cqm-reports 2.1.1 → 3.0.0.pre.alpha.1

checksums.yaml

@@ -1,7 +1,7 @@
 ---
-SHA1:
-  metadata.gz: 6af15ff075a9533c61c844f95c5adc741e999dec
-  data.tar.gz: 2cf3f0aeb6c3e1744e5e2f8a45a8d0e90a1ab5a1
+SHA256:
+  metadata.gz: 61e09a4750ca628e10f1e92fe0d37c28058ab629b59fcbc520ef167d369296a3
+  data.tar.gz: 1035c18714e2ca53bdd527e91ebac55b96e5737cba137c105c8a1b2577418d3d
 SHA512:
-  metadata.gz: a4ab0c6c763b00dfa1c7985110969e6262ecc977d9a6509ca64c82e3979e6fd6e27f1bd888ae05ac5eaeecf600645a7cfea95d7013f8a5b01d1b85e865d80f52
-  data.tar.gz: fdfe64bbfb95f37e11dae78380147076daeb9b155a05eadb663c063191ffb9155390af0ae32a6f9643d87d852d605a87cb6fd48c4dc1cf0c9f631a7f929c4538
+  metadata.gz: e1566656c60a1836df5e4846b6b07669ddddfb81c0aeee0bc0302790bc70abb0fea8711d6722e87f5ca02174ed535ffe7a04a7b4709c1800c5e03a37a07d7e7a
+  data.tar.gz: 3fb48e9b465962a7a7130a49879bb9b812bf59fb2ff94af064af571da1b3c92775861d262cd8dbbf66168e0020ad998de34389e4dcba9d1fed4b66e9753a99da

data/Gemfile

@@ -4,8 +4,6 @@ gemspec :development_group => :test
 
 gem 'mongoid', '~> 6.4.2'
 
-# gem 'cqm-models', git: 'https://github.com/projecttacoma/cqm-models.git', branch: 'master'
-
 gem 'protected_attributes_continued'
 
 group :development, :test do
@@ -28,5 +26,6 @@ group :test do
   gem 'minitest', '~> 5.3'
   gem 'minitest-reporters'
   gem 'awesome_print', :require => 'ap'
+  gem 'cqm-validators'
   gem 'nokogiri-diff'
 end

data/README.md

@@ -18,33 +18,6 @@ Starting with version **2.0.0** released on 6/20/2019, cqm-reports versioning ha
 
 For the versions available, see [tags on this repository](https://github.com/projecttacoma/cqm-validators/tags).
 
-=======
-Importing QRDA
-==========
-
-A QRDA document can be imported into a CQM::Patient (defined in [cqm-models](https://github.com/projecttacoma/cqm-models)) using the following commands.
-
-        doc = Nokogiri::XML(file)
-        patient, warnings = QRDA::Cat1::PatientImporter.instance.parse_cat1(doc)
-
-Exporting QRDA Category I
-==========
-
-Exporting a QRDA document from a CQM::Patient (defined in [cqm-models](https://github.com/projecttacoma/cqm-models)) using the following command.
-
-        Qrda1R5.new(patient, measures, options).render
-* patient is a [CQM::Patient](https://github.com/projecttacoma/cqm-models/blob/master/app/models/cqm/patient.rb)
-* measures is an array of [CQM::Measure](https://github.com/projecttacoma/cqm-models/blob/master/app/models/cqm/measure.rb)
-* options is a hash that can be used to pass in:
-  * provider
-  * patient_addresses
-  * patient_telecoms
-  * start_time
-  * end_time
-  * submission_program 
-
-QRDA export requires the [mustache](https://github.com/mustache/mustache) gem 
-
 ## License
 
 Copyright 2019 The MITRE Corporation

data/lib/{cqm_report.rb → cqm-reports.rb}

@@ -18,6 +18,7 @@ require_relative 'html-export/qdm-patient/qdm_patient.rb'
 require_relative 'qrda-export/catI-r5/qrda1_r5.rb'
 require_relative 'qrda-export/catIII-r2-1/qrda3_r21.rb'
 
