Merge branch 'develop' of barrel.mitre.org:hdata-patient-server/hdata…

…-patient-server into develop

Gemfile.lock

@@ -1,6 +1,6 @@
 GIT
   remote: http://github.com/projectcypress/health-data-standards.git
-  revision: b9c81c7707a17819bc92ce4f92c05bddbdba32a5
+  revision: e431176e7d3bf12aaa77953b14a4b8b1de054b4f
   branch: develop
   specs:
     health-data-standards (0.7.1)
@@ -75,7 +75,7 @@ GEM
       configatron
       hashie
     curb (0.7.18)
-    daemons (1.1.7)
+    daemons (1.1.8)
     devise (2.0.0)
       bcrypt-ruby (~> 3.0)
       orm_adapter (~> 0.0.3)
@@ -195,7 +195,7 @@ GEM
       tilt (~> 1.3)
     sax-machine (0.0.20)
       nokogiri (> 0.0.0)
-    slop (2.4.3)
+    slop (2.4.4)
     sprockets (2.1.2)
       hike (~> 1.2)
       rack (~> 1.0)

app/controllers/entries_controller.rb

@@ -1,8 +1,6 @@
 class EntriesController < ApplicationController
-  before_filter :get_section_name
-  before_filter :find_entry, except: "index"
-
-  respond_to :atom, :xml
+  before_filter :set_up_section
+  before_filter :find_entry, only: "show"
 
   def index
     @entries = @record.send(@section_name)
@@ -12,18 +10,35 @@ def index
   end
 
   def show
-    render :json => @entry.attributes
+    respond_to do |wants|
+      wants.json {render :json => @entry.attributes}
+      wants.xml do
+        exporter = @extension.exporters['application/xml']
+        render :xml => exporter.export(@entry)
+      end
+    end
   end
-
 
   private
 
-  def get_section_name
+  def set_up_section
     @section_name = params[:section]
+    sr = SectionRegistry.instance
+    @extension = sr.extension_from_path(params[:section])
+    unless @extension
+      render text: 'Section Not Found', status: 404
+    end
   end
 
   def find_entry
-    @entry = @record.send(@section_name).find(params[:id])
+    if BSON::ObjectId.legal?(params[:id])
+      @entry = @record.send(@section_name).find(:first, conditions: {id: params[:id]})
+      unless @entry
+        render text: 'Entry Not Found', status: 404
+      end
+    else
+      render text: 'Not a valid identifier for a section document', status: 400
+    end
   end
 
 end

config/initializers/hdata_sections.rb

@@ -0,0 +1,21 @@
+require 'section_registry'
+
+##############################################################
+# Register all the sections we will use in the web application
+############################################################## 
+sr = SectionRegistry.instance
+
+sr.add_section('allergies', 'http://projecthdata.org/hdata/schemas/2009/06/allergy', 'Allergies')
+sr.add_section('care_goals', 'http://projecthdata.org/hdata/schemas/2009/06/care_goal', 'Care Goals')
+sr.add_section('conditions', 'http://projecthdata.org/hdata/schemas/2009/06/condition', 'Conditions')
+sr.add_section('encounters', 'http://projecthdata.org/hdata/schemas/2009/06/encounter', 'Encounters')
+sr.add_section('immunizations', 'http://projecthdata.org/hdata/schemas/2009/06/immunization', 'Immunizations')
+sr.add_section('medical_equipment', 'http://projecthdata.org/hdata/schemas/2009/06/medical_equipment', 'Medical Equipment')
+sr.add_section('medications', 'http://projecthdata.org/hdata/schemas/2009/06/medication', 'Medications')
+sr.add_section('procedures', 'http://projecthdata.org/hdata/schemas/2009/06/procedure', 'Procedures')
+sr.add_section('results', 'http://projecthdata.org/hdata/schemas/2009/06/result', 'Lab Results') do |importers, exporters|
+  importers['application/xml'] = HealthDataStandards::Import::GreenCda::ResultImporter.instance
+  exporters['application/xml'] = HealthDataStandards::Export::GreenCda::ExportGenerator.create_exporter_for(:result)
+end
+sr.add_section('social_history', 'http://projecthdata.org/hdata/schemas/2009/06/social_history', 'Social History')
+sr.add_section('vital_signs', 'http://projecthdata.org/hdata/schemas/2009/06/result', 'Vital Signs')

lib/section_registry.rb

@@ -1,6 +1,9 @@
 require 'ostruct'
 
 # A registry where hData extensionIds can be mapped to url paths and vice versa
+#
+# Note - This class gets configured in config/initializers/hdata_sections.rb
+#
 class SectionRegistry
   include Singleton
 
