender/rx_nav_ruby/blob/master/lib/rx_nav/ndfrt.rb)
+
+  * all_records_by_kind
+  * get_info
+  * find_by_name(name, kind?)
+  * find_by_id(type, id)
+  * find_by({type: x, id: y} OR {name: x, kind: y})
+  * possible_roles
+  * possible_properties
+  * possible_kinds
+  * possible_types
+  * possible_associations
+  * possible_options_for(type)
+  * api_version
+
+### [RxNorm](https://github.com/jbender/rx_nav_ruby/blob/master/lib/rx_nav/rx_norm.rb)
+
+  * search_by_name(name, options?)
+  * find_rxcui_by_id(type, id)
+  * find_rxcui_by_name(name)
+  * find_drugs_by_name(name)
+  * spelling_suggestions(name)
+  * status(id)
+  * properties(id)
+  * quantity(id)
+  * strength(id)
+
+### [RxTerms](https://github.com/jbender/rx_nav_ruby/blob/master/lib/rx_nav/rx_terms.rb)
+
+  * all_concepts
+  * all_info(id)
 
 ## Contributing
 

data/Rakefile

@@ -1 +1,7 @@
-require "bundler/gem_tasks"
+require 'rspec/core/rake_task'
+
+RSpec::Core::RakeTask.new(:spec) do |t|
+  t.pattern = 'spec/**/*_spec.rb'
+end
+
+task default: :spec

data/lib/rx_nav.rb

@@ -24,4 +24,8 @@ module RxNav
     return RxNav.nori.parse(Net::HTTP.get request)
   end
 
+  def self.ensure_array obj
+    (obj && !obj.is_a?(Array)) ? [obj] : obj
+  end
+
 end

data/lib/rx_nav/concept.rb

@@ -28,10 +28,10 @@ module RxNav
 
     # Supplementary calls to fetch info from other DBs
     # Note: these methods return false if no information was found
-    
+
     def get_terms_info
       rxcui = get_rxcui
-      info = RxNav::RxTerms.get_info(rxcui)
+      info = RxNav::RxTerms.all_info(rxcui)
       merge_concept info
     end
 
@@ -58,7 +58,8 @@ module RxNav
         if self.nui.nil?
           raise "This concept doesn't have a nui or rxcui"
         else
-          self.rxcui = RxNav::RxNorm.find_rxcui_by_id('nui', self.nui)
+           rxcui = RxNav::RxNorm.find_rxcui_by_id('nui', self.nui)
+           self.rxcui = rxcui.is_a?(Array) ? rxcui.first : rxcui
         end
       end
       # If we had to look it up, use that, otherwise use the model's
@@ -85,7 +86,7 @@ module RxNav
       str.gsub(/\w+/) { |w| w.capitalize } if str.is_a? String
     end
 
-    def merge_concept concept
+    def merge_concept concept_hash
       if concept_hash.nil? || concept_hash.empty?
         return false
       else
@@ -99,4 +100,4 @@ module RxNav
     end
 
   end
-end
+end

data/lib/rx_nav/ndfrt.rb

@@ -38,7 +38,7 @@ module RxNav
         type  = type.upcase
         id    = id.to_s
         query = "/idType=#{type}&idString=#{id}"
-        return get_concepts query
+        get_concepts query
       end
 
       def find_by_name name, kind = nil
@@ -47,24 +47,27 @@ module RxNav
           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
+        get_concepts query
+      end
+
+      # PLEASE NOTE:
+      # These methods were deprecated in the Sept 2014 release of ND-FRT
+      #
+      # 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?
@@ -79,7 +82,7 @@ module RxNav
         data = get_response_hash(query)[:group_concepts][:concept]
         return data.map { |c| RxNav::Concept.new c }
       end
-  
+
       private
 
       def get_response_hash query
@@ -94,8 +97,7 @@ module RxNav
       def get_concepts query
         data = get_response_hash(query)[:group_concepts]
         if data && data[:concept]
-          concepts = data[:concept]
-          concepts = [concepts] unless concepts.is_a?(Array)
+          concepts = RxNav.ensure_array data[:concept]
           return concepts.map { |c| RxNav::Concept.new(c) }
         else
           return nil

