health-data-standards 0.1.0

data/lib/health-data-standards/export/rendering_context.rb

@@ -0,0 +1,14 @@
+require 'ostruct'
+
+module HealthDataStandards
+  module Export
+    class RenderingContext < OpenStruct
+      include TemplateHelper
+      include ViewHelper
+
+      def my_binding
+        binding
+      end
+    end
+  end
+end

data/lib/health-data-standards/export/template_helper.rb

@@ -0,0 +1,35 @@
+module HealthDataStandards
+  module Export
+    module TemplateHelper
+      attr_accessor :template_format
+
+      def template_root
+        File.join(File.dirname(__FILE__), '..', '..', '..', 'templates')
+      end
+
+      def template(template_name)
+        File.read(File.join(template_root, "#{template_name}.#{self.template_format}.erb"))
+      end
+
+      def partial(partial_name)
+        template("_#{partial_name}")
+      end
+
+      def render(params)
+        #binding.pry
+        erb = nil
+        if params[:template]
+          erb = template(params[:template])
+        elsif params[:partial]
+          erb = partial(params[:partial])
+        end
+        locals = params[:locals]
+        locals ||= {}
+        rendering_context = RenderingContext.new(locals)
+        rendering_context.template_format = self.template_format
+        eruby = Erubis::EscapedEruby.new(erb)
+        eruby.result(rendering_context.my_binding)
+      end
+    end
+  end
+end

data/lib/health-data-standards/export/view_helper.rb

@@ -0,0 +1,35 @@
+module HealthDataStandards
+  module Export
+    module ViewHelper
+      def code_display(entry, tag_name='code', extra_content=nil)
+        if entry.single_code_value?
+          code = entry.codes.first[1].first
+          code_system_oid = QME::Importer::CodeSystemHelper.oid_for_code_system(entry.codes.first[0])
+          "<#{tag_name} code=\"#{code}\" codeSystem=\"#{code_system_oid}\" #{extra_content}><originalText>#{ERB::Util.html_escape entry.description}</originalText></#{tag_name}>"
+        else
+          all_codes = []
+          entry.codes.each_pair {|key, values| values.each {|v| all_codes << {:set => key, :value => v}}}
+          first_code = all_codes.first
+          code_string = "<#{tag_name} code=\"#{first_code[:value]}\" codeSystem=\"#{QME::Importer::CodeSystemHelper.oid_for_code_system(first_code[:set])}\">\n"
+          code_string += "<originalText>#{ERB::Util.html_escape entry.description}</originalText>\n"
+          all_codes[1..-1].each do |cv|
+            code_string += "<translation code=\"#{cv[:value]}\" codeSystem=\"#{QME::Importer::CodeSystemHelper.oid_for_code_system(cv[:set])}\"/>\n"
+          end
+          code_string += "</#{tag_name}>"
+          code_string
+        end
+      end
+      
+      def status_code_for(entry)
+        case entry.status.to_s
+        when 'active'
+          '55561003'
+        when 'inactive'
+          '73425007'
+        when 'resolved'
+          '413322009'
+        end
+      end      
+    end
+  end
+end

