health-data-standards 3.4.1 → 3.4.2

checksums.yaml

@@ -1,7 +1,7 @@
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data/README.md

@@ -25,6 +25,19 @@ Please try to follow the [GitHub Coding Style Guides](https://github.com/stylegu
 Change Log
 ==========
 
+3.4.2 - February 28, 2014
+
+* Provider improvements
+** Providers are now exported in QRDA Cat I if they exist on the Record object
+** Provider identifiers are now represented with CDAIdentifiers
+** Provider import will now import any type of identifier
+** Providers can now be arranged in a hierarchy
+** When importing providers from a clincial document, matching to existing providers in MongoDB has been improved to matching on any type of identifier
+* QRDA Cat I importer now imports procedure values regardless of whether the template has them at the root level or nested in an entryRelationship
+* Bug fix - Result importer will no longer double import result values
+* QRDA Cat I importer now imports encounter order end times
+* Bug fix - QRDA Cat I importer now properly imports condition and procedure ordinaltiy
+
 3.4.1 - January 24, 2014
 
 * Fix for JRuby - Nokogiri is now fixed to version 1.6.0 exactly. Version 1.6.1 was breaking the CCR part of the test suite under JRuby. Nokogiri 1.6.0 works properly across Ruby 1.9.3, Ruby 2.0.0 and JRuby 1.7.9

data/lib/health-data-standards.rb

@@ -1,6 +1,7 @@
 require 'erubis'
 require 'active_support'
 require 'mongoid'
+require 'mongoid/tree'
 require 'uuid'
 require 'builder'
 require 'csv'

data/lib/health-data-standards/import/bulk_record_importer.rb

@@ -78,6 +78,11 @@ module HealthDataStandards
 
         record = Record.update_or_create(patient_data)
         record.provider_performances = providers
+        providers.each do |prov| 
+          prov.provider.ancestors.each do |ancestor|
+            record.provider_performances.push(ProviderPerformance.new(start_date: prov.start_date, end_date: prov.end_date, provider: ancestor))  
+          end
+        end
         record.save
         
         {status: 'success', message: 'patient imported', status_code: 201, record: record}

data/lib/health-data-standards/import/bundle/importer.rb

@@ -164,6 +164,14 @@ module HealthDataStandards
             end
 
             contents.each do |document| 
+              if name == "by_patient"
+                # Set the patient_id to the actual _id of
+                # newly created patient record
+                medical_record_id = document['value']['medical_record_id']
+                if patient = Record.by_patient_id(medical_record_id).first
+                  document['value']['patient_id'] = patient.id
+                end
+              end
               document['bundle_id'] = bundle.id
               Mongoid.default_session[collection].insert(document)
             end

data/lib/health-data-standards/import/cat1/encounter_order_importer.rb

@@ -11,6 +11,7 @@ module HealthDataStandards
         def extract_dates(parent_element, entry, element_name="author")
           if parent_element.at_xpath("cda:#{element_name}/cda:time/@value")
             entry.start_time = HL7Helper.timestamp_to_integer(parent_element.at_xpath("cda:#{element_name}/cda:time")['value'])
+            entry.end_time = HL7Helper.timestamp_to_integer(parent_element.at_xpath("cda:#{element_name}/cda:time")['value'])
           end
         end
       end

data/lib/health-data-standards/import/cat1/encounter_performed_importer.rb

@@ -24,10 +24,18 @@ module HealthDataStandards
             extract_reason_description(reason_element, reason, nrh)
             extract_status(reason_element, reason)
             extract_dates(reason_element, reason)
+            extract_workaround_codes(reason_element, reason)
             encounter.reason = reason
           end
         end
 