data/lib/rx_nav/rx_norm.rb

@@ -1,21 +1,23 @@
 module RxNav
   class RxNorm
     class << self
-      
+
       def search_by_name name, options = {}
         options = {max_results: 20, options: 0}.merge(options)
-        
+
         query = "/approximateTerm?term=#{name}"\
                 "&maxEntries=#{options[:max_results]}"\
                 "&options=#{options[:options]}"
 
         # Get the data we care about in the right form
         data = get_response_hash(query)[:approximate_group][:candidate]
-        data = [data] if (data && !data.is_a?(Array))
 
         # If we didn't get anything, say so
         return nil if data.nil?
-        
+
+        # Put it in the right form
+        data = RxNav.ensure_array data
+
         return data.map { |c| RxNav::Concept.new(c) }
       end
 
@@ -65,13 +67,12 @@ module RxNav
 
         status.send("remapped?=", reported_status == 'remapped')
         status.send("active?=", reported_status == 'active')
-        
+
         if status.remapped?
-          concepts = data[:min_concept_group][:min_concept]
-          concepts = [concepts] if (concepts && !concepts.is_a?(Array))
+          concepts = RxNav.ensure_array data[:min_concept_group][:min_concept]
           status.remapped_to = concepts.map { |c| c[:rxcui] }
         end
-        
+
         return status
       end
 
@@ -80,14 +81,27 @@ module RxNav
         return OpenStruct.new get_response_hash(query)[:properties]
       end
 
+      def property id, name
+        query    = "/rxcui/#{id}/property?propName=#{name.upcase}"
+        response = get_response_hash(query)
+
+        concept_group = response[:property_concept_group]
+        return nil unless concept_group
+
+        concepts = concept_group[:property_concept]
+        return concepts ? concepts[:prop_value] : nil
+      end
+
       def quantity id
-        query = "/rxcui/#{id}/quantity"
-        return get_response_hash(query)[:quantity_group][:quantity]
+        property id, "quantity"
       end
 
       def strength id
-        query = "/rxcui/#{id}/strength"
-        return get_response_hash(query)[:strength_group][:strength]
+        property id, "strength"
+      end
+
+      def available_strength id
+        property id, "available_strength"
       end
 
       private
@@ -95,12 +109,12 @@ module RxNav
       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] }
+          data = RxNav.ensure_array data
+          return data.map { |c| c[:id_group][:rxnorm_id] }
         else
           return nil
         end

data/lib/rx_nav/version.rb

@@ -1,3 +1,3 @@
 module RxNav
-  VERSION = "0.1.3"
+  VERSION = "0.2.0"
 end

data/rx_nav.gemspec

@@ -23,4 +23,5 @@ Gem::Specification.new do |spec|
 
   spec.add_development_dependency 'bundler', '~> 1.3'
   spec.add_development_dependency 'rake'
+  spec.add_development_dependency 'rspec', '>= 2.0.0'
 end

