health-data-standards 3.5.3 → 3.6.1

data/lib/health-data-standards/import/green_c32/result_importer.rb

@@ -1,43 +0,0 @@
-module HealthDataStandards
-  module Import
-    module GreenC32
-      class ResultImporter < SectionImporter
-
-        include Singleton
-        
-        #-------------------------------------------------------------------------------
-
-        def initialize
-          super
-          @range = "./gc32:referenceRange"
-          @interpretation = "./gc32:interpretation"
-          @klass = LabResult
-          @base_xpath = "./gc32:result"
-        end
-        
-        #-------------------------------------------------------------------------------
-
-        def import(result_xml)
-          result_xml.root.add_namespace_definition('gc32', "urn:hl7-org:greencda:c32")
-          
-          result_element = result_xml.xpath(@base_xpath)
-          lab_result = @klass.new(reference_range: extract_node_text(result_element.xpath(@range)))
-          
-          extract_result(result_element, lab_result)
-              
-          lab_result
-        end
-        
-        #-------------------------------------------------------------------------------
-        private
-        #-------------------------------------------------------------------------------
-        
-        def extract_result(result_element, lab_result)
-          extract_entry(result_element, lab_result)
-          extract_code(result_element, lab_result, @interpretation, :interpretation)
-        end
-
-      end
-    end
-  end
-end

