cqm-reports 3.0.0.pre.alpha.2 → 3.1.2

checksums.yaml

@@ -1,7 +1,7 @@
 ---
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-  data.tar.gz: 91135435b8c4793991b838440ea33414deb376fee10ff7728bb785cacc8549b8
+  metadata.gz: 9d999a13b64a6a37c2ad61c53c5325162a31eb948e95556a421474eb22cca735
+  data.tar.gz: f4d69a6e256859b77ea3da62a332f48e358ca4a3589d1d08bbf57889b6977f20
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+  data.tar.gz: 5c0b2e94fa51e623b071aecfc34537bc16efed7069d1bac433b178491462679fde863b24b6ee7cce9191b27e320d24fdfa004b0077f6e5be8492524f23cc89e5

data/Gemfile

@@ -17,6 +17,7 @@ group :development do
 end
 
 group :test do
+  gem 'cqm-models', '~> 3.0.3'
   gem 'factory_girl', '~> 4.1.0'
   gem 'tailor', '~> 1.1.2'
   gem 'cane', '~> 2.3.0'
@@ -26,6 +27,5 @@ 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

@@ -11,6 +11,7 @@ Starting with version **2.0.0** released on 6/20/2019, cqm-reports versioning ha
   | X | QRDA Cat 1 | QRDA Cat 3 |
   | --- | --- | --- |
   | 2 | R1 STU5.1 | R1 STU2.1 |
+  | 3 | R1 STU5.2 | R1 STU2.1 |
 
 * **Y** indicates major changes (incompatible API changes)
 
@@ -18,6 +19,32 @@ 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-reports.rb

@@ -5,6 +5,7 @@ require 'ostruct'
 require_relative 'util/code_system_helper'
 require_relative 'util/hqmf_template_helper'
 require_relative 'util/qrda_template_helper'
+require_relative 'util/entity_helper.rb'
 
 require_relative 'qrda-export/helper/frequency_helper.rb'
 require_relative 'qrda-export/helper/aggregate_object_helper.rb'
@@ -18,7 +19,6 @@ 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'
@@ -66,11 +66,11 @@ require_relative 'qrda-import/data-element-importers/physical_exam_recommended_i
 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/program_participation_importer.rb'
 require_relative 'qrda-import/data-element-importers/provider_care_experience_importer.rb'
+require_relative 'qrda-import/data-element-importers/related_person_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 'ext/data_element.rb'
-require_relative 'ext/code.rb'

data/lib/html-export/qdm-patient/data_element/_data_element_other_fields.mustache

