cqm-parsers 0.2.2 → 0.2.3

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA256:
-  metadata.gz: 1b1bca119f15302832fea054a9bcc5ad90736bfe3ad898ec05410ba9932c4fa6
-  data.tar.gz: 94776039cbf7dadafc0b8bf2308cca80b60e298a5291494d3d63d2ade0f852d4
+  metadata.gz: 9485682c59342822202fe6a253ce7bbcbb67b92a428fa04558a093d0995d9765
+  data.tar.gz: e68e467aa5d71626f960a79df31e08569b35cc7faa8c6c35ca893532818e60ae
 SHA512:
-  metadata.gz: 476c7290726a10f52dfb3f65a066516f755d7913be15c74783d5fbc836a2718c7cf65b9580ef309368ec4bdb45d9d6d175881b190660eb94f12d9ed6b2eeed08
-  data.tar.gz: 14d8e37e7fe9c737df8175192d935e3b908a53fa4511ccff107772108ef055375091241206fa964a5c430dcb944b5ce7b05b1bd94b52a5860a902d212843b0ca
+  metadata.gz: 1bc35e9ea6bfadd995d234619315ef036f2f3cfc61e4a3dc8bc35f20bb7f48efe798049642061019fd4351861b906a16989dc54a451dfe32c3bcd56778e72937
+  data.tar.gz: 5fe9cbb48856d6585c433bf33727129d985afd25a71df22f688aab9289904466ac0defbdd7779c9c2fba422c2607d601f4b1519f605970d2bc74ad334e5beea6

data/lib/qrda-export/catI-r5/qrda_templates/diagnostic_study_performed.mustache

@@ -16,6 +16,9 @@
     {{#authorDatetime}}
     {{> qrda_templates/template_partials/_author}}
     {{/authorDatetime}}
+    {{#reason}}
+    {{> qrda_templates/template_partials/_reason}}
+    {{/reason}}
     {{#negationRationale}}
     {{> qrda_templates/template_partials/_reason}}
     {{/negationRationale}}

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

@@ -1,6 +1,6 @@
 <entryRelationship typeCode="RSON">
   <observation classCode="OBS" moodCode="EVN">
-    <templateId root="2.16.840.1.113883.10.20.24.3.88" extension="2014-12-01"/>
+    <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"/>

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

@@ -2,13 +2,11 @@
  <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"/>
-    <!-- Result (QRDA I R3) -->
-    <templateId root="2.16.840.1.113883.10.20.24.3.87" extension="2016-02-01"/>
     <id root="1.3.6.1.4.1.115" extension="{{random_id}}"/>
     {{> _codes}}
     <statusCode code="completed"/>
     {{#relevantPeriod}}
-    {{{relevant_period}}}
+    {{{relevant_period_as_value}}}
     {{/relevantPeriod}}
     {{^relevantPeriod}}
       {{#authorDatetime}}

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

@@ -103,7 +103,11 @@ module Qrda
         end
 
         def code_and_codesystem
-          "code=\"#{self['code']}\" codeSystem=\"#{code_system_oid(self['codeSystem'])}\" codeSystemName=\"#{self['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

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

@@ -51,6 +51,10 @@ module Qrda
           "</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

data/lib/qrda-import/base-importers/demographics_importer.rb

@@ -13,18 +13,18 @@ module QRDA
         patient.dataElements << pcbd
 
         pcs = QDM::PatientCharacteristicSex.new
-        gender_code = patient_element.at_xpath('cda:administrativeGenderCode')['code']
-        pcs.dataElementCodes = [{ code: gender_code, codeSystem: 'AdministrativeGender' }]
+        code_element = patient_element.at_xpath('cda:administrativeGenderCode')
+        pcs.dataElementCodes = [code_if_present(code_element)]
         patient.dataElements << pcs
 
         pcr = QDM::PatientCharacteristicRace.new
-        race_code = patient_element.at_xpath('cda:raceCode')['code']
-        pcr.dataElementCodes = [{ code: race_code, codeSystem: 'cdcrec' }]
+        code_element = patient_element.at_xpath('cda:raceCode')
+        pcr.dataElementCodes = [code_if_present(code_element)]
         patient.dataElements << pcr
 
         pce = QDM::PatientCharacteristicEthnicity.new
-        ethnicity_code = patient_element.at_xpath('cda:ethnicGroupCode')['code']
-        pce.dataElementCodes = [{ code: ethnicity_code, codeSystem: 'cdcrec' }]
+        code_element = patient_element.at_xpath('cda:ethnicGroupCode')
+        pce.dataElementCodes = [code_if_present(code_element)]
         patient.dataElements << pce
 