data/lib/health-data-standards/import/green_c32/section_importer.rb

@@ -1,186 +0,0 @@
-require "time"
-
-module HealthDataStandards
-  module Import
-    module GreenC32
-      class SectionImporter
-        
-        def initialize
-          @description = "./gc32:code/gc32:originalText"
-          @status = "./gc32:status"
-          @value = "./gc32:value"
-        end
-        
-        
-        def import(entry_xml)
-          generic_import(entry_xml)
-        end
-        
-        def generic_import(element_xml, element_name="entry")
-          entry = Entry.new
-          element_xml.root.add_namespace_definition('gc32', "urn:hl7-org:greencda:c32")
-          element = element_xml.at_xpath("./gc32:#{element_name}")
-          extract_entry(element, entry)
-          entry
-        end
-        
-        def extract_code(element, entry, xpath="./gc32:code", attribute=:codes)
-          
-          code_element = element.at_xpath(xpath)
-
-          return unless code_element
-
-          codes = build_code(code_element)
-          
-          code_element.xpath("./gc32:translation").each do |trans|
-            codes.merge!(build_code(trans))
-          end
-          
-          entry.write_attribute(attribute, codes)
-        end
-        
-        def extract_description(element, entry)
-          description = element.at_xpath(@description)
-          entry.description = extract_node_text(description)
-        end
-        
-        def extract_status(element, entry)
-          status = extract_node_text(element.at_xpath(@status))
-          return unless status
-          entry.status = status
-        end
-        
-        def extract_effective_time(element, entry)
-          if element.at_xpath("./gc32:effectiveTime/gc32:start")
-            extract_interval(element,entry)  
-          else
-            extract_time(element, entry)
-          end
-        end
-        
-        def extract_name(element, entry, name_element="name")
-          name_element = element.at_xpath("./gc32:#{name_element}")
-          return unless name_element
-          entry.title = name_element.at_xpath("./gc32:title").try(:content)
-          entry.given_name = name_element.at_xpath("./gc32:givenName").try(:content)
-          entry.family_name = name_element.at_xpath("./gc32:familyName").try(:content)
-        end
-        
-        def extract_time(element, entry, xpath = "./gc32:effectiveTime", attribute = "time")
-          datetime = element.at_xpath(xpath)
-          
-          return unless datetime && datetime['value']
-          
-          entry.write_attribute(attribute, Time.parse(datetime['value']).utc.to_i)
-        end
-        
-        def extract_interval(element, entry, element_name="effectiveTime")
-          extract_time(element, entry, "./gc32:#{element_name}/gc32:start", "start_time")
-          extract_time(element, entry, "./gc32:#{element_name}/gc32:end", "end_time")
-        end
-        
-        def extract_quantity(element, xpath)
-          value_element = element.at_xpath(xpath)
-          
-          return unless value_element
-          
-          node_value = extract_node_attribute(value_element, "amount", true)
-          node_units = extract_node_attribute(value_element, "unit")
-          
-          return {} unless node_value
-          
-          {"scalar" => node_value, "units" => node_units}
-        end
-        
-        def extract_value(element, entry)
-          pq = extract_quantity(element, @value)
-          if pq.present?
-            entry.values << PhysicalQuantityResultValue.new(pq)
-          end
-        end
-        
-        def extract_entry(element, entry)
-          extract_code(element, entry)
-          extract_description(element, entry)
-          extract_status(element, entry)
-          extract_value(element, entry)
-          extract_effective_time(element, entry)
-          entry.description = element.at_xpath("./gc32:freeText").try(:inner_text)
-          entry
-        end
-        
-        def extract_organization(organization_element)
-          org_id = extract_node_text(organization_element.xpath("./gc32:id"))
-          organization = org_id ? Organization.find(org_id) : Organization.new
-          organization ||= Organization.new
-          # if organization.new_record?
-          # else
-            organization.name = extract_node_text(organization_element.xpath("./gc32:name"))
-            organization.addresses = organization_element.xpath("./gc32:address").map { |addr| extract_address(addr)  }
-            organization.telecoms = organization_element.xpath("./gc32:telecom").map { |tele| extract_telecom(tele) }
-            # organization.save!
-          # end
-          
-          return organization
-        end
-
-        def extract_facility(facility_element)
-          facility = Facility.new
-          facility.name = extract_node_text(facility_element.xpath("./gc32:name"))
-          facility.addresses = facility_element.xpath("./gc32:address").map { |addr| extract_address(addr)  }
-          facility.telecoms = facility_element.xpath("./gc32:telecom").map { |tele| extract_telecom(tele) }
-          start_time = facility_element.at_xpath("./gc32:duration/gc32:start").try(:text)
-          if start_time
-            facility.start_time = Time.parse(start_time).utc.to_i
-          end
-          end_time = facility_element.at_xpath("./gc32:duration/gc32:end").try(:text)
-          if end_time
-            facility.end_time = Time.parse(end_time).utc.to_i
-          end
-          facility
-        end
-        
-        def extract_address(address_element)
-          return unless address_element
-          address = Address.new
-          address.use = address_element['use']
-          address.street = address_element.xpath("./gc32:street").map { |st| extract_node_text(st)  }
-          address.city = extract_node_text(address_element.xpath("./gc32:city"))
-          address.state = extract_node_text(address_element.xpath("./gc32:state"))
-          address.zip = extract_node_text(address_element.xpath("./gc32:postalCode"))
-          address
-        end
-        
-        def extract_telecom(telecom_element)
-          return unless telecom_element
-          telecom = Telecom.new
-          telecom.use = extract_node_attribute(telecom_element, :type)
-          telecom.value = extract_node_attribute(telecom_element, :value)
-          telecom.preferred = extract_node_attribute(telecom_element, :preferred)
-          telecom
-        end
-                
-        private
-        
-        def build_code(code_element)
-          code_system_oid = extract_node_attribute(code_element, "codeSystem")
-          code = extract_node_attribute(code_element, "code")
-          code_system = HealthDataStandards::Util::CodeSystemHelper.code_system_for(code_system_oid)
-          {code_system => [code]}
-        end
-        
-        def extract_node_attribute(node, attribute_name, to_num=false)
-          return if node.nil? || (node.respond_to?(:empty?) && node.empty?)
-          attribute = node.attribute(attribute_name.to_s)
-          value = attribute ? attribute.value : nil
-          return unless value && value != ""
-          to_num ? value.to_f : value
-        end
-        
-        def extract_node_text(node)
-          node ? node.inner_text : nil
-        end
-      end
-    end
-  end
-end

data/lib/health-data-standards/import/green_c32/social_history_importer.rb

@@ -1,13 +0,0 @@
-module HealthDataStandards
-  module Import
-    module GreenC32
-      class SocialHistoryImporter < SectionImporter
-        include Singleton
-        
-        def import(sh_xml)
-          generic_import(sh_xml, "socialHistory")
-        end
-      end
-    end
-  end
-end

