cqm-parsers 0.2.3 → 3.1.0.0

data/lib/qrda-export/catI-r5/qrda_templates/template_partials/_component.mustache

@@ -1,11 +0,0 @@
-<entryRelationship typeCode="REFR">
-     <observation classCode="OBS" moodCode="EVN">
-        <!-- Component -->
-        <templateId root="2.16.840.1.113883.10.20.24.3.149" extension="2017-08-01" />
-        <id root="{{random_id}}"/>
-        {{#code}}
-        <code {{> _code}}/>
-        {{/code}}
-        {{{result_value}}}
-    </observation>
-</entryRelationship>

data/lib/qrda-export/catI-r5/qrda_templates/template_partials/_encounter_diagnosis.mustache

@@ -1,19 +0,0 @@
-<entryRelationship typeCode="REFR">
-  <act classCode="ACT" moodCode="EVN">
-    <templateId extension="2015-08-01" root="2.16.840.1.113883.10.20.22.4.80"/>
-    <code code="29308-4" codeSystem="2.16.840.1.113883.6.1" codeSystemName="LOINC" displayName="Diagnosis"/>
-    <entryRelationship typeCode="SUBJ">
-      <observation classCode="OBS" moodCode="EVN">
-        <!--  Problem observation template -->
-        <templateId extension="2015-08-01" root="2.16.840.1.113883.10.20.22.4.4"/>
-        <id root="{{random_id}}"/>
-        <code code="29308-4" codeSystem="2.16.840.1.113883.6.1">
-          <translation code="282291009" codeSystem="2.16.840.1.113883.6.96"/>
-        </code>
-        <statusCode code="completed"/>
-        {{{relevant_period}}}
-        <value {{> _code}} xsi:type="CD"/>
-      </observation>
-    </entryRelationship>
-  </act>
-</entryRelationship>

data/lib/qrda-export/catI-r5/qrda_templates/template_partials/_encounter_facility_location.mustache

@@ -1,16 +0,0 @@
-<participant typeCode="LOC">
-  <!-- Facility Location template -->
-  <templateId extension="2017-08-01" root="2.16.840.1.113883.10.20.24.3.100"/>
-  <time>
-    {{{facility_period}}}
-  </time>
-  <participantRole classCode="SDLOC">
-    {{#code}}
-    <code {{> _code}}/>
-    {{/code}}
-    <telecom nullFlavor="UNK"/>
-    <playingEntity classCode="PLC">
-      <name/>
-    </playingEntity>
-  </participantRole>
-</participant>

data/lib/qrda-export/catI-r5/qrda_templates/template_partials/_mediation_frequency.mustache

@@ -1,3 +0,0 @@
-<effectiveTime xsi:type="PIVL_TS" institutionSpecified="true" operator="A">
-  <period value="1" unit="d"/>
-</effectiveTime>

data/lib/qrda-export/catI-r5/qrda_templates/template_partials/_medication_details.mustache

@@ -1,11 +0,0 @@
-{{#route}}
-<routeCode {{> _code}}/>
-{{/route}}
-{{#negated}}
-	<doseQuantity nullFlavor="NA"/>
-{{/negated}}
-{{^negated}}
-{{#dosage}}
-	<doseQuantity value="{{value}}" unit="{{unit}}"/>
-{{/dosage}}
-{{/negated}}

data/lib/qrda-export/catI-r5/qrda_templates/template_partials/_ordinality.mustache

@@ -1 +0,0 @@
-<priorityCode {{> _code}}/>

data/lib/qrda-export/catI-r5/qrda_templates/template_partials/_principal_diagnosis.mustache

@@ -1,8 +0,0 @@
-<entryRelationship typeCode="REFR">
-  <observation classCode="OBS" moodCode="EVN">
-      <templateId root="2.16.840.1.113883.10.20.24.3.152" extension="2017-08-01"/>
-      <id root="{{random_id}}"/>
-      <code code="8319008" codeSystem="2.16.840.1.113883.6.96" displayName="Principal Diagnosis" codeSystemName="SNOMED"/>
-      <value {{> _code}} xsi:type="CD"/>
-  </observation>
-</entryRelationship>

data/lib/qrda-export/catI-r5/qrda_templates/template_partials/_reason.mustache

@@ -1,12 +0,0 @@
-<entryRelationship typeCode="RSON">
-  <observation classCode="OBS" moodCode="EVN">
-    <templateId root="2.16.840.1.113883.10.20.24.3.88" extension="2017-08-01"/>
-    <id root="1.3.6.1.4.1.115" extension="{{random_id}}" />
-    <code code="77301-0" codeSystem="2.16.840.1.113883.6.1" displayName="reason" codeSystemName="LOINC"/>
-    <statusCode code="completed"/>
-    {{#relevantPeriod}}
-    {{{relevant_period}}}
-    {{/relevantPeriod}}
-    <value {{> _code}} xsi:type="CD"/>
-  </observation>
-</entryRelationship>

data/lib/qrda-export/catI-r5/qrda_templates/template_partials/_related_to.mustache

