health-data-standards 2.2.1 → 3.0.3

data/lib/health-data-standards/models/cqm/bundle.rb

@@ -0,0 +1,45 @@
+module HealthDataStandards
+  module CQM
+
+    class Bundle
+      include Mongoid::Document
+      store_in collection: 'bundles'
+      field :title, type: String
+      field :version, type: String
+      field :license, type: String
+      field :extensions, type: Array
+      field :effective_date
+      field :measure_period_start
+      field :records, type: Array
+      field :active, type: Boolean
+
+      validates_presence_of :version
+
+      def self.active
+        self.where({active: true})
+      end
+
+      def measures
+      	 HealthDataStandards::CQM::Measure.where({bundle_id: self.id}).order_by([["id", :asc],["sub_id",:asc]])
+      end
+
+      def records
+      	Record.where(bundle_id: self._id, test_id: nil).order_by([["last", :asc]])
+      end
+
+
+      def value_sets
+        HealthDataStandards::SVS::ValueSet.in(bundle_id: self.id)
+      end
+
+      def delete
+        self.measures.destroy
+        self.records.destroy
+        self.value_sets.destroy
+        super
+      end
+
+
+	   end
+  end
+end

data/lib/health-data-standards/models/cqm/measure.rb

@@ -0,0 +1,36 @@
+module HealthDataStandards
+  module CQM
+
+  	class Measure
+		  include Mongoid::Document
+		  store_in collection: 'measures'
+		  field :id, type: String
+		  field :sub_id, type: String
+		  field :name, type: String
+		  field :subtitle, type: String
+		  field :short_subtitle, type: String
+		  field :hqmf_id, type: String
+		  field :hqmf_set_id, type: String
+		  field :hqmf_version_number, type: String
+		  field :nqf_id, type: String
+		  field :type, type: String
+		  field :category, type: String
+		  field :population_ids , type: Hash
+		  field :oids, type: Array 
+		  field :data_criteria, type: Array
+		  scope :top_level_by_type , ->(type){where({"type"=> type}).any_of({"sub_id" => nil}, {"sub_id" => "a"})}
+		  scope :top_level , any_of({"sub_id" => nil}, {"sub_id" => "a"})
+		  scope :order_by_id_sub_id, order_by([["id", :asc],["sub_id", :asc]])
+		  index({oids: 1})
+		  index({hqmf_id: 1})
+		  index({category: 1})
+		  index "bundle_id" => 1
+		  
+		  validates_presence_of :id
+		  validates_presence_of :name
+		  
+
+
+		end
+	end
+end

data/lib/health-data-standards/models/guarantor.rb

@@ -4,6 +4,7 @@ class Guarantor
   embeds_one :organization
   embeds_one :person
   
+  field :time, type: Integer
   field :start_time, type: Integer
   field :end_time, type: Integer
   

data/lib/health-data-standards/models/insurance_provider.rb

@@ -1,5 +1,6 @@
 class InsuranceProvider
   include Mongoid::Document
+  include ThingWithCodes
   
   embedded_in :record, class_name: 'Record'
   embeds_one :payer, class_name: "Organization"
@@ -14,5 +15,6 @@ class InsuranceProvider
   field :relationship, type: Hash
   field :financial_responsibility_type, type: Hash
   field :name, type: String
+  field :free_text, type: String
   
 end

data/lib/health-data-standards/models/order_information.rb

@@ -7,6 +7,8 @@ class OrderInformation
   field :orderExpirationDateTime, type: Integer
   field :orderDateTime, type: Integer
   