data/lib/health-data-standards/import/green_c32/support_importer.rb

@@ -1,22 +0,0 @@
-module HealthDataStandards
-  module Import
-    module GreenC32
-      class SupportImporter < SectionImporter
-        include Singleton
-        
-        def import(support_doc)
-          support_doc.root.add_namespace_definition('gc32', "urn:hl7-org:greencda:c32")
-          support_element = support_doc.at_xpath("./gc32:support")
-          support = Support.new(type: support_element.at_xpath("./gc32:type").try(:content),
-                                relationship: support_element.at_xpath("./gc32:relationship").try(:text))
-          extract_name(support_element, support)
-          support.address = extract_address(support_element.at_xpath("./gc32:address"))
-          support.telecom = extract_telecom(support_element.at_xpath("./gc32:telecom"))
-          support.mothers_maiden_name = support_element.at_xpath("./gc32:mothersMaidenName").try(:text)
-          support
-        end
-        
-      end
-    end
-  end
-end

data/lib/health-data-standards/import/green_c32/vital_sign_importer.rb

@@ -1,21 +0,0 @@
-module HealthDataStandards
-  module Import
-    module GreenC32
-      # This really needs to get refactored to share code with result importer
-      class VitalSignImporter < ResultImporter
-
-        include Singleton
-        
-        #-------------------------------------------------------------------------------
-
-        def initialize
-          super
-          @range = "./gc32:referenceRange"
-          @klass = VitalSign
-          @base_xpath = "./gc32:vitalSign"
-        end
-
-      end
-    end
-  end
-end

data/templates/gc32/_address.gc32.erb

@@ -1,9 +0,0 @@
-<% tag_name ||= "address"%>
-<<%=tag_name%>>
-  <% address.street.each do |street| %>
-    <street><%= street %></street>
-  <% end %>
-  <city><%= address.city %></city>
-  <state><%= address.state %></state>
-  <postalCode><%= address.zip %></postalCode>
-</<%=tag_name%>>

data/templates/gc32/_advance_directive.gc32.erb

@@ -1,5 +0,0 @@
-<advanceDirective xmlns="urn:hl7-org:greencda:c32">
-  <%== gc32_code_display advance_directive, 'preferred_code_sets' => ['SNOMED-CT'] %>
-  <%== gc32_effective_time(advance_directive)%>
-  <freeText><%= advance_directive.description %></freeText>
-</advanceDirective>

data/templates/gc32/_allergy.gc32.erb

@@ -1,12 +0,0 @@
-<allergy xmlns="urn:hl7-org:greencda:c32" id="<%=allergy.id%>">
-  <%== render partial: "entry_attributes", locals: {entry: allergy, code_sets: ['SNOMED-CT', "RxNorm", "FDA"]}%>
-  <% if allergy.type %>
-  <%== gc32_code_display allergy, "tag_name" => "type", "attribute" => "type", 'preferred_code_sets' => ['RxNorm', 'SNOMED-CT'] %>
-  <% end %>
-  <% if allergy.reaction && allergy.reaction['code'] %>
-      <reaction code="<%= allergy.reaction['code'] %>" codeSystem="<%= allergy.reaction['code_system'] %>" />
-  <% end %>
-  <% if allergy.severity && !allergy.severity.empty? %>
-  <%== gc32_code_display allergy, "tag_name" => "severity", "attribute" => "severity", 'preferred_code_sets' => ['SNOMED-CT'] %>
-  <% end %>
-</allergy>

data/templates/gc32/_care_goal.gc32.erb

@@ -1,8 +0,0 @@
-<%
-type = case care_goal
-       when LabResult then "result"
-       else
-         care_goal.class.name.underscore
-       end
-%>
-<%== render partial: type, locals: {type => care_goal} %>

data/templates/gc32/_condition.gc32.erb

@@ -1,10 +0,0 @@
-<condition id="<%= condition.id %>" <% unless condition.cause_of_death.nil? %>causeOfDeath="<%= condition.cause_of_death %>"<% end %> xmlns="urn:hl7-org:greencda:c32">
-  <%== render partial: "entry_attributes", locals: {entry: condition, code_sets: ['SNOMED-CT', "ICD-9-CM", "ICD-10-CM"]}%>
-  <% if condition.priority %>
-    <priority><%= condition.priority %></priority>
-  <% end %>
-  <type><%= condition.type %></type>
-  <% condition.treating_provider.each do |tp| %>
-  <%== render partial: 'provider', locals: {provider: tp} %>
-  <% end %>
-</condition>