@@ -1,6 +0,0 @@
-<sdtc:inFulfillmentOf1 typeCode="FLFS">
-  <sdtc:templateId root="2.16.840.1.113883.10.20.24.3.150" extension="2017-08-01"/>
-  <sdtc:actReference classCode="ACT" moodCode="EVN">
-    <sdtc:id root="1.3.6.1.4.1.115" extension="{{{as_id}}}"/>
-  </sdtc:actReference>
-</sdtc:inFulfillmentOf1>

data/lib/qrda-export/catI-r5/qrda_templates/template_partials/_results.mustache

@@ -1,19 +0,0 @@
-<entryRelationship typeCode="REFR">
- <observation classCode="OBS" moodCode="EVN">
-    <!-- Conforms to C-CDA R2 Result Observation (V2) -->
-    <templateId root="2.16.840.1.113883.10.20.22.4.2" extension="2015-08-01"/>
-    <id root="1.3.6.1.4.1.115" extension="{{random_id}}"/>
-    {{> _codes}}
-    <statusCode code="completed"/>
-    {{#relevantPeriod}}
-    {{{relevant_period_as_value}}}
-    {{/relevantPeriod}}
-    {{^relevantPeriod}}
-      {{#authorDatetime}}
-      {{{author_effective_time}}}
-      {{/authorDatetime}}
-    {{/relevantPeriod}}
-    {{{result_value}}}
- </observation>
-</entryRelationship>
-

data/lib/qrda-export/catI-r5/qrda_templates/template_partials/_severity.mustache

@@ -1,8 +0,0 @@
-<entryRelationship typeCode="REFR">
-  <observation classCode="OBS" moodCode="EVN">
-    <templateId root="2.16.840.1.113883.10.20.22.4.8" extension="2014-06-09" />
-    <code code="SEV" codeSystem="2.16.840.1.113883.5.4" />
-    <statusCode code="completed" />
-    <value xsi:type="CD" {{> _code}}/>
-  </observation>
-</entryRelationship>