         provider_element = doc.xpath("//cda:entry/cda:observation[cda:templateId/@root = '2.16.840.1.113883.10.20.24.3.55']")
@@ -38,6 +38,12 @@ module QRDA
         patient.extendedData = {}
         patient.extendedData['insurance_providers'] = JSON.generate([ip])
       end
+
+      def code_if_present(code_element)
+        return unless code_element && code_element['codeSystem'] && code_element['code']
+
+        QDM::Code.new(code_element['code'], HQMF::Util::CodeSystemHelper.code_system_for(code_element['codeSystem']))
+      end
     end
   end
 end

data/lib/qrda-import/base-importers/section_importer.rb

@@ -139,7 +139,7 @@ module QRDA
           if negation_indicator.eql?('true')
             entry.negationRationale = code_if_present(reason_element.first)
           else
-            entry.reason = code_if_present(reason_element.first)
+            entry.reason = code_if_present(reason_element.first) unless @entry_does_not_have_reason
           end
         end
         extract_negated_code(coded_parent_element, entry)

data/lib/qrda-import/data-element-importers/communication_from_patient_to_provider_importer.rb

@@ -3,6 +3,7 @@ module QRDA
     class CommunicationFromPatientToProviderImporter < SectionImporter
       def initialize(entry_finder = QRDA::Cat1::EntryFinder.new("./cda:entry/cda:act[cda:templateId/@root = '2.16.840.1.113883.10.20.24.3.2']"))
         super(entry_finder)
+        @entry_does_not_have_reason = true
         @id_xpath = './cda:id'
         @code_xpath = './cda:code'
         @author_datetime_xpath = "./cda:author/cda:time"

data/lib/qrda-import/data-element-importers/communication_from_provider_to_patient_importer.rb

@@ -3,6 +3,7 @@ module QRDA
     class CommunicationFromProviderToPatientImporter < SectionImporter
       def initialize(entry_finder = QRDA::Cat1::EntryFinder.new("./cda:entry/cda:act[cda:templateId/@root = '2.16.840.1.113883.10.20.24.3.3']"))
         super(entry_finder)
+        @entry_does_not_have_reason = true
         @id_xpath = './cda:id'
         @code_xpath = './cda:code'
         @author_datetime_xpath = "./cda:author/cda:time"

data/lib/qrda-import/data-element-importers/communication_from_provider_to_provider_importer.rb

@@ -3,6 +3,7 @@ module QRDA
     class CommunicationFromProviderToProviderImporter < SectionImporter
       def initialize(entry_finder = QRDA::Cat1::EntryFinder.new("./cda:entry/cda:act[cda:templateId/@root = '2.16.840.1.113883.10.20.24.3.4']"))
         super(entry_finder)
+        @entry_does_not_have_reason = true
         @id_xpath = './cda:id'
         @code_xpath = './cda:code'
         @author_datetime_xpath = "./cda:author/cda:time"

data/lib/qrda-import/data-element-importers/diagnosis_importer.rb

@@ -5,7 +5,7 @@ module QRDA
         super(entry_finder)
         @id_xpath = './cda:entryRelationship/cda:observation/cda:id'
         @code_xpath = "./cda:entryRelationship/cda:observation[cda:templateId/@root = '2.16.840.1.113883.10.20.24.3.135']/cda:value"
-        @author_datetime_xpath = "./cda:author/cda:time"
+        @author_datetime_xpath = "./cda:entryRelationship/cda:observation[cda:templateId/@root = '2.16.840.1.113883.10.20.24.3.135']/cda:author/cda:time"
         @prevalence_period_xpath = "./cda:entryRelationship/cda:observation[cda:templateId/@root = '2.16.840.1.113883.10.20.24.3.135']/cda:effectiveTime"
         @anatomical_location_site_xpath = "./cda:entryRelationship/cda:observation[cda:templateId/@root = '2.16.840.1.113883.10.20.24.3.135']/cda:targetSiteCode"
         @severity_xpath = "./cda:entryRelationship/cda:observation[cda:templateId/@root = '2.16.840.1.113883.10.20.24.3.135']/cda:entryRelationship/cda:observation[cda:templateId/@root='2.16.840.1.113883.10.20.22.4.8']/cda:value"

data/lib/qrda-import/data-element-importers/diagnostic_study_performed_importer.rb