+        def extract_workaround_codes(parent_element, entry)
+          value = parent_element.at_xpath("./cda:value")
+          entry['code'] = value['code']
+          entry['code_system'] = CodeSystemHelper.code_system_for(value['codeSystem'])
+          entry['codeSystemName'] = CodeSystemHelper.code_system_for(value['codeSystem'])
+        end
+
         def extract_admit_time(parent_element, encounter)
           encounter.admit_time = encounter.start_time
         end

data/lib/health-data-standards/import/cat1/patient_importer.rb

@@ -40,7 +40,7 @@ module HealthDataStandards
                                              generate_importer(ProcedureOrderImporter, nil, '2.16.840.1.113883.3.560.1.62', 'ordered'),
                                              generate_importer(ProcedurePerformedImporter, "//cda:procedure[cda:templateId/@root = '2.16.840.1.113883.10.20.24.3.64']", '2.16.840.1.113883.3.560.1.6'),
                                              generate_importer(CDA::ProcedureImporter, "//cda:procedure[cda:templateId/@root = '2.16.840.1.113883.10.20.24.3.66']", '2.16.840.1.113883.3.560.1.63'),
-                                             generate_importer(CDA::ProcedureImporter, "//cda:observation[cda:templateId/@root = '2.16.840.1.113883.10.20.24.3.69']", '2.16.840.1.113883.3.560.1.21'),
+                                             generate_importer(CDA::ProcedureImporter, "//cda:observation[cda:templateId/@root = '2.16.840.1.113883.10.20.24.3.69']", '2.16.840.1.113883.3.560.1.21'), #risk category assessment
                                              generate_importer(CDA::ProcedureImporter, "//cda:observation[cda:templateId/@root = '2.16.840.1.113883.10.20.24.3.18']", '2.16.840.1.113883.3.560.1.103', 'performed'), #diagnostic study performed
                                              generate_importer(DiagnosticStudyOrderImporter, nil, '2.16.840.1.113883.3.560.1.40', 'ordered')]
 

data/lib/health-data-standards/import/cda/condition_importer.rb

@@ -37,7 +37,7 @@ module HealthDataStandards
         def extract_ordinality(parent_element, entry)
           ordinality_element = parent_element.at_xpath(@ordinality_xpath)
           if ordinality_element
-            entry.ordinality = {CodeSystemHelper.code_system_for(ordinality_element['codeSystem']) => [ordinality_element['code']]}
+            entry.ordinality = {"code" => ordinality_element['code'], "code_system" => CodeSystemHelper.code_system_for(ordinality_element['codeSystem']), "codeSystemName" => CodeSystemHelper.code_system_for(ordinality_element['codeSystem']), CodeSystemHelper.code_system_for(ordinality_element['codeSystem']) => [ordinality_element['code']]}
           end
         end
 

data/lib/health-data-standards/import/cda/medical_equipment_importer.rb

@@ -31,7 +31,7 @@ module HealthDataStandards
         def extract_anatomical_structure(entry_element, entry)
           site = entry_element.at_xpath(@anatomical_xpath)
           if site
-            entry.anatomical_structure = {CodeSystemHelper.code_system_for(site['codeSystem']) => [site['code']]}
+            entry.anatomical_structure = {"code" => site['code'], "code_system" => CodeSystemHelper.code_system_for(site['codeSystem']), "codeSystemName" => CodeSystemHelper.code_system_for(site['codeSystem']), CodeSystemHelper.code_system_for(site['codeSystem']) => [site['code']]}
           end
         end
       end

data/lib/health-data-standards/import/cda/procedure_importer.rb

@@ -8,7 +8,7 @@ module HealthDataStandards
         def initialize(entry_finder=EntryFinder.new("//cda:section[cda:templateId/@root!='2.16.840.1.113883.3.88.11.83.124']//cda:procedure"))
           super(entry_finder)
           @entry_class = Procedure
-          @value_xpath = ".//cda:observation[cda:templateId/@root='2.16.840.1.113883.10.20.24.3.87']/cda:value"
+          @value_xpath = "./cda:value | ./cda:entryRelationship[@typeCode='REFR']/cda:observation/cda:value"
           @ordinality_xpath = "./cda:priorityCode"
         end
 