data/lib/qrda-export/helper/cat_1_view_helper.rb

@@ -1,146 +0,0 @@
-module Qrda
-  module Export
-    module Helper
-      module Cat1ViewHelper
-        def random_id
-          UUID.generate
-        end
-
-        def as_id
-          self[:value]
-        end
-
-        def object_id
-          self[:_id]
-        end
-
-        def submission_program
-          @submission_program
-        end
-
-        def provider
-          JSON.parse(@provider.to_json) if @provider
-        end
-
-        def provider_addresses
-          @provider['addresses']
-        end
-
-        def provider_street
-          self['street'].join('')
-        end
-
-        def provider_npi
-          @provider['cda_identifiers'].map { |cda| cda['extension'] if cda['root'] == '2.16.840.1.113883.4.6' }.compact.first
-        end
-
-        def provider_tin
-          @provider['cda_identifiers'].map { |cda| cda['extension'] if cda['root'] == '2.16.840.1.113883.4.2' }.compact.first
-        end
-
-        def provider_ccn
-          @provider['cda_identifiers'].map { |cda| cda['extension'] if cda['root'] == '2.16.840.1.113883.4.336' }.compact.first
-        end
-
-        def provider_type_code
-          @provider['specialty']
-        end
-
-        def mrn
-          @patient.extendedData['medical_record_number']
-        end
-
-        def given_name
-          @patient.givenNames.join(' ')
-        end
-
-        def family_name
-          @patient.familyName
-        end
-
-        def birthdate
-          @patient.birthDatetime.to_formatted_s(:number)
-        end
-
-        def gender
-          @patient.dataElements.where(hqmfOid: '2.16.840.1.113883.10.20.28.3.55').first.dataElementCodes.first['code']
-        end
-
-        def race
-          @patient.dataElements.where(hqmfOid: '2.16.840.1.113883.10.20.28.3.59').first.dataElementCodes.first['code']
-        end
-
-        def ethnic_group
-          @patient.dataElements.where(hqmfOid: '2.16.840.1.113883.10.20.28.3.56').first.dataElementCodes.first['code']
-        end
-
-        def insurance_provider
-          @insurance_provider
-        end
-
-        def insurance_provider_code_and_code_system
-          "code=\"#{self['codes'].values.first[0]}\" codeSystem=\"#{code_system_oid(self['codes'].keys.first)}\" codeSystemName=\"#{self['codes'].keys.first}\""
-        end
-
-        def measures
-          @measures.only(:hqmf_id, :hqmf_set_id, :description).as_json
-        end
-
-        def negation_ind
-          self[:negationRationale].nil? ? "" : "negationInd=\"true\""
-        end
-
-        def negated
-          self[:negationRationale].nil? ? false : true
-        end
-
-        def multiple_codes?
-          self[:dataElementCodes].size > 1
-        end
-
-        def code_system_oid(name)
-          Qrda::Export::Helper::CodeSystemHelper.oid_for_code_system(name)
-        end
-
-        def code_and_codesystem
-          if self['codeSystem'] == 'NA_VALUESET'
-            "nullFlavor=\"NA\" sdtc:valueSet=\"#{self['code']}\""
-          else
-            "code=\"#{self['code']}\" codeSystem=\"#{code_system_oid(self['codeSystem'])}\" codeSystemName=\"#{self['codeSystem']}\""
-          end
-        end
-
-        def primary_code_and_codesystem
-          "code=\"#{self[:dataElementCodes][0]['code']}\" codeSystem=\"#{code_system_oid(self[:dataElementCodes][0]['codeSystem'])}\" codeSystemName=\"#{self[:dataElementCodes][0]['codeSystem']}\""
-        end
-
-        def translation_codes_and_codesystem_list
-          translation_list = ""
-          self[:dataElementCodes].each_with_index do |_dec, index|
-            next if index.zero?
-            translation_list += "<translation code=\"#{self[:dataElementCodes][index]['code']}\" codeSystem=\"#{code_system_oid(self[:dataElementCodes][index]['codeSystem'])}\" codeSystemName=\"#{self[:dataElementCodes][index]['codeSystem']}\"/>"
-          end
-          translation_list
-        end
-
-        def result_value
-          return "<value xsi:type=\"CD\" nullFlavor=\"UNK\"/>" unless self['result']
-          result_string = if self['result'].is_a? Array
-                            result_value_as_string(self['result'][0])
-                          elsif self['result'].is_a? Hash
-                            result_value_as_string(self['result'])
-                          elsif !self['result'].nil?
-                            "<value xsi:type=\"PQ\" value=\"#{self['result']}\" unit=\"1\"/>"
-                          end
-          result_string
-        end
-
-        def result_value_as_string(result)
-          return "<value xsi:type=\"CD\" nullFlavor=\"UNK\"/>" unless result
-          return "<value xsi:type=\"CD\" code=\"#{result['code']}\" codeSystem=\"#{code_system_oid(result['codeSystem'])}\" codeSystemName=\"#{result['codeSystem']}\"/>" if result['code']
-          return "<value xsi:type=\"PQ\" value=\"#{result['value']}\" unit=\"#{result['unit']}\"/>" if result['unit']
-        end
-      end
-    end
-  end
-end

data/lib/qrda-export/helper/code_system_helper.rb

@@ -1,77 +0,0 @@
-module Qrda
-  module Export
-    module Helper
-      # General helpers for working with codes and code systems
-      class CodeSystemHelper
-        CODE_SYSTEMS = {
-          '2.16.840.1.113883.6.1' =>    'LOINC',
-          '2.16.840.1.113883.6.96' =>   'SNOMED-CT',
-          '2.16.840.1.113883.6.12' =>   'CPT',
-          '2.16.840.1.113883.6.88' =>   'RxNorm',
-          '2.16.840.1.113883.6.103' =>  'ICD-9-CM',
-          '2.16.840.1.113883.6.104' =>  'ICD-9-PCS',
-          '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' =>   'HCP',
-          '2.16.840.1.113883.6.285' =>   'HCPCS',
-          '2.16.840.1.113883.5.2' => "HL7 Marital Status",
-          '2.16.840.1.113883.12.292' => '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',
-          '2.16.840.1.113883.5.1076' => "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",
-          '2.16.840.1.113883.3.221.5' => "Source of Payment Typology",
-          '2.16.840.1.113883.6.13' => 'CDT',
-          '2.16.840.1.113883.18.2' => 'AdministrativeSex'
-        }
-        
-        CODE_SYSTEM_ALIASES = {
-          'FDA SPL' => 'NCI Thesaurus',
-          'HSLOC' => 'HL7 Healthcare Service Location',
-          'SOP' => "Source of Payment Typology"
-        }
-        
-        # Some old OID are still around in data, this hash maps retired OID values to 
-        # the new value
-        OID_ALIASES = {
-          '2.16.840.1.113883.6.59' => '2.16.840.1.113883.12.292' # CVX
-        }
-        
-        # Returns the name of a code system given an oid
-        # @param [String] oid of a code system
-        # @return [String] the name of the code system as described in the measure definition JSON
-        def self.code_system_for(oid)
-          oid = OID_ALIASES[oid] if OID_ALIASES[oid]
-          CODE_SYSTEMS[oid] || "Unknown"
-        end
-        
-        # Returns the oid for a code system given a codesystem name
-        # @param [String] the name of the code system
-        # @return [String] the oid of the code system
-        def self.oid_for_code_system(code_system)
-          code_system = CODE_SYSTEM_ALIASES[code_system] if CODE_SYSTEM_ALIASES[code_system]
-          CODE_SYSTEMS.invert[code_system]
-        end
-        
-        # Returns the whole map of OIDs to code systems
-        # @terurn [Hash] oids as keys, code system names as values
-        def self.code_systems
-          CODE_SYSTEMS
-        end
-      end
-    end
-  end
-end
-