+require_relative 'qrda-import/entry_package.rb'
 require_relative 'qrda-import/cda_identifier.rb'
 require_relative 'qrda-import/narrative_reference_handler.rb'
 require_relative 'qrda-import/entry_finder.rb'
@@ -66,9 +67,10 @@ require_relative 'qrda-import/data-element-importers/procedure_order_importer.rb
 require_relative 'qrda-import/data-element-importers/procedure_performed_importer.rb'
 require_relative 'qrda-import/data-element-importers/procedure_recommended_importer.rb'
 require_relative 'qrda-import/data-element-importers/provider_care_experience_importer.rb'
-require_relative 'qrda-import/data-element-importers/provider_characteristic_importer.rb'
 require_relative 'qrda-import/data-element-importers/substance_administered_importer.rb'
 require_relative 'qrda-import/data-element-importers/substance_order_importer.rb'
 require_relative 'qrda-import/data-element-importers/substance_recommended_importer.rb'
 require_relative 'qrda-import/data-element-importers/symptom_importer.rb'
-require_relative 'qrda-import/patient_importer.rb'
+require_relative 'qrda-import/patient_importer.rb'
+require_relative 'ext/data_element.rb'
+require_relative 'ext/code.rb'

data/lib/ext/code.rb

@@ -0,0 +1,11 @@
+module QDM
+  class Code    
+    def ==(other)
+      return false unless other.is_a? QDM::Code
+
+      (code == other.code) && (system == other.system) && (version == other.version)
+    end
+
+    alias eql? ==
+  end
+end

data/lib/ext/data_element.rb

@@ -0,0 +1,24 @@
+module QDM
+  class DataElement
+    def merge!(other)
+      # ensure they're the same category (e.g. 'encounter')
+      return unless qdmCategory == other.qdmCategory
+
+      # ensure they're the same status (e.g. 'performed'), and that they both have a status set (or that they both don't)
+      return if respond_to?(:qdmStatus) && !other.respond_to?(:qdmStatus)
+      return if !respond_to?(:qdmStatus) && other.respond_to?(:qdmStatus)
+      return if respond_to?(:qdmStatus) && other.respond_to?(:qdmStatus) && qdmStatus != other.qdmStatus
+      
+      # iterate over non-code fields
+      fields.each_key do |field|
+        next if field[0] == '_' || %w[dataElementCodes qdmCategory qdmVersion qdmStatus].include?(field)
+        
+        if send(field).nil?
+          send(field + '=', other.send(field))
+        end
+      end
+
+      self.dataElementCodes = dataElementCodes.concat(other.dataElementCodes).uniq
+    end
+  end
+end

data/lib/html-export/qdm-patient/qdm_patient.rb

@@ -17,7 +17,7 @@ class QdmPatient < Mustache
   def data_elements
     de_hash = {}
     @qdmPatient.dataElements.each do |data_element|
-      de_hash[data_element._type] ? de_hash[data_element._type].element_list << data_element : de_hash[data_element._type] = { title: data_element._type, element_list: [data_element] }
+      de_hash[data_element._type] ? de_hash[data_element._type][:element_list] << data_element : de_hash[data_element._type] = { title: data_element._type, element_list: [data_element] }
     end
     JSON.parse(de_hash.values.to_json)
   end
@@ -27,11 +27,11 @@ class QdmPatient < Mustache
   end
 
   def code_code_system_string
-    "#{self['code']} (#{HQMF::Util::CodeSystemHelper.code_system_for(self['codeSystemOid'])})"
+    "#{self['code']} (#{HQMF::Util::CodeSystemHelper.code_system_for(self['system'])})"
   end
 
   def code_system_name
-    HQMF::Util::CodeSystemHelper.code_system_for(self['codeSystemOid'])
+    HQMF::Util::CodeSystemHelper.code_system_for(self['system'])
   end
 
   def result_string

data/lib/qrda-export/catI-r5/_header.mustache

@@ -6,9 +6,9 @@
 <!-- QRDA templateId -->
 <templateId root="2.16.840.1.113883.10.20.24.1.1" extension="2017-08-01"/>
 <!-- QDM-based QRDA templateId -->
-<templateId root="2.16.840.1.113883.10.20.24.1.2" extension="2018-10-01"/>
+<templateId root="2.16.840.1.113883.10.20.24.1.2" extension="2017-08-01"/>
 <!-- CMS QRDA templateId -->
-<templateId root="2.16.840.1.113883.10.20.24.1.3" extension="2019-02-01"/>
+<templateId root="2.16.840.1.113883.10.20.24.1.3" extension="2018-02-01"/>
 <!-- This is the globally unique identifier for this QRDA document -->
 <id root="{{random_id}}"/>
 <!-- QRDA document type code -->

