health-data-standards 2.2.1 → 3.0.3

data/lib/health-data-standards/import/c32/allergy_importer.rb

@@ -1,47 +0,0 @@
-module HealthDataStandards
-  module Import
-    module C32
-      class AllergyImporter < SectionImporter
-    
-        def initialize
-          @entry_xpath = "//cda:observation[cda:templateId/@root='2.16.840.1.113883.10.20.1.18']"
-          @code_xpath = "./cda:participant/cda:participantRole/cda:playingEntity/cda:code"
-          @description_xpath = "./cda:code/cda:originalText/cda:reference[@value] | ./cda:text/cda:reference[@value]"
-          @type_xpath = "./cda:code"
-          @reaction_xpath = "./cda:entryRelationship[@typeCode='MFST']/cda:observation[cda:templateId/@root='2.16.840.1.113883.10.20.1.54']/cda:value"
-          @severity_xpath = "./cda:entryRelationship[@typeCode='SUBJ']/cda:observation[cda:templateId/@root='2.16.840.1.113883.10.20.1.55']/cda:value"
-          @status_xpath   = "./cda:entryRelationship[@typeCode='REFR']/cda:observation[cda:templateId/@root='2.16.840.1.113883.10.20.1.39']/cda:value"
-          @id_map = {}
-        end
-    
-        # Traverses that HITSP C32 document passed in using XPath and creates an Array of Entry
-        # objects based on what it finds                          
-        # @param [Nokogiri::XML::Document] doc It is expected that the root node of this document
-        #        will have the "cda" namespace registered to "urn:hl7-org:v3"
-        #        measure definition
-        # @return [Array] will be a list of Entry objects
-        def create_entries(doc,id_map = {})
-          @id_map = id_map
-          allergy_list = []
-          entry_elements = doc.xpath(@entry_xpath)
-          entry_elements.each do |entry_element|
-            allergy = Allergy.new
-            extract_codes(entry_element, allergy)
-            extract_dates(entry_element, allergy)
-            extract_description(entry_element, allergy, id_map)
-            extract_negation(entry_element, allergy)
-            
-            extract_status(entry_element, allergy)
-            allergy.type = extract_code(entry_element, @type_xpath)
-            allergy.reaction = extract_code(entry_element, @reaction_xpath)
-            allergy.severity = extract_code(entry_element, @severity_xpath)
-            
-            allergy_list << allergy
-          end
-          allergy_list
-        end
-        
-      end
-    end
-  end
-end

data/lib/health-data-standards/import/c32/medical_equipment_importer.rb

@@ -1,45 +0,0 @@
-module HealthDataStandards
-  module Import
-    module C32
-      class MedicalEquipmentImporter < SectionImporter
-        
-        def initialize
-          @entry_xpath = "//cda:section[cda:templateId/@root='2.16.840.1.113883.3.88.11.83.128']/cda:entry/cda:supply"
-          @code_xpath = "./cda:participant/cda:participantRole/cda:playingDevice/cda:code"
-          @description_xpath = "./cda:code/cda:originalText/cda:reference[@value] | ./cda:text/cda:reference[@value]"
-          @check_for_usable = true
-        end
-        
-        def create_entries(doc,id_map = {})
-          entry_list = []
-          entry_elements = doc.xpath(@entry_xpath)
-          entry_elements.each do |entry_element|
-            entry = create_entry(entry_element, id_map)
-            if @check_for_usable
-              entry_list << entry if entry.usable?
-            else
-              entry_list << entry
-            end
-          end
-          entry_list
-        end
-        
-        def create_entry(entry_element, id_map={})
-          entry = MedicalEquipment.new
-          extract_codes(entry_element, entry)
-          extract_dates(entry_element, entry)
-          extract_value(entry_element, entry)
-          
-          extract_description(entry_element, entry, id_map)
-          extract_manufacturer(entry_element, entry)
-          entry
-        end
-        
-        def extract_manufacturer(entry_element, entry)
-          manufacturer = entry_element.at_xpath("./cda:participant/cda:participantRole/cda:scopingEntity/cda:desc").try(:inner_text)
-          entry.manufacturer = manufacturer.strip if manufacturer
-        end
-      end
-    end
-  end
-end