data/templates/gc32/_encounter.gc32.erb

@@ -1,28 +0,0 @@
-<encounter xmlns="urn:hl7-org:greencda:c32" id="<%= encounter.id %>">
-  <%== render partial: "entry_attributes", locals: {entry: encounter, code_sets: ["CPT", "SNOMED-CT"]}%>
-  <% if encounter.discharge_disposition %>
-  <%== gc32_code_display encounter, "tag_name" => "dischargeDisposition", 'attribute' => "discharge_disposition", 'preferred_code_sets' => ["NUBC"] %>
-  <% end %>
-  <% if encounter.admit_type%>
-  <%== gc32_code_display encounter, "tag_name" => "admissionType", 'attribute' => "admit_type", 'preferred_code_sets' => ["NUBC"] %>
-  <% end %>
-  <% if provider %>
-  <%== render partial: 'provider', locals: {provider: encounter.performer, tag_name: 'performer'}%>
-  <% end %>
-  <% facility = encounter.facility %>
-  <% if facility %>
-  <facility>
-      <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 %>
-    <%== gc32_interval(encounter, "duration", :admit_time, :discharge_time) %>
-  </facility>
-  <% end %>
-  <% if encounter.performer %>
-  <%== render partial: 'provider', locals: {provider: encounter.performer} %>
-  <% end %>
-</encounter>

data/templates/gc32/_entry.gc32.erb

@@ -1,3 +0,0 @@
-<entry xmlns="urn:hl7-org:greencda:c32" id="<%= entry.id %>">
-  <%== render partial: "entry_attributes", locals: {entry: entry, code_sets: ["SNOMED-CT", "LOINC"]}%>
-</entry>

data/templates/gc32/_entry_attributes.gc32.erb

@@ -1,10 +0,0 @@
-<% if entry.codes.empty? %>
-  <code />
-<% else %>  
-  <%== gc32_code_display entry, "tag_name" => "code", 'preferred_code_sets' => code_sets %>
-<% end %>
-<% if entry.status_code && !entry.status_code.empty? %>
-<%== gc32_code_display entry, "tag_name" => "status", "attribute" => "status_code", 'preferred_code_sets' => ['SNOMED-CT', "HL7 ActStatus"] %>
-<% end %>
-<freeText><%=entry.description %></freeText>
-<%== gc32_effective_time(entry)%>

data/templates/gc32/_immunization.gc32.erb

@@ -1,9 +0,0 @@
-<immunization xmlns="urn:hl7-org:greencda:c32" id="<%= immunization.id%>" <% if refused %> refused="true" <% end %>>
-  <%== render partial: "entry_attributes", locals: {entry: immunization, code_sets: ["RxNorm", "CVX", "FDA"]}%>
-  <% if immunization.series_number %>
-    <seriesNumber><%= immunization.series_number %></seriesNumber>
-  <% end %>
-  <% if immunization.refusal_reason %>
-  <%== gc32_code_display immunization, "tag_name" => "refusalReason", "attribute" => "refusal_reason", "preferred_code_sets" => ["HL7 ActNoImmunicationReason"] %>
-  <% end %>
-</immunization>

data/templates/gc32/_insurance_provider.gc32.erb

@@ -1,28 +0,0 @@
-  <insuranceProvider xmlns="urn:hl7-org:greencda:c32" id="<%=insurance_provider.id%>">
-  <insuranceType code="<%== insurance_provider.type %>" codeSystem="2.16.840.1.113883.3.88.12.3221.5.2" />
-  <%== render partial: "organization", locals: {organization: insurance_provider.payer, tag_name: payer} %>
-  <% if insurance_provider.subscriber %>
-    <subscriber>
-      <%== render partial: 'person_attributes', locals: {person: insurance_provider.subscriber} %>
-    </subscriber>
-  <% end %>
-  <% if insurance_provider.relationship %>
-  <%== gc32_code_display insurance_provider, "attribute" => "relationship", "tag_name" => "relationshipToSubscriber" %>
-  <% end %>
-  <% insurance_provider.guarantors.each do |g| %>
-  <guarantor>
-    <%== gc32_interval(insurance_provider, "financialResponsibilityDateRange", :start_time, :end_time) %>
-    <% if g.organization %>
-      <%== render partial: 'organization', locals: {organization: g.organization}%>
-    <% elsif g.person%>
-      <person>
-        <%== render partial: 'person_attributes', locals: {person: g.person} %>
-      </person>
-    <% end %>
-  </guarantor>
-  <% end %>
-  <healthPlanName><%=insurance_provider.name%></healthPlanName>
-  <% if insurance_provider.description%>
-    <freeText><%= insurance_provider.description%></freeText>
-  <% end %>
-</insuranceProvider>