@@ -27,7 +27,7 @@ module HealthDataStandards
         def extract_ordinality(parent_element, procedure)
           ordinality_element = parent_element.at_xpath(@ordinality_xpath)
           if ordinality_element
-            procedure.ordinality = {CodeSystemHelper.code_system_for(ordinality_element['codeSystem']) => [ordinality_element['code']]}
+            procedure.ordinality = {"code" => ordinality_element['code'], "code_system" => CodeSystemHelper.code_system_for(ordinality_element['codeSystem']), "codeSystemName" => CodeSystemHelper.code_system_for(ordinality_element['codeSystem']), CodeSystemHelper.code_system_for(ordinality_element['codeSystem']) => [ordinality_element['code']]}
           end
         end
 

data/lib/health-data-standards/import/cda/provider_importer.rb

@@ -31,7 +31,14 @@ module HealthDataStandards
         def extract_provider_data(performer, use_dates=true, entity_path="./cda:assignedEntity")
           provider = {}
           entity = performer.xpath(entity_path)
-          
+
+          cda_idents = []
+          entity.xpath("./cda:id").each do |cda_ident|
+            ident_root = cda_ident['root']
+            ident_extension = cda_ident['extension']
+            cda_idents.push(CDAIdentifier.new(root: ident_root, extension: ident_extension)) if ident_root.present?
+          end
+
           name = entity.at_xpath("./cda:assignedPerson/cda:name")
           provider[:title]        = extract_data(name, "./cda:prefix")
           provider[:given_name]   = extract_data(name, "./cda:given[1]")
@@ -51,7 +58,8 @@ module HealthDataStandards
           provider[:telecoms] = performer.xpath("./cda:assignedEntity/cda:telecom").try(:map) {|te| import_telecom(te)}
           
           provider[:npi] = npi if Provider.valid_npi?(npi)
-          
+          provider[:cda_identifiers] = cda_idents
+
           provider
         end
       

data/lib/health-data-standards/import/cda/result_importer.rb

@@ -9,7 +9,6 @@ module HealthDataStandards
         
         def create_entry(entry_element, nrh = NarrativeReferenceHandler.new)
           result = super
-          extract_value(entry_element, result)
           extract_interpretation(entry_element, result)
           extract_reference_range(entry_element, result)
           extract_negation(entry_element, result)

data/lib/health-data-standards/import/cda/section_importer.rb

@@ -160,12 +160,12 @@ module HealthDataStandards
           unless negation_indicator.nil?
             entry.negation_ind = negation_indicator.eql?('true')
             if entry.negation_ind
-              negation_reason_element = parent_element.at_xpath("./cda:entryRelationship[@typeCode='RSON']/cda:act[cda:templateId/@root='2.16.840.1.113883.10.20.1.27']/cda:code")
+              negation_reason_element = parent_element.at_xpath("./cda:entryRelationship[@typeCode='RSON']/cda:observation[cda:templateId/@root='2.16.840.1.113883.10.20.24.3.88']/cda:value | ./cda:entryRelationship[@typeCode='RSON']/cda:act[cda:templateId/@root='2.16.840.1.113883.10.20.1.27']/cda:code")
               if negation_reason_element
                 code_system_oid = negation_reason_element['codeSystem']
                 code = negation_reason_element['code']
                 code_system = HealthDataStandards::Util::CodeSystemHelper.code_system_for(code_system_oid)
-                entry.negation_reason = {'code' => code, 'codeSystem' => code_system}
+                entry.negation_reason = {'code' => code, 'code_system' => code_system, 'codeSystem' => code_system}
               end
             end
           end

data/lib/health-data-standards/import/provider_import_utils.rb

@@ -6,13 +6,19 @@ module ProviderImportUtils
   end
   
   def find_or_create_provider(provider_hash)
-    provider = Provider.where(npi: provider_hash[:npi]).first if provider_hash[:npi] && !provider_hash[:npi].empty?
+    provider = Provider.by_npi(provider_hash[:npi]).first if provider_hash[:npi] && !provider_hash[:npi].empty?
     unless provider
       if provider_hash[:npi]
         provider = Provider.create(provider_hash)
+        provider.npi = provider_hash[:npi]
       else
         provider ||= Provider.resolve_provider(provider_hash) if Provider.respond_to? :resolve_provider
-        
+
+        ident_roots = provider_hash[:cda_identifiers].map {|ident| ident.root}
+        ident_extensions = provider_hash[:cda_identifiers].map {|ident| ident.extension}
+        unless ident_roots.size == 0
+          provider ||= Provider.in("cda_identifiers.root" => ident_roots).and.in("cda_identifiers.extension" => ident_extensions).first
+        end
         provider_query = {:title => provider_hash[:title],            
                             :given_name => provider_hash[:given_name],  
                             :family_name=> provider_hash[:family_name],