+  belongs_to :provider
+  
   alias :order_number :orderNumber
   alias :order_number= :orderNumber=
   alias :quantity_ordered :quantityOrdered

data/lib/health-data-standards/models/record.rb

@@ -1,25 +1,26 @@
 class Record
   include Mongoid::Document
   
-  field :title, type: String # TODO
+  field :title, type: String
   field :first, type: String
   field :last, type: String
   field :gender, type: String
   field :birthdate, type: Integer
-  field :deathdate, type: Integer # TODO
-  field :religious_affilication, type: Hash # TODO
+  field :deathdate, type: Integer
+  field :religious_affiliation, type: Hash
   field :effective_time, type: Integer
   field :race, type: Hash
   field :ethnicity, type: Hash
-  field :languages, type: Array
+  field :languages, type: Array, default: []
   field :test_id, type: Moped::BSON::ObjectId
-  field :marital_status, type: Hash # TODO
+  field :marital_status, type: Hash
   field :medical_record_number, type: String
   field :expired, type: Boolean
   field :clinicalTrialParticipant, type: Boolean   # Currently not implemented in the C32 importer
                                                    # because it cannot be easily represented in a
                                                    # HITSP C32
 
+  index "last" => 1                                                   
   embeds_many :allergies
   embeds_many :care_goals, class_name: "Entry" # This can be any number of different entry types
   embeds_many :conditions

data/lib/health-data-standards/models/svs/value_set.rb

@@ -14,7 +14,7 @@ module HealthDataStandards
       index "concepts.code_system" => 1
       index "concepts.code_system_name" => 1
       index "concepts.display_name" => 1
-      
+      index "bundle_id" => 1
       scope :by_oid, ->(oid){where(:oid => oid)}
 
       # Provides an Array of Hashes. Each code system gets its own Hash

data/lib/health-data-standards/railtie.rb

@@ -0,0 +1,11 @@
+module HealthDataStandards
+  class Railtie < Rails::Railtie
+    initializer 'Rails logger' do
+      HealthDataStandards.logger = Rails.logger
+    end
+    rake_tasks do
+      Dir[File.join(File.dirname(__FILE__),'tasks/*.rake')].each { |f| load f }
+    end
+
+  end
+end