data/templates/gc32/_medical_equipment.gc32.erb

@@ -1,6 +0,0 @@
-<medicalEquipment xmlns="urn:hl7-org:greencda:c32" id="<%= medical_equipment.id%>">
-  <%== render partial: "entry_attributes", locals: {entry: medical_equipment, code_sets: ["SNOMED-CT", "LOINC"]}%>
-  <% if medical_equipment.values.first %>
-    <%== quantity_display medical_equipment.values.first, "quantity" %>
-  <% end %>
-</medicalEquipment>

data/templates/gc32/_medication.gc32.erb

@@ -1,91 +0,0 @@
-<medication xmlns="urn:hl7-org:greencda:c32" id="<%=medication.id%>">
-  <%== render partial: "entry_attributes", locals: {entry: medication, code_sets: ["RxNorm", "CVX", "FDA"]}%>
-  <% if medication.administration_timing %>
-    <administrationTiming institutionSpecified="<%= medication.administration_timing['institution_specified'] %>">
-      <period amount="<%=medication.administration_timing['period']['value'] %>" unit="<%= medication.administration_timing['period']['unit']%>" />
-    </administrationTiming>
-  <% end %>
-  <% if medication.route %>
-  <%== gc32_code_display medication, "tag_name" => "route", "attribute" => "route", "preferred_code_sets" => ["NCI Thesaurus"] %>
-  <% end %> 
-  <% if medication.site %>
-  <%== gc32_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 %>
-  <%== gc32_code_display medication, "tag_name" => "productForm", "attribute" => "product_form", "preferred_code_sets" => ["FDA", "NCI Thesaurus"]  %>
-  <% end %>
-  <% if medication.delivery_method %>
-    <%== gc32_code_display medication, "tag_name" => "deliveryMethod", "attribute" => "delivery_method", "preferred_code_sets" => medication.delivery_method.keys %>
-  <% end %>
-  <% if medication.type_of_medication%>
-  <%== gc32_code_display medication, "tag_name" => "type", "attribute" => "type_of_medication", "preferred_code_sets" => ["SNOMED-CT"] %>
-  <% end %>
-  <% if medication.status_of_medication%>
-  <%== gc32_code_display medication, "tag_name" => "statusOfMedication", "attribute" => "status_of_medication", "preferred_code_sets" => ["SNOMED-CT"] %>
-  <% end %>
-  <%if medication.indication%>
-  <%== gc32_code_display medication, "tag_name" => "indication", "attribute" => "indication", "preferred_code_sets" => ["SNOMED-CT"] %>
-  <% end %>
-  <% if medication.vehicle %>
-  <%== gc32_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>
-    <% if fh.dispense_date %>
-      <dispenseDate value="<%=Time.at(fh.dispense_date).xmlschema%>" />
-    <% end %>
-    <%== 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 %>>
-      <% if oi.quantity_ordered %>
-      <%== quantity_display oi.quantity_ordered, "quantityOrdered" %>
-      <% end %>
-      <% if oi.order_date_time %>
-        <orderedDateTime value="<%=Time.at(oi.order_date_time).xmlschema%>" />
-      <% end %>
-      <% if oi.order_expiration_date_time %>
-        <expirationDateTime value="<%=Time.at(oi.order_expiration_date_time).xmlschema%>" />
-      <% end %>
-    </orderInformation>
-  <% end %>
-  <% include_providers ||= false %>
-  <% if include_providers %>
-  <prescribers>
-  <% medication.order_information.each do |oi| %>
-    <% if oi.provider %>
-      <%== render partial: 'provider', locals: {provider: oi.provider, tag_name: 'prescriber'} %>
-    <% end %>
-  <% end %>
-  </prescribers>
-  <pharmacists>
-  <% medication.fulfillment_history.each do |fh| %>
-    <% if oi.provider %>
-      <%== render partial: 'provider', locals: {provider: fh.provider, tag_name: 'pharmacist'} %>
-    <% end %>
-  <% end %>
-  </pharmacists>
-  <% end %> 
-</medication>