data/lib/qrda-export/catI-r5/qrda1_r5.mustache

@@ -12,8 +12,8 @@
           <!-- This is the templateId for Patient Data section -->
           <templateId root="2.16.840.1.113883.10.20.17.2.4"/>
           <!-- This is the templateId for Patient Data QDM section -->
-          <templateId extension="2018-10-01" root="2.16.840.1.113883.10.20.24.2.1"/>
-          <templateId extension="2019-02-01" root="2.16.840.1.113883.10.20.24.2.1.1"/>
+          <templateId extension="2017-08-01" root="2.16.840.1.113883.10.20.24.2.1"/>
+          <templateId extension="2018-02-01" root="2.16.840.1.113883.10.20.24.2.1.1"/>
           <code code="55188-7" codeSystem="2.16.840.1.113883.6.1"/>
           <title>Patient Data</title>
           <text/>
@@ -178,10 +178,6 @@
             {{> qrda_templates/provider_care_experience}}
           {{/provider_care_experience}}
 
-          {{#provider_characteristic}}
-            {{> qrda_templates/provider_characteristic}}
-          {{/provider_characteristic}}
-
           {{#substance_administered}}
             {{> qrda_templates/medication_administered}}
           {{/substance_administered}}

data/lib/qrda-export/catI-r5/qrda1_r5.rb

@@ -13,33 +13,11 @@ class Qrda1R5 < Mustache
     @qdmPatient = patient.qdmPatient
     @measures = measures
     @provider = options[:provider]
-    @patient_address_option = options[:patient_addresses]
-    @patient_telecom_option = options[:patient_telecoms]
     @performance_period_start = options[:start_time]
     @performance_period_end = options[:end_time]
     @submission_program = options[:submission_program]
   end
 
-  def patient_addresses
-    @patient_address_option ||= [CQM::Address.new(
-      use: 'HP',
-      street: ['202 Burlington Rd.'],
-      city: 'Bedford',
-      state: 'MA',
-      zip: '01730',
-      country: 'US'
-    )]
-    JSON.parse(@patient_address_option.to_json)
-  end
-
-  def patient_telecoms
-    @patient_telecom_option ||= [CQM::Telecom.new(
-      use: 'HP',
-      value: '555-555-2003'
-    )]
-    JSON.parse(@patient_telecom_option.to_json)
-  end
-
   def patient_characteristic_payer
     JSON.parse(@qdmPatient.get_data_elements('patient_characteristic', 'payer').to_json)
   end
@@ -195,7 +173,7 @@ class Qrda1R5 < Mustache
   def physical_exam_order
     JSON.parse(@qdmPatient.get_data_elements('physical_exam', 'order').to_json)
   end
-
+  
   def physical_exam_performed
     JSON.parse(@qdmPatient.get_data_elements('physical_exam', 'performed').to_json)
   end
@@ -220,10 +198,6 @@ class Qrda1R5 < Mustache
     JSON.parse(@qdmPatient.dataElements.where(hqmfOid: { '$in' => HQMF::Util::HQMFTemplateHelper.get_all_hqmf_oids('provider_care_experience', '') }).to_json)
   end
 
-  def provider_characteristic
-    JSON.parse(@qdmPatient.get_data_elements('provider_characteristic', nil).to_json)
-  end
-
   def substance_administered
     JSON.parse(@qdmPatient.get_data_elements('substance', 'administered').to_json)
   end
@@ -235,7 +209,7 @@ class Qrda1R5 < Mustache
   def substance_recommended
     JSON.parse(@qdmPatient.get_data_elements('substance', 'recommended').to_json)
   end
-
+  
   def symptom
     JSON.parse(@qdmPatient.get_data_elements('symptom', nil).to_json)
   end