data/lib/health-data-standards/import/c32/procedure_importer.rb

@@ -1,62 +0,0 @@
-module HealthDataStandards
-  module Import
-    module C32
-
-      # TODO Extract Discharge Disposition
-      class ProcedureImporter < SectionImporter
-
-        def initialize
-          #scoped to not look in the plan of care section so planned procedures do not end up mixed with
-          #past procedures
-          @entry_xpath = "//cda:section[cda:templateId/@root!='2.16.840.1.113883.3.88.11.83.124']//cda:procedure"
-          @code_xpath = "./cda:code"
-          @description_xpath = "./cda:code/cda:originalText/cda:reference[@value] | ./cda:text/cda:reference[@value] "
-          @check_for_usable = true               # Pilot tools will set this to false
-        end
-
-        # Traverses that HITSP C32 document passed in using XPath and creates an Array of Entry
-        # objects based on what it finds                          
-        # @param [Nokogiri::XML::Document] doc It is expected that the root node of this document
-        #        will have the "cda" namespace registered to "urn:hl7-org:v3"
-        #        measure definition
-        # @return [Array] will be a list of Entry objects
-        def create_entries(doc,id_map = {})
-          procedure_list = []
-          entry_elements = doc.xpath(@entry_xpath)
-          entry_elements.each do |entry_element|
-            procedure = create_entry(entry_element, id_map)
-            if @check_for_usable
-              procedure_list << procedure if procedure.usable?
-            else
-              procedure_list << procedure
-            end
-          end
-          procedure_list
-        end
-        
-        def create_entry(entry_element, id_map={})
-          procedure = Procedure.new
-          extract_codes(entry_element, procedure)
-          extract_dates(entry_element, procedure)
-          extract_description(entry_element, procedure, id_map)
-          extract_performer(entry_element, procedure)
-          extract_site(entry_element, procedure)
-          extract_negation(entry_element, procedure)
-          procedure
-        end
-
-        private
-
-        def extract_performer(parent_element, procedure)
-          performer_element = parent_element.at_xpath("./cda:performer")
-          procedure.performer = import_actor(performer_element) if performer_element
-        end
-
-        def extract_site(parent_element, procedure)
-          procedure.site = extract_code(parent_element, "./cda:targetSiteCode")
-        end
-
-      end
-    end
-  end
-end

data/lib/health-data-standards/import/c32/result_importer.rb

@@ -1,56 +0,0 @@
-module HealthDataStandards
-  module Import
-    module C32
-      class ResultImporter < SectionImporter
-        def initialize
-          @entry_xpath = "//cda:observation[cda:templateId/@root='2.16.840.1.113883.3.88.11.83.15.1'] | //cda:observation[cda:templateId/@root='2.16.840.1.113883.3.88.11.83.15']"
-          @code_xpath = "./cda:code"
-          @description_xpath = "./cda:code/cda:originalText/cda:reference[@value] | ./cda:text/cda:reference[@value] "
-          @check_for_usable = true               # Pilot tools will set this to false
-        end
-    
-        # Traverses that HITSP C32 document passed in using XPath and creates an Array of Entry
-        # objects based on what it finds                          
-        # @param [Nokogiri::XML::Document] doc It is expected that the root node of this document
-        #        will have the "cda" namespace registered to "urn:hl7-org:v3"
-        #        measure definition
-        # @return [Array] will be a list of Entry objects
-        def create_entries(doc,id_map = {})
-          result_list = []
-          entry_elements = doc.xpath(@entry_xpath)
-          entry_elements.each do |entry_element|
-            result = create_entry(entry_element, id_map)
-            if @check_for_usable
-              result_list << result if result.usable?
-            else
-              result_list << result
-            end
-          end
-          result_list
-        end
-        
-        def create_entry(entry_element, id_map={})
-          result = LabResult.new
-          extract_codes(entry_element, result)
-          extract_dates(entry_element, result)
-          extract_value(entry_element, result)
-          extract_description(entry_element, result, id_map)
-          extract_interpretation(entry_element, result)
-          extract_negation(entry_element, result)
-          result
-        end
-    
-        private
-        def extract_interpretation(parent_element, result)
-          interpretation_element = parent_element.at_xpath("./cda:interpretationCode")
-          if interpretation_element
-            code = interpretation_element['code']
-            code_system = CodeSystemHelper.code_system_for(interpretation_element['codeSystem'])
-            result.interpretation = {'code' => code, 'codeSystem' => code_system}
-          end
-        end
-    
-      end
-    end
-  end
-end