@@ -30,25 +33,4 @@ def add_section(path, extension_id, name)
   def extension_from_path(path)
     @extensions.find {|e| e.path == path}
   end
-end
-
-
-##############################################################
-# Register all the sections we will use in the web application
-############################################################## 
-sr = SectionRegistry.instance
-
-sr.add_section('allergies', 'http://projecthdata.org/hdata/schemas/2009/06/allergy', 'Allergies')
-sr.add_section('care_goals', 'http://projecthdata.org/hdata/schemas/2009/06/care_goal', 'Care Goals')
-sr.add_section('conditions', 'http://projecthdata.org/hdata/schemas/2009/06/condition', 'Conditions')
-sr.add_section('encounters', 'http://projecthdata.org/hdata/schemas/2009/06/encounter', 'Encounters')
-sr.add_section('immunizations', 'http://projecthdata.org/hdata/schemas/2009/06/immunization', 'Immunizations')
-sr.add_section('medical_equipment', 'http://projecthdata.org/hdata/schemas/2009/06/medical_equipment', 'Medical Equipment')
-sr.add_section('medications', 'http://projecthdata.org/hdata/schemas/2009/06/medication', 'Medications')
-sr.add_section('procedures', 'http://projecthdata.org/hdata/schemas/2009/06/procedure', 'Procedures')
-sr.add_section('results', 'http://projecthdata.org/hdata/schemas/2009/06/result', 'Lab Results') do |importers, exporters|
-  importers['application/xml'] = HealthDataStandards::Import::GreenCda::ResultImporter.instance
-  exporters['application/xml'] = HealthDataStandards::Export::GreenCda::ExportGenerator.create_exporter_for(:result)
-end
-sr.add_section('social_history', 'http://projecthdata.org/hdata/schemas/2009/06/social_history', 'Social History')
-sr.add_section('vital_signs', 'http://projecthdata.org/hdata/schemas/2009/06/result', 'Vital Signs')
+end

test/factories.rb

@@ -5,6 +5,18 @@
     birthdate -790874989
     gender 'M'
     sequence(:medical_record_number) {|n| n}
+
+    trait :with_lab_results do
+      results {|r| [r.association(:lab_result)]}
+    end
+  end
+
+  factory :lab_result do
+    description 'LDL Cholesterol'
+    time 1285387200
+    codes({'CPT' => ['83721'], 'LOINC' => ['2089-1']})
+    value({'scalar' => 127, 'units' => 'mg/dL'})
+    reference_range '70 mg/dL - 160 mg/dL'
   end
 
 

test/functional/entries_controller_test.rb

@@ -0,0 +1,48 @@
+require 'test_helper'
+
+class EntriesControllerTest < ActionController::TestCase
+  setup do
+    @record = FactoryGirl.create(:record, :with_lab_results)
+  end
+
+  test "get a result as xml" do
+    request.env['HTTP_ACCEPT'] = Mime::XML
+    get :show, {record_id: @record.medical_record_number, section: 'results', id: @record.results.first.id}
+    doc = Nokogiri::XML::Document.parse(response.body)
+    assert_response :success
+    assert_equal "result", doc.children.first.name
+  end
+
+  test "get a result as JSON" do
+    request.env['HTTP_ACCEPT'] = Mime::JSON
+    get :show, {record_id: @record.medical_record_number, section: 'results', id: @record.results.first.id}
+    doc = JSON.parse(response.body)
+    assert_response :success
+    assert_equal "LDL Cholesterol", doc['description']
+  end
+
+  test "get a section that doesn't exist" do
+    request.env['HTTP_ACCEPT'] = Mime::XML
+    get :show, {record_id: @record.medical_record_number, section: 'bacon', id: @record.results.first.id}
+    assert_response :missing
+  end
+
+  test "get section Atom feed" do
+    request.env['HTTP_ACCEPT'] = 'application/atom+xml'
+    get :index, {record_id: @record.medical_record_number, section: 'results'}
+    assert_response :success
+    rss = Feedzirra::Feed.parse(@response.body)
+    assert_not_nil(rss.entries)
+    assert_equal(1, rss.entries.size)
+    assert rss.entries[0].links[0].include? "/records/#{@record.medical_record_number}/results/#{@record.results.first.id}"
+  end
+
+  test "get a document that doesn't exist" do
+    request.env['HTTP_ACCEPT'] = Mime::XML
+    get :show, {record_id: @record.medical_record_number, section: 'results', id: 'bacon'}
+    assert_response 400
+
+    get :show, {record_id: @record.medical_record_number, section: 'results', id: ('0' * 24)}
+    assert_response :missing
+  end
+end

test/unit/section_registry_test.rb

@@ -1,5 +1,4 @@
 require 'test_helper'
-require 'section_registry'
 
 class SectionRegistryTest < ActiveSupport::TestCase
   test 'finding an extension by path' do