@@ -7,8 +7,8 @@ module QRDA
         @code_xpath = './cda:code'
         @relevant_period_xpath = "./cda:effectiveTime"
         @author_datetime_xpath = "./cda:author/cda:time"
-        @result_xpath = "./cda:entryRelationship[@typeCode='REFR']/cda:observation/cda:value"
-        @result_datetime_xpath = "./cda:entryRelationship[@typeCode='REFR']/cda:observation/cda:effectiveTime"
+        @result_xpath = "./cda:entryRelationship[@typeCode='REFR']/cda:observation[cda:templateId/@root = '2.16.840.1.113883.10.20.22.4.2']/cda:value"
+        @result_datetime_xpath = "./cda:entryRelationship[@typeCode='REFR']/cda:observation[cda:templateId/@root = '2.16.840.1.113883.10.20.22.4.2']/cda:effectiveTime"
         @status_xpath = "./cda:entryRelationship/cda:observation[cda:templateId/@root = '2.16.840.1.113883.10.20.24.3.93']/cda:value"
         @method_xpath = './cda:methodCode'
         @facility_location_xpath = "./cda:participant[cda:templateId/@root = '2.16.840.1.113883.10.20.24.3.100']/cda:participantRole[@classCode='SDLOC']/cda:code"

data/lib/qrda-import/data-element-importers/laboratory_test_performed_importer.rb

@@ -9,8 +9,8 @@ module QRDA
         @author_datetime_xpath = "./cda:author/cda:time"
         @status_xpath = "./cda:entryRelationship/cda:observation[cda:templateId/@root = '2.16.840.1.113883.10.20.24.3.93']/cda:value"
         @method_xpath = './cda:methodCode'
-        @result_xpath = "./cda:entryRelationship[@typeCode='REFR']/cda:observation/cda:value"
-        @result_datetime_xpath = "./cda:entryRelationship[@typeCode='REFR']/cda:observation/cda:effectiveTime"
+        @result_xpath = "./cda:entryRelationship[@typeCode='REFR']/cda:observation[cda:templateId/@root = '2.16.840.1.113883.10.20.22.4.2']/cda:value"
+        @result_datetime_xpath = "./cda:entryRelationship[@typeCode='REFR']/cda:observation[cda:templateId/@root = '2.16.840.1.113883.10.20.22.4.2']/cda:effectiveTime"
         @components_xpath = "./cda:entryRelationship/cda:observation[cda:templateId/@root = '2.16.840.1.113883.10.20.24.3.149']"
         @entry_class = QDM::LaboratoryTestPerformed
       end

data/lib/qrda-import/data-element-importers/substance_administered_importer.rb

@@ -3,6 +3,7 @@ module QRDA
     class SubstanceAdministeredImporter < MedicationAdministeredImporter
       def initialize(entry_finder = QRDA::Cat1::EntryFinder.new("./cda:entry/cda:substanceAdministration[cda:templateId/@root = '2.16.840.1.113883.10.20.24.3.42']"))
         super(entry_finder)
+        @entry_does_not_have_reason = true
         @entry_class = QDM::SubstanceAdministered
       end
 

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: cqm-parsers
 version: !ruby/object:Gem::Version
-  version: 0.2.2
+  version: 0.2.3
 platform: ruby
 authors:
 - The MITRE Corporation
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2019-01-25 00:00:00.000000000 Z
+date: 2019-04-30 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: mustache
@@ -30,14 +30,14 @@ dependencies:
     requirements:
     - - "~>"
       - !ruby/object:Gem::Version
-        version: 1.8.0
+        version: 2.0.1
   type: :runtime
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
     - - "~>"
       - !ruby/object:Gem::Version
-        version: 1.8.0
+        version: 2.0.1
 - !ruby/object:Gem::Dependency
   name: erubis
   requirement: !ruby/object:Gem::Requirement
@@ -142,14 +142,14 @@ dependencies:
     requirements:
     - - "~>"
       - !ruby/object:Gem::Version
-        version: 1.8.5
+        version: 1.10.3
   type: :runtime
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
     - - "~>"
       - !ruby/object:Gem::Version
-        version: 1.8.5
+        version: 1.10.3
 - !ruby/object:Gem::Dependency
   name: highline
   requirement: !ruby/object:Gem::Requirement
@@ -411,7 +411,7 @@ required_rubygems_version: !ruby/object:Gem::Requirement
       version: '0'
 requirements: []
 rubyforge_project: 
-rubygems_version: 2.7.7
+rubygems_version: 2.7.9
 signing_key: 
 specification_version: 4
 summary: A library for parsing HQMF documents.