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

@@ -0,0 +1,51 @@
+class Entry
+
+  include Mongoid::Document
+
+  embedded_in :entry_list, polymorphic: true
+
+  field :description, type: String
+  field :time, type: Integer
+  field :start_time, type: Integer
+  field :end_time, type: Integer
+  field :status, type: Symbol
+  field :codes, type: Hash
+  field :value, type: Hash
+
+  def single_code_value?
+    codes.size == 1 && codes.first[1].size == 1
+  end
+
+  def codes_to_s
+    codes.map {|code_set, codes| "#{code_set}: #{codes.join(', ')}"}.join(' ')
+  end
+  
+  def times_to_s
+    if start_time.present? || end_time.present?
+      start_string = start_time ? Time.at(start_time).to_formatted_s(:long_ordinal) : 'UNK'
+      end_string = end_time ? Time.at(end_time).to_formatted_s(:long_ordinal) : 'UNK'
+      "#{start_string} - #{end_string}"
+    elsif time.present?
+      Time.at(time).to_formatted_s(:long_ordinal)
+    end
+  end
+  
+  def to_effective_time(xml)
+    if time.present?
+      xml.effectiveTime("value" => Time.at(time).utc.to_formatted_s(:number))
+    else
+      xml.effectiveTime do
+        if start_time.present?
+          xml.low("value" => Time.at(start_time).utc.to_formatted_s(:number))
+        else
+          xml.low("nullFlavor" => "UNK")
+        end
+        if end_time.present?
+          xml.high("value" => Time.at(end_time).utc.to_formatted_s(:number))          
+        else
+          xml.high("nullFlavor" => "UNK")          
+        end
+      end
+    end
+  end
+end

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

@@ -0,0 +1,21 @@
+class Record
+
+  include Mongoid::Document
+
+  field :first, type: String
+  field :last, type: String
+  field :gender, type: String
+  field :birthdate, type: Integer
+  field :race, type: String
+  field :ethnicity, type: String
+  field :test_id, type: BSON::ObjectId
+
+  [:allergies, :care_goals, :conditions, :encounters, :immunizations, :medical_equipment,
+   :medications, :procedures, :results, :social_history, :vital_signs].each do |section|
+    embeds_many section, as: :entry_list, class_name: "Entry"
+  end
+  
+  def over_18?
+    Time.at(birthdate) < Time.now.years_ago(18)
+  end
+end

data/templates/_allergies.c32.erb

@@ -0,0 +1,57 @@
+<component>
+  <!--Allergies/Reactions-->
+  <section>
+    <templateId root="2.16.840.1.113883.3.88.11.83.102" assigningAuthorityName="HITSP/C83"/>
+    <templateId root="1.3.6.1.4.1.19376.1.5.3.1.3.13" assigningAuthorityName="IHE PCC"/>
+    <templateId root="2.16.840.1.113883.10.20.1.2" assigningAuthorityName="HL7 CCD"/>
+    <!--Allergies/Reactions section template-->
+    <code code="48765-2" codeSystem="2.16.840.1.113883.6.1" codeSystemName="LOINC" displayName="Allergies"/>
+    <title>Allergies and Adverse Reactions</title>
+    <%== render :partial => 'narrative_block', :locals => {:entries => entries, :section => 'allergies'} %>
+    <% entries.each_with_index do |entry, i| -%>
+    <entry typeCode="DRIV">
+      <act classCode="ACT" moodCode="EVN">
+        <templateId root="2.16.840.1.113883.3.88.11.83.6"/>
+        <templateId root="2.16.840.1.113883.10.20.1.27"/>
+        <templateId root="1.3.6.1.4.1.19376.1.5.3.1.4.5.3"/>
+        <templateId root="1.3.6.1.4.1.19376.1.5.3.1.4.5.1"/>
+        <!--Allergy act template -->
+        <id root="<%= UUID.generate %>"/>
+        <code nullFlavor="NA"/>
+        <statusCode code="active"/>
+        <effectiveTime>
+          <low value="<%= Time.at(entry.time).utc.to_formatted_s(:number) %>"/>
+        </effectiveTime>
+        <entryRelationship typeCode="SUBJ" inversionInd="false">
+          <observation classCode="OBS" moodCode="EVN">
+            <templateId root="2.16.840.1.113883.10.20.1.18"/>
+            <templateId root="2.16.840.1.113883.10.20.1.28"/>
+            <templateId root="1.3.6.1.4.1.19376.1.5.3.1.4.6"/>
+            <templateId root="1.3.6.1.4.1.19376.1.5.3.1.4.5"/>
+            <id root="<%= UUID.generate %>"/>
+            <code code="416098002" codeSystem="2.16.840.1.113883.6.96" displayName="drug allergy" codeSystemName="SNOMED CT">
+              <originalText><reference value="#allergies-desc-<%= i %>"/></originalText>
+            </code>
+            <text>
+              <reference value="#allergies-desc-<%= i %>"/>
+            </text>
+            <statusCode code="completed"/>
+            <effectiveTime>
+              <low value="<%= Time.at(entry.time).utc.to_formatted_s(:number) %>"/>
+            </effectiveTime>
+            <value xsi:type="CD" nullFlavor="UNK"/>
+            <participant typeCode="CSM">
+              <participantRole classCode="MANU">
+                <playingEntity classCode="MMAT">
+                  <%== render :partial => 'code_with_reference', :locals => {:entry => entry, :i => i, :section => 'allergies'} %>
+                  <name><%= entry.description %></name>
+                </playingEntity>
+              </participantRole>
+            </participant>
+          </observation>
+        </entryRelationship>
+      </act>
+    </entry>
+    <% end -%>
+  </section>
+</component>