data/lib/health-data-standards/tasks/bundle.rake

@@ -0,0 +1,107 @@
+require 'health-data-standards'
+
+db_name = ENV['DB_NAME'] || 'test'
+
+namespace :bundle do
+  desc 'Import a quality bundle into the database.'
+  task :import, [:bundle_path,  :delete_existing,  :update_measures, :type] => [:environment] do |task, args|
+    raise "The path to the measures zip file must be specified" unless args.bundle_path
+    options = {:clear_db => (args.delete_existing == "true"),
+    					 :type => args.type ,
+    					 :update_measures => (args.update_measures == "true")
+    					}
+
+    bundle = File.open(args.bundle_path)    
+    importer = HealthDataStandards::Import::Bundle::Importer
+    bundle_contents = importer.import(bundle, options)
+    
+    puts "Successfully imported bundle at: #{args.bundle_path}"
+    puts "\t Imported into environment: #{Rails.env.upcase}" if defined? Rails 
+    puts "\t Loaded #{args.type || 'all'} measures"
+    puts "\t Measures Loaded: #{bundle_contents.measures.count}"
+    puts "\t Test Patients Loaded: #{bundle_contents.records.count}"
+    puts "\t Extensions Loaded: #{bundle_contents[:extensions].count}"
+  end
+  
+  # this task is most likely temporary.  Once Bonnie can handle both EP and EH measures together, this would no longer be required.
+  desc 'Merge two bundles into one.'
+  task :merge, [:bundle_one,:bundle_two] do |t, args|
+    raise "Two bundle zip file paths to be merged must be specified" unless args.bundle_one && args.bundle_two
+    
+    tmpdir = Dir.mktmpdir
+    ['measures','patients','library_functions','results', 'sources', 'value_sets'].each do |dir|
+      
+      FileUtils.mkdir_p(File.join(tmpdir, 'output', dir))
+      
+    end
+      
+    begin
+      
+      ({'one'=>args.bundle_one,'two'=>args.bundle_two}).each do |key, source|
+        Zip::ZipFile.open(source) do |zip_file|
+          zip_file.each do |f|
+            f_path=File.join(tmpdir, key, f.name)
+            FileUtils.mkdir_p(File.dirname(f_path))
+            zip_file.extract(f, f_path) unless File.exist?(f_path)
+          end
+        end
+      end
+      
+      
+      ['measures','patients','library_functions', 'sources'].each do |dir|
+        ['one','two'].each do |key|
+          FileUtils.mv(Dir.glob(File.join(tmpdir,key,dir,'*')), File.join(tmpdir,'output',dir))
+        end
+      end
+
+      ['value_sets'].each do |dir|
+        FileUtils.mkdir_p(File.join(tmpdir,'output',dir,'json'))
+        FileUtils.mkdir_p(File.join(tmpdir,'output',dir,'xml'))
+        ['one','two'].each do |key|
+          ['json', 'xml'].each do |type|
+            FileUtils.mv(Dir.glob(File.join(tmpdir,key,dir,type,'*')), File.join(tmpdir,'output',dir,type))
+          end
+        end
+      end
+      
+      Dir.glob(File.join(tmpdir,'one','results','*.json')).each do |result_path_one|
+        json_one = JSON.parse(File.new(result_path_one).read)
+        result_filename = Pathname.new(result_path_one).basename.to_s
+        json_two = JSON.parse(File.new(File.join(tmpdir,'two','results',result_filename)).read)
+        File.open(File.join(tmpdir,'output','results',result_filename), 'w') {|f| f.write(JSON.pretty_generate(json_one + json_two)) }
+      end
+      
+      json_one = JSON.parse(File.new(File.join(tmpdir,'one','bundle.json')).read)
+      json_two = JSON.parse(File.new(File.join(tmpdir,'two','bundle.json')).read)
+      json_out = {}
+
+      json_out.merge! json_one
+
+      ['measures','patients','extensions'].each do |key|
+        json_out[key] = (json_one[key] + json_two[key]).uniq
+      end
+      
+      version = json_out['version']
+
+      File.open(File.join(tmpdir,'output','bundle.json'), 'w') {|f| f.write(JSON.pretty_generate(json_out)) }
+      date_string = Time.now.strftime("%Y-%m-%d")
+
+      out_zip = File.join('tmp','bundles',"bundle-merged-#{date_string}-#{version}.zip")
+      FileUtils.remove_entry_secure out_zip if File.exists?(out_zip)
+      Zip::ZipFile.open(out_zip, 'w') do |zipfile|
+        path = File.join(tmpdir,'output')
+        Dir[File.join(path,'**','**')].each do |file|
+          zipfile.add(file.sub(path+'/',''),file)
+        end
+      end
+      
+      puts "wrote merged bundle to: #{out_zip}"
+
+    ensure
+      FileUtils.remove_entry_secure tmpdir
+    end
+    
+  
+  end
+  
+end

data/lib/health-data-standards/util/code_system_helper.rb

@@ -13,17 +13,25 @@ module HealthDataStandards
         '2.16.840.1.113883.6.4' =>   'ICD-10-PCS',
         '2.16.840.1.113883.6.90' =>   'ICD-10-CM',
         '2.16.840.1.113883.6.14' =>   'HCPCS',
+        '2.16.840.1.113883.5.2' => "HL7 Marital Status",
         '2.16.840.1.113883.6.59' =>   'CVX',
         '2.16.840.1.113883.5.83' => 'HITSP C80 Observation Status',
         '2.16.840.1.113883.3.26.1.1' => 'NCI Thesaurus',
         '2.16.840.1.113883.3.88.12.80.20' => 'FDA',
+        "2.16.840.1.113883.4.9" => "UNII",
+        "2.16.840.1.113883.6.69" => "NDC",
         '2.16.840.1.113883.5.14' => 'HL7 ActStatus',
         '2.16.840.1.113883.6.259' => 'HL7 Healthcare Service Location',
         '2.16.840.1.113883.12.112' => 'DischargeDisposition',
         '2.16.840.1.113883.5.4' => 'HL7 Act Code',
         '2.16.840.1.113883.1.11.18877' => 'HL7 Relationship Code',
         '2.16.840.1.113883.6.238' => 'CDC Race',
-        '2.16.840.1.113883.6.177' => 'NLM MeSH'
+        '2.16.840.1.113883.6.177' => 'NLM MeSH',
+        '2.16.840.1.113883.5.1076' => "Religious Affiliation",
+        '2.16.840.1.113883.1.11.19717' => "HL7 ActNoImmunicationReason",
+        '2.16.840.1.113883.3.88.12.80.33' => "NUBC",
+        '2.16.840.1.113883.1.11.78' => "HL7 Observation Interpretation",
+        '2.16.840.1.114222.4.11.3591' => "Source of Payment Typology"
       }
       