data/spec/concept_spec.rb

@@ -0,0 +1,64 @@
+require 'spec_helper'
+
+describe RxNav::Concept do
+  context 'new concept' do
+    subject { RxNav::Concept.new }
+    it { is_expected.to be_kind_of(OpenStruct) }
+    it { is_expected.to respond_to(:name) }
+    it { is_expected.to respond_to(:kind) }
+    it { is_expected.to respond_to(:nui) }
+    it { is_expected.to respond_to(:to_s) }
+    it { is_expected.to respond_to(:get_terms_info) }
+    it { is_expected.to respond_to(:get_ndfrt_info) }
+    it { is_expected.to respond_to(:get_norm_info) }
+  end
+
+  context 'NDF-RT concept "N0000152900"' do
+    let(:nui) { "N0000152900" }
+    let(:concept) { RxNav::NDFRT.get_info nui }
+    subject { concept }
+
+    context "#name" do
+      subject { concept.name }
+      it { is_expected.to be_kind_of(String) }
+      it { is_expected.to eq("Acetic Acid 2%/Hydrocortisone 1% Soln,Otic") }
+    end
+
+    context "#kind" do
+      subject { concept.kind }
+      it { is_expected.to be_kind_of(String) }
+      it { is_expected.to eq("Drug") }
+    end
+
+    context "#nui" do
+      subject { concept.nui }
+      it { is_expected.to be_kind_of(String) }
+      it { is_expected.to eq(nui) }
+    end
+
+    context "#to_s" do
+      subject { concept.to_s }
+      it { is_expected.to be_kind_of(String) }
+      it { is_expected.to eq(concept.name) }
+    end
+
+    context "#get_terms_info" do
+      let(:original) { concept }
+      subject { concept.get_terms_info }
+      it { is_expected.to be_kind_of(RxNav::Concept) }
+    end
+
+    context "#get_ndfrt_info" do
+      let(:original) { concept }
+      subject { concept.get_ndfrt_info }
+      it { is_expected.to be_kind_of(RxNav::Concept) }
+    end
+
+    context "#get_norm_info" do
+      let(:original) { concept }
+      subject { concept.get_norm_info }
+      it { is_expected.to be_kind_of(RxNav::Concept) }
+    end
+
+  end
+end

data/spec/ndfrt_spec.rb

@@ -0,0 +1,116 @@
+require 'spec_helper'
+require 'support/api'
+require 'support/array_type'
+
+describe RxNav::NDFRT do
+
+  describe "remote endpoints" do
+    url      = "http://rxnav.nlm.nih.gov/REST/Ndfrt"
+    response = Net::HTTP.get(URI("#{url}/json"))
+    subject  { JSON.parse(response)["resourceList"]["resource"] }
+
+    include_examples 'uses valid endpoints', [
+      "#{url}/version",
+      "#{url}/associationList",
+      "#{url}/typeList",
+      "#{url}/kindList",
+      "#{url}/propertyList",
+      "#{url}/roleList",
+      "#{url}/idType={idType}&idString={idString}",
+      "#{url}/search?conceptName={conceptName}&kindName={kindName}",
+      "#{url}/allInfo/{nui}",
+      "#{url}/allconcepts?kind=yourKinds"
+    ]
+  end
+
+  describe "#api_version" do
+    subject { RxNav::NDFRT.api_version }
+
+    it { is_expected.to be_kind_of(String) }
+  end
+
+  describe "#possible_associations" do
+    subject { RxNav::NDFRT.possible_associations }
+
+    include_examples 'should be an array of', String
+  end
+
+  describe "#possible_types" do
+    subject { RxNav::NDFRT.possible_types }
+
+    include_examples 'should be an array of', String
+  end
+
+  describe "#possible_kinds" do
+    subject { RxNav::NDFRT.possible_kinds }
+
+    include_examples 'should be an array of', String
+  end
+
+  describe "#possible_properties" do
+    subject { RxNav::NDFRT.possible_properties }
+
+    include_examples 'should be an array of', String
+  end
+
+  describe "#possible_roles" do
+    subject { RxNav::NDFRT.possible_roles }
+
+    include_examples 'should be an array of', String
+  end
+
+  describe "#find_by_id for type RXCUI and id 161" do
+    subject { RxNav::NDFRT.find_by_id 'RXCUI', '161' }
+
+    include_examples 'should be an array of', RxNav::Concept
+  end
+
+  describe "#find_by_name morphine without kind" do
+    subject { RxNav::NDFRT.find_by_name 'morphine' }
+
+    include_examples 'should be an array of', RxNav::Concept
+  end
+
+  describe "#find_by_name morphine with kind ingredient" do
+    subject { RxNav::NDFRT.find_by_name 'morphine', 'ingredient' }
+
+    include_examples 'should be an array of', RxNav::Concept
+  end
+
+  describe "#find_by with hash of name" do
+    it "should return the same as find_by_name" do
+      @generic_find = RxNav::NDFRT.find_by name: 'morphine'
+      @specific_find = RxNav::NDFRT.find_by_name 'morphine'
+      expect(@generic_find).to eq(@specific_find)
+    end
+  end
+
+  describe "#find_by with hash of name and kind" do
+    it "should return the same as find_by_name" do
+      @generic_find = RxNav::NDFRT.find_by name: 'morphine', kind: 'ingredient'
+      @specific_find = RxNav::NDFRT.find_by_name 'morphine', 'ingredient'
+      expect(@generic_find).to eq(@specific_find)
+    end
+  end
+
+  describe "#find_by with hash of type and id" do
+    it "should return the same as find_by_name" do
+      @generic_find = RxNav::NDFRT.find_by type: 'RXCUI', id: '161'
+      @specific_find = RxNav::NDFRT.find_by_id 'RXCUI', '161'
+      expect(@generic_find).to eq(@specific_find)
+    end
+  end
+
+  describe "#all_records_by_kind" do
+    subject { RxNav::NDFRT.all_records_by_kind "pharmacokinetics" }
+
+    include_examples 'should be an array of', RxNav::Concept
+  end
+
+  describe "#get_info" do
+    subject { RxNav::NDFRT.get_info "N0000152900" }
+
+    it { is_expected.to be_kind_of(RxNav::Concept) }
+  end
+
+end