data/templates/_care_goals.c32.erb

@@ -0,0 +1,24 @@
+<component>
+  <!--Plan of Care-->
+  <section>
+    <templateId root="2.16.840.1.113883.3.88.11.83.124" assigningAuthorityName="HITSP/C83"/>
+    <templateId root="1.3.6.1.4.1.19376.1.5.3.1.3.31" assigningAuthorityName="IHE PCC"/>
+    <templateId root="2.16.840.1.113883.10.20.2.7" assigningAuthorityName="HL7 CCD"/>
+    <templateId root="2.16.840.1.113883.10.20.1.10" assigningAuthorityName="HL7 CCD"/>
+    <!--Plan of Care section template-->
+    <code code="18776-5" codeSystem="2.16.840.1.113883.6.1" codeSystemName="LOINC" displayName="Treatment plan"/>
+    <%== render :partial => 'narrative_block', :locals => {:entries => entries, :section => 'plan_of_care'} %>
+    <% entries.each do |entry| -%>
+    <entry typeCode="DRIV">
+      <observation classCode="OBS" moodCode="RQO">
+        <templateId root="2.16.840.1.113883.10.20.1.25"/>
+        <!-- Plan of Activity activity template -->
+        <id root="<%= UUID.generate %>"/>
+        <%== code_display(entry) %>
+        <statusCode code="new"/>
+        <effectiveTime value="<%= Time.at(entry.time).utc.to_formatted_s(:number) %>"/>
+      </observation>
+    </entry>
+    <% end -%>
+  </section>
+</component>

data/templates/_code_with_reference.c32.erb

@@ -0,0 +1,8 @@
+<% if entry.single_code_value? 
+  code = entry.codes.first[1].first
+  code_system_oid = QME::Importer::CodeSystemHelper.oid_for_code_system(entry.codes.first[0])
+  -%>
+<code code="<%= code %>" codeSystem="<%= code_system_oid %>">
+  <originalText><reference value="#<%= section %>-desc-<%= i %>"/></originalText>
+</code>
+<% end -%>