data/lib/qrda-export/helper/date_helper.rb

@@ -1,89 +0,0 @@
-module Qrda
-  module Export
-    module Helper
-      module DateHelper
-        def value_or_null_flavor(time)
-          # this is a bit of a hack for a defineded undefined date
-          if time && DateTime.parse(time).year < 3000
-            "value='#{DateTime.parse(time).utc.to_formatted_s(:number)}'"
-          else
-            "nullFlavor='UNK'"
-          end
-        end
-
-        def performance_period_start
-          @performance_period_start.to_formatted_s(:number)
-        end
-
-        def performance_period_end
-          @performance_period_end.to_formatted_s(:number)
-        end
-
-        def current_time
-          Time.now.utc.to_formatted_s(:number)
-        end
-
-        def author_time
-          "<time #{value_or_null_flavor(self['authorDatetime'])}/>"
-        end
-
-        def author_effective_time
-          "<effectiveTime #{value_or_null_flavor(self['authorDatetime'])}/>"
-        end
-
-        def expired_date_time
-          "<effectiveTime>"\
-          "<low #{value_or_null_flavor(self['expiredDatetime'])}/>"\
-          "</effectiveTime>"
-        end
-
-        def prevalence_period
-          "<effectiveTime>"\
-          "<low #{value_or_null_flavor(self['prevalencePeriod']['low'])}/>"\
-          "<high #{value_or_null_flavor(self['prevalencePeriod']['high'])}/>"\
-          "</effectiveTime>"
-        end
-
-        def relevant_period
-          "<effectiveTime>"\
-          "<low #{value_or_null_flavor(self['relevantPeriod']['low'])}/>"\
-          "<high #{value_or_null_flavor(self['relevantPeriod']['high'])}/>"\
-          "</effectiveTime>"
-        end
-
-        def relevant_period_as_value
-          "<effectiveTime #{value_or_null_flavor(self['relevantPeriod']['low'])}/>"
-        end
-
-        def insurance_provider_period
-          start_time = self['start_time'] ? DateTime.strptime(self['start_time'].to_s, '%s').to_s : nil
-          end_time = self['end_time'] ? DateTime.strptime(self['end_time'].to_s, '%s').to_s : nil
-          "<effectiveTime>"\
-          "<low #{value_or_null_flavor(start_time)}/>"\
-          "<high #{value_or_null_flavor(end_time)}/>"\
-          "</effectiveTime>"
-        end
-
-        def medication_duration_effective_time
-          "<effectiveTime xsi:type=\"IVL_TS\">"\
-          "<low #{value_or_null_flavor(self['relevantPeriod']['low'])}/>"\
-          "<high #{value_or_null_flavor(self['relevantPeriod']['high'])}/>"\
-          "</effectiveTime>"
-        end
-
-        def facility_period
-          "<low #{value_or_null_flavor(self['locationPeriod']['low'])}/>"\
-          "<high #{value_or_null_flavor(self['locationPeriod']['high'])}/>"
-        end
-
-        def incision_datetime
-          "<effectiveTime #{value_or_null_flavor(self['incisionDatetime'])}/>"
-        end
-
-        def completed_prevalence_period
-          self['prevalencePeriod']['high'] ? true : false
-        end
-      end
-    end
-  end
-end