data/lib/qrda-export/catI-r5/qrda_header/_record_target.mustache

@@ -1,20 +1,14 @@
 <recordTarget>
   <patientRole>
     <id extension="{{mrn}}" root="1.3.6.1.4.1.115" />
-    {{#patient_addresses}}
-      <addr use="{{use}}">
-        {{#street}}
-          <streetAddressLine>{{.}}</streetAddressLine>
-        {{/street}}
-        <city>{{city}}</city>
-        <state>{{state}}</state>
-        <postalCode>{{zip}}</postalCode>
-        <country>{{country}}</country>
-      </addr>
-    {{/patient_addresses}}
-    {{#patient_telecoms}}
-      <telecom use="{{use}}" value="tel:{{value}}"/>
-    {{/patient_telecoms}}
+    <addr use="HP">
+      <streetAddressLine>202 Burlington Rd.</streetAddressLine>
+      <city>Bedford</city>
+      <state>MA</state>
+      <postalCode>01730</postalCode>
+      <country>US</country>
+    </addr>
+    <telecom use="WP" value="tel:+1-781-271-3000"/>
     <patient>
       {{#patient}}
         <name>
@@ -27,9 +21,6 @@
           <administrativeGenderCode {{> _code}}/>
         {{/dataElementCodes}}
       {{/patient_characteristic_sex}}
-      {{^patient_characteristic_sex}}
-          <administrativeGenderCode nullFlavor="UNK"/>
-      {{/patient_characteristic_sex}}
       {{#patient_characteristic_birthdate}}
         {{{birth_date_time}}}
       {{/patient_characteristic_birthdate}}
@@ -38,20 +29,16 @@
           <raceCode {{> _code}}/>
         {{/dataElementCodes}}
       {{/patient_characteristic_race}}
-      {{^patient_characteristic_race}}
-          <raceCode nullFlavor="UNK"/>
-      {{/patient_characteristic_race}}
       {{#patient_characteristic_ethnicity}}
         {{#dataElementCodes}}
           <ethnicGroupCode {{> _code}}/>
         {{/dataElementCodes}}
       {{/patient_characteristic_ethnicity}}
-      {{^patient_characteristic_ethnicity}}
-          <ethnicGroupCode nullFlavor="UNK"/>
-      {{/patient_characteristic_ethnicity}}
       <languageCommunication>
+        <templateId root="2.16.840.1.113883.3.88.11.83.2" assigningAuthorityName="HITSP/C83"/>
+        <templateId root="1.3.6.1.4.1.19376.1.5.3.1.2.1" assigningAuthorityName="IHE/PCC"/>
         <languageCode code="eng"/>
       </languageCommunication>
     </patient>
   </patientRole>
-</recordTarget>
+</recordTarget>

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

@@ -5,10 +5,10 @@
     <id root="1.3.6.1.4.1.115" extension="{{object_id}}"/>
     <code code="ASSERTION" codeSystem="2.16.840.1.113883.5.4"/>
     <statusCode code="completed"/>
-    {{#relevantPeriod}}
-      <!-- QDM Attribute: Relevant Period -->
-      {{{relevant_period}}}
-    {{/relevantPeriod}}
+    {{#relevantDatetime}}
+      <!-- QDM Attribute: Relevant dateTime -->
+      {{{relevant_date_time}}}
+    {{/relevantDatetime}}
     <value xsi:type="CD" code="281647001" displayName="Adverse reaction" codeSystem="2.16.840.1.113883.6.96" codeSystemName="SNOMED CT"/>
     {{#authorDatetime}}
       <!-- QDM Attribute: Author dateTime -->

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

@@ -6,8 +6,13 @@
     <templateId root="2.16.840.1.113883.10.20.24.3.147" extension="2017-08-01"/>
     <id root="1.3.6.1.4.1.115" extension="{{object_id}}"/>
     <code code="ASSERTION" codeSystem="2.16.840.1.113883.5.4"/>
-    <statusCode code="completed" />
     {{#prevalencePeriod}}
+    {{#completed_prevalence_period}}
+    <statusCode code="completed" />
+    {{/completed_prevalence_period}}
+    {{^completed_prevalence_period}}
+    <statusCode code="active" />
+    {{/completed_prevalence_period}}
     <!-- QDM Attribute: Prevalence Period -->
     {{{prevalence_period}}}
     {{/prevalencePeriod}}

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

@@ -8,7 +8,7 @@
         {{/category}}
         {{^category}}
           <!-- QDM Attribute: Category -->
-          <code nullFlavor="NA"/>
+          <code nullFlavor="UNK"/>
         {{/category}}
         <statusCode code="completed"/>
         {{#relevantPeriod}}
@@ -48,7 +48,7 @@
         {{/negationRationale}}
         <entryRelationship typeCode="REFR">
           <observation classCode="OBS" moodCode="EVN">
-            <templateId root="2.16.840.1.113883.10.20.24.3.88" extension="2017-08-01"/>
+            <templateId root="2.16.840.1.113883.10.20.24.3.88" extension="2014-12-01"/>
             <id root="1.3.6.1.4.1.115" extension="{{object_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/diagnosis.mustache