data/templates/_conditions.c32.erb

@@ -0,0 +1,61 @@
+<component>
+  <!--Problems-->
+  <section>
+    <templateId root="2.16.840.1.113883.3.88.11.83.103" assigningAuthorityName="HITSP/C83"/>
+    <templateId root="1.3.6.1.4.1.19376.1.5.3.1.3.6" assigningAuthorityName="IHE PCC"/>
+    <templateId root="2.16.840.1.113883.10.20.1.11" assigningAuthorityName="HL7 CCD"/>
+    <!--Problems section template-->
+    <code code="11450-4" codeSystem="2.16.840.1.113883.6.1" codeSystemName="LOINC" displayName="Problem list"/>
+    <title>Problems</title>
+    <%== render :partial => 'narrative_block', :locals => {:entries => entries, :section => 'conditions'} %>
+    <% entries.each_with_index do |entry, i| -%>
+    <entry typeCode="DRIV">
+      <act classCode="ACT" moodCode="EVN">
+        <templateId root="2.16.840.1.113883.3.88.11.83.7" assigningAuthorityName="HITSP C83"/>
+        <templateId root="2.16.840.1.113883.10.20.1.27"/>
+        <templateId root="1.3.6.1.4.1.19376.1.5.3.1.4.5.1" assigningAuthorityName="IHE PCC"/>
+        <templateId root="1.3.6.1.4.1.19376.1.5.3.1.4.5.2" assigningAuthorityName="IHE PCC"/>
+        <!-- Problem act template -->
+        <id root="<%= UUID.generate %>"/>
+        <code nullFlavor="NA"/>
+        <% if entry.status.eql? 'resolved' -%>
+        <statusCode code="completed"/>
+        <% else -%>
+        <statusCode code="active"/>
+        <% end -%>
+        <effectiveTime>
+          <low value="<%= Time.at(entry.time).utc.to_formatted_s(:number) %>"/>
+        </effectiveTime>
+        <entryRelationship typeCode="SUBJ" inversionInd="false">
+          <observation classCode="OBS" moodCode="EVN">
+            <templateId root="1.3.6.1.4.1.19376.1.5.3.1.4.5" assigningAuthorityName="IHE PCC"/>
+            <templateId root="2.16.840.1.113883.10.20.1.28" assigningAuthorityName="CCD"/>
+            <!--Problem observation template - NOT episode template-->
+            <id root="<%= UUID.generate %>"/>
+            <code code="64572001" displayName="Condition" codeSystem="2.16.840.1.113883.6.96" codeSystemName="SNOMED-CT"/>
+            <text>
+              <reference value="#conditions-desc-<%= i %>"/>
+            </text>
+            <statusCode code="completed"/>
+            <effectiveTime>
+              <low value="<%= Time.at(entry.time).utc.to_formatted_s(:number) %>"/>
+            </effectiveTime>
+            <%== code_display(entry, 'value', 'xsi:type="CD"') %>
+            <% if entry.status -%>
+            <entryRelationship typeCode="REFR">
+              <observation classCode="OBS" moodCode="EVN">
+                <templateId root="2.16.840.1.113883.10.20.1.50"/>
+                <!-- Problem status observation template -->
+                <code code="33999-4" codeSystem="2.16.840.1.113883.6.1" displayName="Status"/>
+                <statusCode code="completed"/>
+                <value xsi:type="CE" code="<%= status_code_for(entry) %>" codeSystem="2.16.840.1.113883.6.96"/>
+              </observation>
+            </entryRelationship>
+            <% end -%>
+          </observation>
+        </entryRelationship>
+      </act>
+    </entry>
+    <% end -%>
+  </section>
+</component>