       CODE_SYSTEM_ALIASES = {

data/lib/hqmf-generator/attribute.xml.erb

@@ -0,0 +1,11 @@
+	<subjectOf>
+		<measureAttribute>
+			<id root="2.16.840.1.113883.3.100.1" extension="<%= attribute.id %>"/>
+			<code code="<%= attribute.code %>">
+				<displayName value="<%= attribute.name %>"/>
+			</code>
+			<%- if attribute.value -%>
+			<value xsi:type="ED" value="<%= attribute.value %>"/>
+			<%- end -%>
+		</measureAttribute>
+	</subjectOf>

data/lib/hqmf-generator/characteristic_criteria.xml.erb

@@ -0,0 +1,21 @@
+      <entry typeCode="DRIV">
+        <observationCriteria moodCode="EVN" classCode="OBS">
+          <%= xml_for_template(criteria, is_source_data_criteria) %>
+          <id>
+            <item root="2.16.840.1.113883.3.100.1" extension="<%= criteria.id %>"/>
+          </id>
+          <%= xml_for_code(criteria) %>
+          <%= xml_for_description(criteria) %>
+          <%= xml_for_effective_time(criteria) %>
+          <%- if criteria.value -%>
+          <%= xml_for_value(criteria.value) %>
+          <%- end -%>
+          <definition>
+            <observationReference moodCode="EVN" classCode="OBS">
+              <id root="2.16.840.1.113883.3.100.1" extension="<%= section_name(criteria) %>"/>
+            </observationReference>
+          </definition>
+          <%= xml_for_temporal_references(criteria) %>
+          <%= xml_for_fields(criteria) %>
+        </observationCriteria>
+      </entry>

data/lib/hqmf-generator/code.xml.erb

@@ -0,0 +1,13 @@
+          <%- if criteria.inline_code_list -%>
+          <%- code_system_name = criteria.inline_code_list.keys[0] -%>
+          <%- code = criteria.inline_code_list[code_system_name][0] -%>
+          <%- code_system_oid = oid_for_name(code_system_name) -%>
+          <<%= name %> codeSystemName="<%= code_system_name %>" codeSystem="<%= code_system_oid %>"
+            code="<%= code %>">
+            <displayName value="<%= criteria.title %>"/>
+          </<%= name %>>
+          <%- elsif criteria.code_list_id -%>
+          <<%= name %><%= " xsi:type=\"CD\"" if include_type %> valueSet="<%= criteria.code_list_id %>">
+            <displayName value="<%= criteria.title %>"/>
+          </<%= name %>>
+          <%- end -%>

data/lib/hqmf-generator/condition_criteria.xml.erb

@@ -0,0 +1,22 @@
+      <entry typeCode="DRIV">
+        <observationCriteria  moodCode="EVN" classCode="OBS"<%= " actionNegationInd='true'" if criteria.negation %>>
+          <%= xml_for_template(criteria, is_source_data_criteria) %>
+          <id>
+            <item root="2.16.840.1.113883.3.100.1" extension="<%= criteria.id %>"/>
+          </id>
+          <%= xml_for_description(criteria) %>
+          <%= "<statusCode code=\"#{criteria.status}\"/>" if criteria.status %>
+          <%= xml_for_effective_time(criteria) %>
+          <%= xml_for_reason(criteria) %>
+          <%= xml_for_code(criteria, 'value') %>
+          <definition>
+            <observationReference moodCode="EVN" classCode="OBS">
+              <id root="2.16.840.1.113883.3.100.1" extension="<%= section_name(criteria) %>"/>
+            </observationReference>
+          </definition>
+          <%= xml_for_temporal_references(criteria) %>
+          <%= xml_for_fields(criteria) %>
+          <%= xml_for_derivation(criteria) %>
+          <%= xml_for_subsets(criteria) %>
+        </observationCriteria>
+      </entry>