data/spec/rx_nav_spec.rb

@@ -0,0 +1,14 @@
+require 'spec_helper'
+
+describe "http://rxnav.nlm.nih.gov/REST" do
+  before :all do
+    @url      = URI "http://rxnav.nlm.nih.gov/REST/json"
+    @response = Net::HTTP.get(@url)
+    @json     = JSON.parse(@response)
+  end
+
+  it "should be online" do
+    expect(@json).to_not be_empty
+  end
+
+end

data/spec/rx_norm_spec.rb

@@ -0,0 +1,92 @@
+require 'spec_helper'
+require 'support/api'
+require 'support/array_type'
+
+describe RxNav::RxNorm do
+
+  describe "remote endpoints" do
+    url      = "http://rxnav.nlm.nih.gov/REST"
+    response = Net::HTTP.get(URI("#{url}/json"))
+    subject  { JSON.parse(response)["resourceList"]["resource"] }
+
+    include_examples 'uses valid endpoints', [
+      "#{url}/approximateTerm?term=value&maxEntries=value&option=value",
+      "#{url}/rxcui?idtype=yourIdtype&id=yourId&allsrc=0or1",
+      "#{url}/rxcui?name=yourName&srclist=yourSources&allsrc=0or1&search=0or1or2",
+      "#{url}/drugs?name=yourName",
+      "#{url}/spellingsuggestions?name=yourName",
+      "#{url}/rxcui/{rxcui}/status",
+      "#{url}/rxcui/{rxcui}/properties",
+      "#{url}/rxcui/{rxcui}/property?propName=propName"
+    ]
+  end
+
+  describe "#search_by_name" do
+    subject { RxNav::RxNorm.search_by_name "zocor" }
+
+    include_examples 'should be an array of', RxNav::Concept
+  end
+
+  describe "#find_rxcui_by_id" do
+    describe "NUI search" do
+      subject { RxNav::RxNorm.find_rxcui_by_id "NUI", "N0000148200" }
+      include_examples 'should be an array of', String
+    end
+
+    describe "NDC search" do
+      subject { RxNav::RxNorm.find_rxcui_by_id "NDC", "0781-1506-10" }
+      include_examples 'should be an array of', String
+    end
+  end
+
+  describe "#find_rxcui_by_name" do
+    subject { RxNav::RxNorm.find_rxcui_by_name "lipitor" }
+    include_examples 'should be an array of', String
+  end
+
+  describe "#find_drugs_by_name" do
+    let(:results) { RxNav::RxNorm.find_drugs_by_name "cymbalta" }
+
+    context "at the top level" do
+      subject { results }
+      include_examples 'should be an array of', Hash
+    end
+
+    context "first result" do
+      subject { results.first }
+      it { is_expected.to include(:name) }
+      it { is_expected.to include(:concepts) }
+
+      context 'name' do
+        subject { results.first[:name] }
+        it { is_expected.to be_kind_of(String) }
+      end
+
+      context 'concepts' do
+        subject { results.first[:concepts] }
+        include_examples 'should be an array of', RxNav::Concept
+      end
+    end
+  end
+
+  describe '#spelling_suggestions' do
+    subject { RxNav::RxNorm.spelling_suggestions "ambienn" }
+
+    include_examples 'should be an array of', String
+  end
+
+  describe "#status" do
+    subject { RxNav::RxNorm.status "105048" }
+
+    it { is_expected.to be_kind_of(OpenStruct) }
+    it { is_expected.to respond_to(:active?) }
+    it { is_expected.to respond_to(:remapped?) }
+  end
+
+  describe "#properties" do
+    subject { RxNav::RxNorm.properties "131725" }
+
+    it { is_expected.to be_kind_of(OpenStruct) }
+  end
+
+end