data/templates/_encounters.c32.erb

@@ -0,0 +1,28 @@
+<component>
+  <!--Encounters-->
+  <section>
+    <templateId root="2.16.840.1.113883.3.88.11.83.127" assigningAuthorityName="HITSP/C83"/>
+    <templateId root="1.3.6.1.4.1.19376.1.5.3.1.1.5.3.3" assigningAuthorityName="IHE PCC"/>
+    <templateId root="2.16.840.1.113883.10.20.1.3" assigningAuthorityName="HL7 CCD"/>
+    <!--Encounters section template-->
+    <code code="46240-8" codeSystem="2.16.840.1.113883.6.1" codeSystemName="LOINC" displayName="History of encounters"/>
+    <title>Encounters</title>
+    <%== render :partial => 'narrative_block', :locals => {:entries => entries, :section => 'encounters'} %>
+    <% entries.each_with_index do |entry, i| -%>
+    <entry typeCode="DRIV">
+      <encounter classCode="ENC" moodCode="EVN">
+        <templateId root="2.16.840.1.113883.3.88.11.83.16" assigningAuthorityName="HITSP C83"/>
+        <templateId root="2.16.840.1.113883.10.20.1.21" assigningAuthorityName="CCD"/>
+        <templateId root="1.3.6.1.4.1.19376.1.5.3.1.4.14" assigningAuthorityName="IHE PCC"/>
+        <!-- Encounter activity template -->
+        <id root="<%= UUID.generate %>"/>
+        <%== render :partial => 'code_with_reference', :locals => {:entry => entry, :i => i, :section => 'encounters'} %>
+        <text>
+          <reference value="#encounters-desc-<%= i %>"/>
+        </text>
+        <effectiveTime value="<%= Time.at(entry.time).utc.to_formatted_s(:number) %>"/>
+      </encounter>
+    </entry>
+    <% end -%>
+  </section>
+</component>

data/templates/_immunizations.c32.erb

@@ -0,0 +1,41 @@
+      <component>
+        <!--Immunizations-->
+        <section>
+          <templateId root="2.16.840.1.113883.3.88.11.83.117" assigningAuthorityName="HITSP/C83"/>
+          <templateId root="1.3.6.1.4.1.19376.1.5.3.1.3.23" assigningAuthorityName="IHE PCC"/>
+          <templateId root="2.16.840.1.113883.10.20.1.6" assigningAuthorityName="HL7 CCD"/>
+          <!--Immunizations section template-->
+          <code code="11369-6" codeSystem="2.16.840.1.113883.6.1" codeSystemName="LOINC" displayName="History of immunizations"/>
+          <title>Immunizations</title>
+          <%== render :partial => 'narrative_block', :locals => {:entries => entries, :section => 'immunizations'} %>
+          <% entries.each_with_index do |entry, i| -%>
+          <entry typeCode="DRIV">
+            <substanceAdministration classCode="SBADM" moodCode="EVN" negationInd="false">
+              <templateId root="2.16.840.1.113883.10.20.1.24"/>
+              <templateId root="2.16.840.1.113883.3.88.11.83.13" />
+              <templateId root="1.3.6.1.4.1.19376.1.5.3.1.4.12"/>
+              <!-- Medication activity template -->
+              <id root="<%= UUID.generate %>"/>
+              <code code='IMMUNIZ' codeSystem='2.16.840.1.113883.5.4' codeSystemName='ActCode'/>
+              <text>
+                <reference value="#immunizations-desc-<%= i %>"/>
+              </text>
+              <statusCode code="completed"/>
+              <effectiveTime value="<%= Time.at(entry.time).utc.to_formatted_s(:number) %>"/>
+              <doseQuantity nullFlavor="UNK"/>
+              <consumable>
+                <manufacturedProduct>
+                  <templateId root="2.16.840.1.113883.10.20.1.53"/>
+                  <templateId root="1.3.6.1.4.1.19376.1.5.3.1.4.7.2"/>
+                  <!-- Product template -->
+                  <manufacturedMaterial>
+                    <%== render :partial => 'code_with_reference', :locals => {:entry => entry, :i => i, :section => 'immunizations'} %>
+                    <name><%= entry.description %></name>
+                  </manufacturedMaterial>
+                </manufacturedProduct>
+              </consumable>
+            </substanceAdministration>
+          </entry>
+          <% end -%>
+        </section>
+      </component>