@@ -25,8 +25,13 @@
         <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" />
         {{#prevalencePeriod}}
+        {{#completed_prevalence_period}}
+        <statusCode code="completed" />
+        {{/completed_prevalence_period}}
+        {{^completed_prevalence_period}}
+        <statusCode code="active" />
+        {{/completed_prevalence_period}}
         <!-- QDM Attribute: Prevalence Period -->
         {{{prevalence_period}}}
         {{/prevalencePeriod}}

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

@@ -34,10 +34,6 @@
           <!-- QDM Attribute: Admission Source -->
           {{> qrda_templates/template_partials/_admission_source}}
         {{/admissionSource}}
-        {{#principalDiagnosis}}
-          <!-- QDM Attribute: Principal Diagnosis -->
-          {{> qrda_templates/template_partials/_principal_diagnosis}}
-        {{/principalDiagnosis}}
         {{#diagnoses}}
           <!-- QDM Attribute: Diagnoses -->
           {{> qrda_templates/template_partials/_encounter_diagnosis}}

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

@@ -1,12 +1,7 @@
 <entry>
-    {{#negated}}
-      <substanceAdministration classCode="SBADM" moodCode="EVN" {{{negation_ind}}}>
-    {{/negated}}
-    {{^negated}}
-      <substanceAdministration classCode="SBADM" moodCode="EVN" negationInd="false">
-    {{/negated}}
+  <substanceAdministration classCode="SBADM" moodCode="EVN" {{{negation_ind}}}>
     <!-- C-CDA R2 Immunization Activity -->
-    <templateId root="2.16.840.1.113883.10.20.22.4.52" extension="2015-08-01"/>
+    <templateId root="2.16.840.1.113883.10.20.22.4.52" extension="2014-06-09"/>
     <!-- Immunization Administered -->
     <templateId root="2.16.840.1.113883.10.20.24.3.140" extension="2017-08-01"/>
     <id root="1.3.6.1.4.1.115" extension="{{object_id}}"/>

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

@@ -9,6 +9,8 @@
       <substanceAdministration moodCode="EVN" classCode="SBADM">
         <!-- Medication Activity (consolidation) template -->
         <templateId root="2.16.840.1.113883.10.20.22.4.16" extension="2014-06-09"/> 
+        <!-- Medication, Active template -->
+        <templateId root="2.16.840.1.113883.10.20.24.3.41" extension="2016-02-01"/>
         <id root="1.3.6.1.4.1.115" extension="{{object_id}}"/>
         <text>{{description}}</text>
         <statusCode code="active"/> 

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

@@ -8,10 +8,6 @@
     {{> _codes}}
     <text>{{description}}</text>
     <statusCode code="active"/>
-    {{#ordinality}}
-      <!-- QDM Attribute: Ordinality -->
-      {{> qrda_templates/template_partials/_ordinality}}
-    {{/ordinality}}
     {{#anatomicalLocationSite}}
       <!-- QDM Attribute: Anatomical Location Site -->
       {{> qrda_templates/template_partials/_anatomical_location_site}}

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

@@ -12,10 +12,6 @@
       <!-- QDM Attribute: Relevant Period -->
       {{{relevant_period}}}
     {{/relevantPeriod}}
-    {{#ordinality}}
-      <!-- QDM Attribute: Ordinality -->
-      {{> qrda_templates/template_partials/_ordinality}}
-    {{/ordinality}}
     {{#method}}
       <!-- QDM Attribute: Method -->
       {{> qrda_templates/template_partials/_method}}

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

@@ -9,10 +9,6 @@
     {{> _codes}}
     <text>{{description}}</text>
     <statusCode code="active"/>
-    {{#ordinality}}
-      <!-- QDM Attribute: Ordinality -->
-      {{> qrda_templates/template_partials/_ordinality}}
-    {{/ordinality}}
     {{#anatomicalLocationSite}}
       <!-- QDM Attribute: Anatomical Location Site -->
       {{> qrda_templates/template_partials/_anatomical_location_site}}