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

@@ -3,7 +3,7 @@ class CDAIdentifier
 
   field :root, type: String
   field :extension, type: String
-  embedded_in :entry
+  embedded_in :cda_identifiable, polymorphic: true
 
   def ==(comparison_object)
     if comparison_object.respond_to?(:root) && comparison_object.respond_to?(:extension)

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

@@ -6,7 +6,7 @@ class Entry
   # embedded_in :entry_list, polymorphic: true
   
   embedded_in :record
-  embeds_one :cda_identifier, class_name: "CDAIdentifier"
+  embeds_one :cda_identifier, class_name: "CDAIdentifier", as: :cda_identifiable
   embeds_many :values, class_name: "ResultValue"
   
   field :description, type: String

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

@@ -1,15 +1,43 @@
 class Provider
   include Personable
+  include Mongoid::Tree
   
-  field :npi         , type: String
-  field :tin         , type: String
+  NPI_OID = '2.16.840.1.113883.4.6'
+  TAX_ID_OID = '2.16.840.1.113883.4.2'
+
   field :specialty   , type: String
   field :phone       , type: String
   
   validates_uniqueness_of :npi, allow_blank: true
   
   embeds_one :organization
+  embeds_many :cda_identifiers, class_name: "CDAIdentifier", as: :cda_identifiable
+
+  scope :by_npi, ->(an_npi){ where("cda_identifiers.root" => NPI_OID, "cda_identifiers.extension" => an_npi)}
+
+  def npi=(an_npi)
+    cda_id_npi = self.cda_identifiers.where(root: NPI_OID).first
+    if cda_id_npi
+      cda_id_npi.extension = an_npi
+      cda_id_npi.save!
+    else
+      self.cda_identifiers << CDAIdentifier.new(root: NPI_OID, extension: an_npi)
+    end
+  end
 
+  def npi
+    cda_id_npi = self.cda_identifiers.where(root: NPI_OID).first
+    cda_id_npi ? cda_id_npi.extension : nil
+  end
+
+  def tin=(a_tin)
+    self.cda_identifiers << CDAIdentifier.new(root: TAX_ID_OID, extension: a_tin)
+  end
+
+  def tin
+    cda_id_tin = self.cda_identifiers.where(root: TAX_ID_OID).first
+    cda_id_tin ? cda_id_tin.extension : nil
+  end
 
   def records(effective_date=nil)
     Record.by_provider(self, effective_date)

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

@@ -85,6 +85,12 @@ class Record
     matching_entries_by_section.flatten
   end
 
+  def entries
+    Sections.map do |section|
+      self.send(section)
+    end.flatten
+  end
+
   memoize :entries_for_oid
   
   alias :clinical_trial_participant :clinicalTrialParticipant

data/templates/cat1/_providers.cat1.erb

@@ -0,0 +1,57 @@
+<documentationOf typeCode="DOC">
+  <serviceEvent classCode="PCPR"> <!-- care provision -->
+  <% if patient.provider_performances.empty? -%>
+    <!-- No provider data found in the patient record
+         putting in a fake provider -->
+    <effectiveTime>
+      <low value="20020716"/>
+      <high value="<%= Time.now.utc.to_formatted_s(:number) %>"/>
+    </effectiveTime>
+    <!-- You can include multiple performers, each with an NPI, TIN, CCN. -->
+    <performer typeCode="PRF"> 
+      <time>
+        <low value="20020716"/>
+        <high value="<%= Time.now.utc.to_formatted_s(:number) %>"/>
+      </time>
+      <assignedEntity>
+        <!-- This is the provider NPI -->
+        <id root="2.16.840.1.113883.4.6" extension="111111111" /> 
+        <representedOrganization>
+          <!-- This is the organization TIN -->
+          <id root="2.16.840.1.113883.4.2" extension="1234567" /> 
+          <!-- This is the organization CCN -->
+          <id root="2.16.840.1.113883.4.336" extension="54321" /> 
+        </representedOrganization>
+      </assignedEntity>
+    </performer>
+  <% else -%>
+    <% patient.provider_performances.each do |pp| -%>
+      <effectiveTime>
+        <low <%= value_or_null_flavor(pp.start_date) %>/>
+        <high <%= value_or_null_flavor(pp.end_date) %>/>
+      </effectiveTime>
+      <!-- You can include multiple performers, each with an NPI, TIN, CCN. -->
+      <performer typeCode="PRF"> 
+        <time>
+          <low <%= value_or_null_flavor(pp.start_date) %>/>
+          <high <%= value_or_null_flavor(pp.end_date) %>/>
+        </time>
+        <assignedEntity>
+          <% pp.provider.cda_identifiers.each do |cda_id| -%>
+            <% unless cda_id.root.eql? '2.16.840.1.113883.4.2' -%>
+          <id root="<%= cda_id.root %>" extension="<%= cda_id.extension %>" /> 
+            <% end -%>
+          <% end -%>
+          <representedOrganization>
+            <% pp.provider.cda_identifiers.each do |cda_id| -%>
+            <% if cda_id.root.eql?('2.16.840.1.113883.4.2') -%>
+            <id root="2.16.840.1.113883.4.2" extension="<%= cda_id.extension %>" /> 
+            <% end -%>  
+            <% end -%>
+          </representedOrganization>
+        </assignedEntity>
+      </performer>
+    <% end -%>
+  <% end -%>
+  </serviceEvent>
+</documentationOf>