data/spec/spec_helper.rb

@@ -0,0 +1,4 @@
+require "codeclimate-test-reporter"
+CodeClimate::TestReporter.start
+
+require_relative '../lib/rx_nav'

data/spec/support/api.rb

@@ -0,0 +1,5 @@
+shared_examples 'uses valid endpoints' do |endpoints|
+  endpoints.each do |endpoint|
+    it { should include(endpoint) }
+  end
+end

data/spec/support/array_type.rb

@@ -0,0 +1,5 @@
+shared_examples 'should be an array of' do |klass|
+  it { is_expected.to be_kind_of(Array) }
+  it { is_expected.to_not be_empty }
+  it { is_expected.to all( be_a klass ) }
+end

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: rx_nav
 version: !ruby/object:Gem::Version
-  version: 0.1.3
+  version: 0.2.0
 platform: ruby
 authors:
 - Jonathan Bender
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2014-01-09 00:00:00.000000000 Z
+date: 2015-02-02 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: nori
@@ -66,6 +66,20 @@ dependencies:
     - - ">="
       - !ruby/object:Gem::Version
         version: '0'
+- !ruby/object:Gem::Dependency
+  name: rspec
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: 2.0.0
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: 2.0.0
 description: Ruby wrappers for the RxNav RESTful APIs
 email:
 - jlbender@gmail.com
@@ -75,6 +89,7 @@ extra_rdoc_files: []
 files:
 - ".gitignore"
 - Gemfile
+- Guardfile
 - LICENSE.txt
 - README.md
 - Rakefile
@@ -86,6 +101,13 @@ files:
 - lib/rx_nav/rx_terms.rb
 - lib/rx_nav/version.rb
 - rx_nav.gemspec
+- spec/concept_spec.rb
+- spec/ndfrt_spec.rb
+- spec/rx_nav_spec.rb
+- spec/rx_norm_spec.rb
+- spec/spec_helper.rb
+- spec/support/api.rb
+- spec/support/array_type.rb
 homepage: https://github.com/jbender/rx_nav_ruby
 licenses:
 - MIT
@@ -106,8 +128,15 @@ required_rubygems_version: !ruby/object:Gem::Requirement
       version: '0'
 requirements: []
 rubyforge_project: 
-rubygems_version: 2.2.1
+rubygems_version: 2.2.2
 signing_key: 
 specification_version: 4
 summary: Ruby-based way of interacting with the RxNav APIs (http://rxnav.nlm.nih.gov/APIsOverview.html)
-test_files: []
+test_files:
+- spec/concept_spec.rb
+- spec/ndfrt_spec.rb
+- spec/rx_nav_spec.rb
+- spec/rx_norm_spec.rb
+- spec/spec_helper.rb
+- spec/support/api.rb
+- spec/support/array_type.rb