data/templates/_advance_directive.gc32.erb

@@ -1,8 +0,0 @@
-<advanceDirective xmlns="urn:hl7-org:greencda:c32">
-  <%== code_display advance_directive, 'preferred_code_sets' => ['SNOMED-CT'] %>
-  <effectiveTime>
-    <start><%= time_if_not_nil(advance_directive.start_time, advance_directive.time) %></start>
-    <end><%= time_if_not_nil(advance_directive.end_time) %></end>
-  </effectiveTime>
-  <freeText><%= advance_directive.free_text %></freeText>
-</advanceDirective>

data/templates/_allergy.gc32.erb

@@ -1,23 +0,0 @@
-<allergy xmlns="urn:hl7-org:greencda:c32">
-  <id><%= allergy.id%></id>
-  <%== code_display allergy, "tag_name" => "code", 'preferred_code_sets' => ['SNOMED-CT', "RxNorm", "FDA"] %>
-  <status><%= allergy.status%></status>
-  <freeText><%= allergy.free_text %></freeText>
-  <effectiveTime>
-    <% if allergy.start_time || allergy.end_time %>
-    <start><%= time_if_not_nil(allergy.start_time) %></start>
-    <end><%= time_if_not_nil(allergy.end_time) %></end>
-    <% else %>
-    <%= time_if_not_nil(allergy.time) %>
-    <% end %>
-  </effectiveTime>
-  <% if allergy.type %>
-  <%== code_display allergy, "tag_name" => "type", "attribute" => "type", 'preferred_code_sets' => ['RxNorm', 'SNOMED-CT'] %>
-  <% end %>
-  <% if allergy.reaction %>
-  <%== code_display allergy, "tag_name" => "reaction", "attribute" => "reaction", 'preferred_code_sets' => ['RxNorm', 'SNOMED-CT'] %>
-  <% end %>
-  <% if allergy.severity%>
-  <%== code_display allergy, "tag_name" => "severity", "attribute" => "severity", 'preferred_code_sets' => ['RxNorm', 'SNOMED-CT'] %>
-  <% end %>
-</allergy>

data/templates/_condition.gc32.erb

@@ -1,9 +0,0 @@
-<condition <% unless condition.cause_of_death.nil? %>causeOfDeath="<%= condition.cause_of_death %>"<% end %> xmlns="urn:hl7-org:greencda:c32">
-  <id><%= condition.id %></id>
-  <%== code_display condition, "tag_name" => "code", 'preferred_code_sets' => ['SNOMED-CT'] %>
-  <%== gc32_effective_time(condition)%>
-  <% if condition.priority %>
-    <priority><%= condition.priority %></priority>
-  <% end %>
-  <type><%= condition.type %></type>
-</condition>

data/templates/_encounter.gc32.erb

@@ -1,26 +0,0 @@
-<encounter xmlns="urn:hl7-org:greencda:c32">
-  <id><%= encounter.id %></id>
-  <%== code_display encounter, "tag_name" => "code", 'preferred_code_sets' => ['SNOMED-CT'] %>
-  <% if encounter.status %>
-    <status code="completed"/>
-  <% end %>
-  <%== gc32_effective_time(encounter)%>
-  <%== code_display encounter, "tag_name" => "dishcargeDisposition", 'attribute' => "discharge_disposition" %>
-  <%== code_display encounter, "tag_name" => "admissionType", 'attribute' => "admit_type" %>
-  <% if provider %>
-  <%= render partial: 'provider', locals: {provider: encounter.performer, tag_name: 'performer'}%>
-  <% end %>
-  <% facility = encounter.facility %>
-  <% if facility %>
-  <facility>
-      <id><%= facility.id%></id>
-      <name><%= facility.name%></name>
-      <% facility.addresses.each do |addr| %>
-        <%= render :partial => "address", locals: {address: addr} %>
-      <% end %>
-      <% facility.telecoms.each do |tele| %>
-        <%= render :partial => "telecom", locals: {telecom: tele} %>
-      <% end %>
-    <% end %>
-  </facility>
-</encounter>