data/templates/cat1/show.cat1.erb

@@ -86,35 +86,7 @@
       </representedOrganization>
     </assignedEntity>
   </legalAuthenticator>
-
-  <!-- TODO: This is where the provider information will go.
-       It is currently hard coded, but should be replaced with the providers
-       and the time over which they are performing. --> 
-  <documentationOf typeCode="DOC">
-    <serviceEvent classCode="PCPR"> <!-- care provision -->
-      <effectiveTime>
-        <low value="20020716"/>
-        <high value="<%= Time.now.utc.to_formatted_s(:number) %>"/>
-      </effectiveTime>
-      <!-- You can include multiple performers, each with an NPI, TIN, CCN. -->
-      <performer typeCode="PRF"> 
-        <time>
-          <low value="20020716"/>
-          <high value="<%= Time.now.utc.to_formatted_s(:number) %>"/>
-        </time>
-        <assignedEntity>
-          <!-- This is the provider NPI -->
-          <id root="2.16.840.1.113883.4.6" extension="111111111" /> 
-          <representedOrganization>
-            <!-- This is the organization TIN -->
-            <id root="2.16.840.1.113883.4.2" extension="1234567" /> 
-            <!-- This is the organization CCN -->
-            <id root="2.16.840.1.113883.4.336" extension="54321" /> 
-          </representedOrganization>
-        </assignedEntity>
-      </performer>
-    </serviceEvent>
-  </documentationOf>
+  <%== render :partial => 'providers', :locals => {:patient => patient} %>
   <component>
     <structuredBody>
       <%== render :partial => 'measures', :locals => {:measures => measures} %>

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: health-data-standards
 version: !ruby/object:Gem::Version
-  version: 3.4.1
+  version: 3.4.2
 platform: ruby
 authors:
 - Andy Gregorowicz
@@ -12,7 +12,7 @@ authors:
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2014-01-24 00:00:00.000000000 Z
+date: 2014-02-28 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: rest-client
@@ -56,6 +56,20 @@ dependencies:
     - - ~>
       - !ruby/object:Gem::Version
         version: 3.1.4
+- !ruby/object:Gem::Dependency
+  name: mongoid-tree
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - ~>
+      - !ruby/object:Gem::Version
+        version: 1.0.4
+  type: :runtime
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - ~>
+      - !ruby/object:Gem::Version
+        version: 1.0.4
 - !ruby/object:Gem::Dependency
   name: activesupport
   requirement: !ruby/object:Gem::Requirement
@@ -455,6 +469,7 @@ files:
 - templates/cat1/_medication_details.cat1.erb
 - templates/cat1/_ordinality.cat1.erb
 - templates/cat1/_patient_data.cat1.erb
+- templates/cat1/_providers.cat1.erb
 - templates/cat1/_reason.cat1.erb
 - templates/cat1/_record_target.cat1.erb
 - templates/cat1/_reporting_parameters.cat1.erb