data/lib/hqmf-generator/derivation.xml.erb

@@ -0,0 +1,6 @@
+          <excerpt typeCode="XCRPT">
+            <subsetCode code="<%= criteria.derivation_operator %>"/>
+            <%- criteria.children_criteria.each do |child_id| -%>
+            <%= xml_for_reference_id(child_id) %>
+            <%- end -%>
+          </excerpt>

data/lib/hqmf-generator/description.xml.erb

@@ -0,0 +1 @@
+          <text value="<%= text %>"/>

data/lib/hqmf-generator/document.xml.erb

@@ -0,0 +1,63 @@
+<?xml version="1.0" encoding="utf-8"?>
+<QualityMeasureDocument xmlns="urn:hl7-org:v3" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance">
+  <id root="2.16.840.1.113883.3.100.1" extension="<%= doc.hqmf_id %>" />
+  <code code="57024-2" codeSystem="2.16.840.1.113883.6.1"/>
+  <title value="<%= doc.title %>"/>
+  <text value="<%= doc.description %>"/>
+  <statusCode code="completed" />
+  <setId root="2.16.840.1.113883.3.100.1" extension="<%= doc.hqmf_set_id %>" />
+  <versionNumber value="<%= doc.hqmf_version_number %>"/>
+  <author typeCode="AUT" contextControlCode="OP">
+    <responsibleParty classCode="ASSIGNED" />
+  </author>
+  <custodian typeCode="CST">
+    <responsibleParty classCode="ASSIGNED" />
+  </custodian>
+  <controlVariable>
+    <measurePeriod>
+      <code code="MSRTP" codeSystem="2.16.840.1.113883.3.560">
+        <displayName value="Measurement period"/>
+      </code>
+      <value>
+        <low value="<%= doc.measure_period.low.value %>" />
+        <high value="<%= doc.measure_period.high.value %>" />
+      </value>
+    </measurePeriod>
+  </controlVariable>
+  <%- doc.attributes.each do |attribute| -%>
+  <%= xml_for_attribute(attribute) %>
+  <%- end -%>
+  <component>
+    <dataCriteriaSection>
+      <code code="57025-9" codeSystem="2.16.840.1.113883.6.1"/>
+      <title value="Data Criteria Section"/>
+      <text>This section describes the data criteria.</text>
+      <%- doc.all_data_criteria.each do |data_criteria| -%>
+      <%= xml_for_data_criteria(data_criteria, false) %>
+      <%- end -%>
+      <%- doc.source_data_criteria.each do |data_criteria| -%>
+      <%= xml_for_data_criteria(data_criteria, true) %>
+      <%- end -%>
+    </dataCriteriaSection>
+  </component>
+  <%- doc.populations.each_with_index do |population, population_index| -%>
+  <component>
+    <populationCriteriaSection>
+      <%- if population['stratification'] -%>
+		  <templateId>
+		    <item root="<%= HQMF::Document::STRATIFIED_POPULATION_TEMPLATE_ID %>" identifierName="<%= HQMF::Document::STRATIFIED_POPULATION_TEMPLATE_TITLE %>" controlInformationRoot="<%= population['stratification'] %>"/>
+		  </templateId>
+      <%- end -%>
+      <id root="2.16.840.1.113883.3.100.1" extension="<%= population['id'] || "Population#{population_index}" %>"/>
+      <code code="57026-7" codeSystem="2.16.840.1.113883.6.1"/>
+      <title value="<%= population['title'] %>"/>
+      <text>This section describes the Initial Patient Population,
+        Numerator, Denominator, Denominator Exceptions, and Measure
+        Populations</text>
+      <%- population.keys.each do |criteria_id| -%>
+      <%= xml_for_population_criteria(population, criteria_id) %>
+      <%- end -%>
+    </populationCriteriaSection>
+  </component>
+  <%- end -%>
+</QualityMeasureDocument>