data/templates/_entry.gc32.erb

@@ -1,14 +0,0 @@
-<entry xmlns="urn:hl7-org:greencda:c32">
-  <id><%= entry.id %></id>
-  <%== code_display entry, "tag_name" => "code", 'preferred_code_sets' => ['SNOMED-CT', "LOINC"] %>
-  <status><%= entry.status%></status>
-  <freeText><%=entry.free_text %></freeText>
-  <effectiveTime>
-    <% if entry.start_time || entry.end_time %>
-    <start><%= time_if_not_nil(entry.start_time) %></start>
-    <end><%= time_if_not_nil(entry.end_time) %></end>
-    <% else %>
-    <%= time_if_not_nil(entry.time) %>
-    <% end %>
-  </effectiveTime>
-</entry>

data/templates/_immunization.gc32.erb

@@ -1,11 +0,0 @@
-<immunization <% if refused %> refused="true" <% end %> xmlns="urn:hl7-org:greencda:c32">
-  <id><%= immunization.id %></id>
-  <%== code_display immunization, "preferred_code_sets" => ["RxNorm", "CVX"] %>  
-  <%== gc32_effective_time(immunization)%>
-  <% if immunization.series_number %>
-    <seriesNumber><%= immunization.series_number %></seriesNumber>
-  <% end %>
-  <% if immunization.refusal_reason %>
-  <%== code_display immunization, "tag_name" => "refusalReason", "attribute" => "refusal_reason", "preferred_code_sets" => ["SNOMED-CT"] %>
-  <% end %>
-</immunization>

data/templates/_medical_equipment.gc32.erb

@@ -1,7 +0,0 @@
-<medicalEquipment xmlns="urn:hl7-org:greencda:c32">
-  <id><%= medical_equipment.id %></id>
-  <%== code_display medical_equipment, "tag_name" => "code", 'preferred_code_sets' => ['SNOMED-CT', "LOINC"] %>
-  <status><%= medical_equipment.status%></status>
-  <freeText><%=medical_equipment.free_text %></freeText>
-  <%== gc32_effective_time(medical_equipment)%>
-</medicalEquipment>