@@ -15,8 +15,18 @@
 		<div class="div-table-head--no-border"><span class="criteria-heading">Anatomical Location Site:</span>  {{{code_code_system_string}}}</div>
 	</div>
 {{/anatomicalLocationSite}}
+{{#cause}}
+	<div class="div-head-row">
+		<div class="div-table-head--no-border"><span class="criteria-heading">Cause:</span>  {{{code_code_system_string}}}</div>
+	</div>
+{{/cause}}
+{{#category}}
+	<div class="div-head-row">
+		<div class="div-table-head--no-border"><span class="criteria-heading">Category:</span>  {{{code_code_system_string}}}</div>
+	</div>
+{{/category}}
 {{#components}}
-	{{#code}}	
+	{{#code}}
 		<div class="div-head-row">
 			<div class="div-table-head--no-border"><span class="criteria-heading">Component Code:</span>  {{{code_code_system_string}}}</div>
 		</div>
@@ -27,9 +37,14 @@
 		</div>
 	{{/result}}
 {{/components}}
+{{#daysSupplied}}
+	<div class="div-head-row">
+		<div class="div-table-head--no-border"><span class="criteria-heading">Days Supplied:</span>  {{{daysSupplied}}}</div>
+	</div>
+{{/daysSupplied}}
 {{#diagnoses}}
 	<div class="div-head-row">
-		<div class="div-table-head--no-border"><span class="criteria-heading">Diagnosis:</span>  {{{code_code_system_string}}}</div>
+		<div class="div-table-head--no-border"><span class="criteria-heading">Diagnosis:</span>  {{{nested_code_string}}}</div>
 	</div>
 {{/diagnoses}}
 {{#dischargeDisposition}}
@@ -37,14 +52,24 @@
 		<div class="div-table-head--no-border"><span class="criteria-heading">Discharge Disposition:</span>  {{{code_code_system_string}}}</div>
 	</div>
 {{/dischargeDisposition}}
+{{#dispenser}}
+	<div class="div-head-row">
+		<div class="div-table-head--no-border"><span class="criteria-heading">Dispenser:</span>  {{{entity_string}}}</div>
+	</div>
+{{/dispenser}}
+{{#dosage}}
+	<div class="div-head-row">
+		<div class="div-table-head--no-border"><span class="criteria-heading">Dosage:</span>  {{{unit_string}}}</div>
+	</div>
+{{/dosage}}
 {{#facilityLocation}}
 	<div class="div-head-row">
-		<div class="div-table-head--no-border"><span class="criteria-heading">Facility Location:</span>  {{{code_code_system_string}}}</div>
+		<div class="div-table-head--no-border"><span class="criteria-heading">Facility Location:</span>  {{{nested_code_string}}}</div>
 	</div>
 {{/facilityLocation}}
 {{#facilityLocations}}
 	<div class="div-head-row">
-		<div class="div-table-head--no-border"><span class="criteria-heading">Facility:</span>  {{{facility_string}}}</div>
+		<div class="div-table-head--no-border"><span class="criteria-heading">Facility:</span>  {{{nested_code_string}}}</div>
 	</div>
 {{/facilityLocations}}
 {{#frequency}}
@@ -52,11 +77,31 @@
 		<div class="div-table-head--no-border"><span class="criteria-heading">Frequency:</span>  {{{code_code_system_string}}}</div>
 	</div>
 {{/frequency}}
+{{#identifier}}
+	<div class="div-head-row">
+		<div class="div-table-head--no-border"><span class="criteria-heading">Identifier:</span>  {{{identifier_string}}}</div>
+	</div>
+{{/identifier}}
 {{#lengthOfStay}}
 	<div class="div-head-row">
 		<div class="div-table-head--no-border"><span class="criteria-heading">Length Of Stay:</span>  {{{unit_string}}}</div>
 	</div>
 {{/lengthOfStay}}
+{{#linkedPatientId}}
+	<div class="div-head-row">
+		<div class="div-table-head--no-border"><span class="criteria-heading">Linked Patient Id:</span>  {{{linkedPatientId}}}</div>
+	</div>
+{{/linkedPatientId}}
+{{#medium}}
+	<div class="div-head-row">
+		<div class="div-table-head--no-border"><span class="criteria-heading">Medium:</span>  {{{code_code_system_string}}}</div>
+	</div>
+{{/medium}}
+{{#methodCode}}
+	<div class="div-head-row">
+		<div class="div-table-head--no-border"><span class="criteria-heading">Method:</span>  {{{code_code_system_string}}}</div>
+	</div>
+{{/methodCode}}
 {{#negationRationale}}
 	<div class="div-head-row">
 		<div class="div-table-head--no-border"><span class="criteria-heading">Negation Reason:</span>  {{{code_code_system_string}}}</div>
@@ -67,26 +112,105 @@
 		<div class="div-table-head--no-border"><span class="criteria-heading">Ordinality:</span>  {{{code_code_system_string}}}</div>
 	</div>
 {{/ordinality}}
+{{#participant}}
+	<div class="div-head-row">
+		<div class="div-table-head--no-border"><span class="criteria-heading">Participant:</span>  {{{entity_string}}}</div>
+	</div>
+{{/participant}}
+{{#performer}}
+	<div class="div-head-row">
+		<div class="div-table-head--no-border"><span class="criteria-heading">Performer:</span>  {{{entity_string}}}</div>
+	</div>
+{{/performer}}
+{{#prescriber}}
+	<div class="div-head-row">
+		<div class="div-table-head--no-border"><span class="criteria-heading">Prescriber:</span>  {{{entity_string}}}</div>
+	</div>
+{{/prescriber}}
 {{#principalDiagnosis}}
 	<div class="div-head-row">
 		<div class="div-table-head--no-border"><span class="criteria-heading">Principal Diagnosis:</span>  {{{code_code_system_string}}}</div>
 	</div>
 {{/principalDiagnosis}}
+{{#priority}}
+	<div class="div-head-row">
+		<div class="div-table-head--no-border"><span class="criteria-heading">Priority:</span>  {{{code_code_system_string}}}</div>
+	</div>
+{{/priority}}
+{{#rank}}
+	<div class="div-head-row">
+		<div class="div-table-head--no-border"><span class="criteria-heading">Rank:</span>  {{{rank}}}</div>
+	</div>
+{{/rank}}
 {{#reason}}
 	<div class="div-head-row">
 		<div class="div-table-head--no-border"><span class="criteria-heading">Reason:</span>  {{{code_code_system_string}}}</div>
 	</div>
 {{/reason}}
+{{#recipient}}
+	<div class="div-head-row">
+		<div class="div-table-head--no-border"><span class="criteria-heading">Recipient:</span>  {{{entity_string}}}</div>
+	</div>
+{{/recipient}}
+{{#recorder}}
+	<div class="div-head-row">
+		<div class="div-table-head--no-border"><span class="criteria-heading">Recorder:</span>  {{{entity_string}}}</div>
+	</div>
+{{/recorder}}
+{{#referenceRange}}
+	<div class="div-head-row">
+		<div class="div-table-head--no-border"><span class="criteria-heading">Reference Range Start:</span>  {{{low}}}</div>
+	</div>
+	<div class="div-head-row">
+		<div class="div-table-head--no-border"><span class="criteria-heading">Reference Range End:</span>  {{{high}}}</div>
+	</div>
+{{/referenceRange}}
+{{#refills}}
+	<div class="div-head-row">
+		<div class="div-table-head--no-border"><span class="criteria-heading">Refills:</span>  {{{refills}}}</div>
+	</div>
+{{/refills}}
+{{#relatedTo}}
+{{! TODO: relatedTo is an array of strings, which are ids of dataElements, and not very useful to the user}}
+	<div class="div-head-row">
+		<div class="div-table-head--no-border"><span class="criteria-heading">Related To:</span>  {{{relatedTo}}}</div>
+	</div>
+{{/relatedTo}}
+{{#relationship}}
+	<div class="div-head-row">
+		<div class="div-table-head--no-border"><span class="criteria-heading">Relationship:</span>  {{{code_code_system_string}}}</div>
+	</div>
+{{/relationship}}
+{{#requester}}
+	<div class="div-head-row">
+		<div class="div-table-head--no-border"><span class="criteria-heading">Requester:</span>  {{{entity_string}}}</div>
+	</div>
+{{/requester}}
 {{#route}}
 	<div class="div-head-row">
 		<div class="div-table-head--no-border"><span class="criteria-heading">Route:</span>  {{{code_code_system_string}}}</div>
 	</div>
 {{/route}}
+{{#sender}}
+	<div class="div-head-row">
+		<div class="div-table-head--no-border"><span class="criteria-heading">Sender:</span>  {{{entity_string}}}</div>
+	</div>
+{{/sender}}
+{{#setting}}
+	<div class="div-head-row">
+		<div class="div-table-head--no-border"><span class="criteria-heading">Setting:</span>  {{{code_code_system_string}}}</div>
+	</div>
+{{/setting}}
 {{#severity}}
 	<div class="div-head-row">
 		<div class="div-table-head--no-border"><span class="criteria-heading">Severity:</span>  {{{code_code_system_string}}}</div>
 	</div>
 {{/severity}}
+{{#supply}}
+	<div class="div-head-row">
+		<div class="div-table-head--no-border"><span class="criteria-heading">Supply:</span>  {{{unit_string}}}</div>
+	</div>
+{{/supply}}
 {{#status}}
 	<div class="div-head-row">
 		<div class="div-table-head--no-border"><span class="criteria-heading">Status:</span>  {{{code_code_system_string}}}</div>
@@ -103,4 +227,4 @@
 	</div>
 {{/result}}
 </div>
-</div>
+</div>