data/templates/_medical_equipment.c32.erb

@@ -0,0 +1,34 @@
+<component>
+  <!--Medical Equipment - Not C32-->
+  <section>
+    <templateId root="2.16.840.1.113883.3.88.11.83.128" assigningAuthorityName="HITSP/C83"/>
+    <templateId root="2.16.840.1.113883.10.20.1.7" assigningAuthorityName="CCD"/>
+    <templateId root="1.3.6.1.4.1.19376.1.5.3.1.1.5.3.5" assigningAuthorityName="IHE PCC"/>
+    <!-- Medical equipment section template -->
+    <code code="46264-8" codeSystem="2.16.840.1.113883.6.1"/>
+    <title>Medical Equipment</title>
+    <%== render :partial => 'narrative_block', :locals => {:entries => entries, :section => 'medical_equipment'} %>
+    <% entries.each_with_index do |entry, i| -%>
+    <entry typeCode="DRIV">
+      <supply classCode="SPLY" moodCode="EVN">
+        <templateId root="2.16.840.1.113883.10.20.1.34"/>
+        <!-- Supply activity template -->
+        <id root="<%= UUID.generate %>"/>
+        <statusCode code="completed"/>
+        <effectiveTime value="<%= Time.at(entry.time).utc.to_formatted_s(:number) %>"/>
+        <participant typeCode="DEV">
+          <participantRole classCode="MANU">
+            <templateId root="2.16.840.1.113883.10.20.1.52"/>
+            <!-- Product instance template -->
+            <addr/>
+            <telecom/>
+            <playingDevice>
+              <%== code_display(entry) %>
+            </playingDevice>
+          </participantRole>
+        </participant>
+      </supply>
+    </entry>
+    <% end -%>
+  </section>
+</component>

data/templates/_medications.c32.erb

@@ -0,0 +1,40 @@
+<component>
+  <!--Medications-->
+  <section>
+    <templateId root="2.16.840.1.113883.10.20.1.8" assigningAuthorityName="HL7 SDTC CCD"/>
+    <templateId root="2.16.840.1.113883.3.88.11.83.112" assigningAuthorityName="HITSP"/>
+    <templateId root="1.3.6.1.4.1.19376.1.5.3.1.3.19" assigningAuthorityName="IHE"/>
+    <code code="10160-0" displayName="History of medication use" codeSystem="2.16.840.1.113883.6.1" codeSystemName="LOINC"/>
+    <title>Medications - Prescription and Non-Prescription</title>
+    <%== render :partial => 'narrative_block', :locals => {:entries => entries, :section => 'medications'} %>
+    <% entries.each_with_index do |entry, i| -%>
+    <entry>
+      <!--CCD Medication activity - Required-->
+      <substanceAdministration classCode="SBADM" moodCode="EVN">
+        <templateId root="2.16.840.1.113883.10.20.1.24" assigningAuthorityName="HL7 SDTC CCD"/>
+        <templateId root="2.16.840.1.113883.3.88.11.83.8"/>
+        <templateId root="1.3.6.1.4.1.19376.1.5.3.1.4.7"/>
+        <templateId root="1.3.6.1.4.1.19376.1.5.3.1.4.7.1"/>
+        <id root="<%= UUID.generate %>"/>
+        <statusCode code="completed"/>
+        <effectiveTime xsi:type="IVL_TS">
+          <low value="<%= Time.at(entry.time).utc.to_formatted_s(:number) %>"/>
+          <high nullFlavor="UNK"/>
+        </effectiveTime>
+        <consumable>
+          <!--CCD Product - Required-->
+          <manufacturedProduct classCode="MANU">
+            <templateId root="2.16.840.1.113883.10.20.1.53" assigningAuthorityName="HL7 SDTC CCD"/>
+            <templateId root="2.16.840.1.113883.3.88.11.83.8.2"/>
+            <templateId root="1.3.6.1.4.1.19376.1.5.3.1.4.7.2"/>
+            <manufacturedMaterial>
+              <%== render :partial => 'code_with_reference', :locals => {:entry => entry, :i => i, :section => 'medications'} %>
+              <name><%= entry.description %></name>
+            </manufacturedMaterial>
+          </manufacturedProduct>
+        </consumable>
+      </substanceAdministration>
+    </entry>
+    <% end -%>
+  </section>
+</component>