data/templates/_medication.gc32.erb

@@ -1,72 +0,0 @@
-<medication>
-  <id><%= medication.id%></id>
-  <%== code_display medication, "preferred_code_sets" => ["RxNorm", "CVX"] %>
-  <freeText><%= medication.free_text%></freeText>
-  <%== gc32_effective_time(medication)%>
-  <% if medication.administration_timing %>
-    <administrationTiming institutionSpecified="<%= medication.administration_timing[:insitution_specified] %>">
-      <%== quantity_display medication.administration_timing["period"], :period %>
-    </administrationTiming>
-  <% end %>
-  <% if medication.route %>
-  <%== code_display medication, "tag_name" => "route", "attribute" => "route", "preferred_code_sets" => ["NCI Thesaurus"] %>
-  <% end %> 
-  <% if medication.site %>
-  <%== code_display medication, "tag_name" => "site", "attribute" => "site", "preferred_code_sets" => ["SNOMED-CT"] %>
-  <% end %>
-  <%== quantity_display medication.dose, :dose %>
-  <% if medication.dose_indicator %>
-  <doseIndication><%medication.dose_indicator%></doseIndication>
-  <% end %>
-  <% if medication.dose_restriction %>
-  <doseRestriction>
-    <numerator><%= medication.dose_restriction["numerator"]%></numerator>
-    <denominator><%= medication.dose_restriction["denominator"]%></denominator>
-  </doseRestriction>
-  <% end %>
-  <% if medication.product_form %>
-  <%== code_display medication, "tag_name" => "productForm", "attribute" => "product_form", "preferred_code_sets" => ["NCI Thesaurus"]  %>
-  <% end %>
-  <% if medication.delivery_method %>
-    <%== code_display medication, "tag_name" => "deliveryMethod", "attribute" => "delivery_method", "preferred_code_sets" => medication.delivery_method.keys %>
-  <% end %>
-  <% if medication.type_of_medication%>
-  <%== code_display medication, "tag_name" => "type", "attribute" => "type_of_medication", "preferred_code_sets" => ["SNOMED-CT"] %>
-  <% end %>
-  <% if medication.status_of_medication%>
-  <%== code_display medication, "tag_name" => "statusOfMedication", "attribute" => "status_of_medication", "preferred_code_sets" => ["SNOMED-CT"] %>
-  <% end %>
-  <%if medication.indication%>
-  <%== code_display medication, "tag_name" => "indication", "attribute" => "indication", "preferred_code_sets" => ["SNOMED-CT"] %>
-  <% end %>
-  <% if medication.vehicle %>
-  <%== code_display medication, "tag_name" => "vehicle", "attribute" => "vehicle", "preferred_code_sets" => ["SNOMED-CT"] %>
-  <% end%>
-  
-  <% if medication.dose_indicator %>
-    <doseIndicator><%= medication.dose_indicator %></doseIndicator>
-  <% end %>
-  
-  <% if medication.patient_instructions %>
-    <patientInstructions><%=medication.patient_instructions%></patientInstructions>
-  <% end %>
-  
-  <% if medication.fulfillment_instructions %>
-    <fulfillmentInstructions><%=medication.fulfillment_instructions%></fulfillmentInstructions>
-  <% end %>
-  <% medication.fulfillment_history.each do |fh| %>
-  <fulfillmentHistory <%if (fh.fill_status) %> fillStatus="<%=fh.fill_status%>" <% end %>
-    <% if fh.fill_number %> fillNumber="<%=fh.fill_number%>" <% end %>>
-    <prescriptionNumber><%=fh.prescription_number%></prescriptionNumber>
-    <dispenseDate><%= Time.at(fh.dispense_date).utc%></dispenseDate>
-    <%== quantity_display fh.quantity_dispensed, :quantityDispensed %>
-  </fulfillmentHistory>
-  <% end %>
-  <% medication.order_information.each do |oi| %>
-    <orderInformation <% if oi.order_number %><%= "orderNumber=\"#{oi.order_number}\"" %> <% end %> <% if oi.fills %> <%= "fills=\"#{oi.fills}\"" %> <% end %>>
-      <%== quantity_display oi.quantity_ordered, "quantityOrdered" %>
-      <orderDateTime><%= Time.at(oi.order_date_time).utc%></orderDateTime>
-      <expirationDateTime><%= Time.at(oi.order_expiration_date_time).utc%></expirationDateTime>
-    </orderInformation>
-  <% end %>
-</medication>

data/templates/_organization.gc32.erb

@@ -1,10 +0,0 @@
-<organization>
-  <id><%= organization.id%></id>
-  <name><%= organization.name%></name>
-  <% organization.addresses.each do |addr| %>
-    <%= render :partial => "address", locals: {address: addr} %>
-  <% end %>
-  <% organization.telecoms.each do |tele| %>
-    <%= render :partial => "telecom", locals: {telecom: tele} %>
-  <% end %>
-</organization>

data/templates/_procedure.gc32.erb

@@ -1,10 +0,0 @@
-<procedure xmlns="urn:hl7-org:greencda:c32">
-  <id><%= procedure.id %></id>
-  <%== code_display procedure, "tag_name" => "code", 'preferred_code_sets' => ['SNOMED-CT'] %>
-  <status><%= procedure.status%></status>
-  <freeText><%=procedure.free_text %></freeText>
-  <%== gc32_effective_time(procedure)%>
-  <% if procedure.site %>
-    <%== code_display procedure, "tag_name" => "site", "attribute" => "site", "preferred_code_sets" => ["SNOMED-CT"] %>
-  <% end %>
-</procedure>

data/templates/_provider.gc32.erb

@@ -1,19 +0,0 @@
-<% tag_name ||= "provider" %>
-<<%=tag_name%>>
-  <id><%=provider.id%></id>
-  <name>
-    <title><%=provider.title%></title>
-    <givenName><%= provider.given_name%></givenName>
-    <familyName><%= provider.family_name%></familyName>
-  </name>
-  <npi>1234567890</npi>
-  <specialty></specialty>
-  <% provider.addresses.each do |addr| %>
-    <%= render :partial => "address", locals: {address: addr} %>
-  <% end %>
-  <% provider.telecoms.each do |tele| %>
-    <%= render :partial => "telecom", locals: {telecom: tele} %>
-  <% end %>
-  <%= render :partial => "organization", locals: { organization: provider.organization } %>
-  
-</<%=tag_name%>>