data/lib/html-export/qdm-patient/data_element/_data_element_times.mustache

@@ -10,6 +10,11 @@
 		</div>
 	{{/end_time?}}
 {{/relevantPeriod}}
+{{#relevantDatetime}}
+	<div class="div-head-row">
+		<div class="div-table-head--no-border"><span class="criteria-heading">Relevant Date/Time:</span>  {{{relevantDatetime}}}</div>
+	</div>
+{{/relevantDatetime}}
 {{#prevalencePeriod}}
 	<div class="div-head-row">
 	    <div class="div-table-head--no-border"><span class="criteria-heading">Prevalence Period Start:</span>  {{{low}}}</div>
@@ -20,6 +25,16 @@
 		</div>
 	{{/end_time?}}
 {{/prevalencePeriod}}
+{{#participationPeriod}}
+	<div class="div-head-row">
+		<div class="div-table-head--no-border"><span class="criteria-heading">Participation Period Start:</span>  {{{low}}}</div>
+	</div>
+	{{#end_time?}}
+		<div class="div-head-row">
+			<div class="div-table-head--no-border"><span class="criteria-heading">Participation Period End:</span>  {{{high}}}</div>
+		</div>
+	{{/end_time?}}
+{{/participationPeriod}}
 {{#authorDatetime}}
 	<div class="div-head-row">
 		<div class="div-table-head--no-border"><span class="criteria-heading">Author Date/Time:</span>  {{{authorDatetime}}}</div>
@@ -40,5 +55,25 @@
 		<div class="div-table-head--no-border"><span class="criteria-heading">Incision Date/Time:</span>  {{{incisionDatetime}}}</div>
 	</div>
 {{/incisionDatetime}}
+{{#receivedDatetime}}
+	<div class="div-head-row">
+		<div class="div-table-head--no-border"><span class="criteria-heading">Received Date/Time:</span>  {{{receivedDatetime}}}</div>
+	</div>
+{{/receivedDatetime}}
+{{#sentDatetime}}
+	<div class="div-head-row">
+		<div class="div-table-head--no-border"><span class="criteria-heading">Sent Date/Time:</span>  {{{sentDatetime}}}</div>
+	</div>
+{{/sentDatetime}}
+{{#birthDatetime}}
+	<div class="div-head-row">
+		<div class="div-table-head--no-border"><span class="criteria-heading">Birth Date/Time:</span>  {{{birthDatetime}}}</div>
+	</div>
+{{/birthDatetime}}
+{{#expiredDatetime}}
+	<div class="div-head-row">
+		<div class="div-table-head--no-border"><span class="criteria-heading">Expired Date/Time:</span>  {{{expiredDatetime}}}</div>
+	</div>
+{{/expiredDatetime}}
+</div>
 </div>
-</div>

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

@@ -3,7 +3,7 @@
   <head>
     <meta http-equiv="Content-Type" content="text/html; charset=UTF-8" />
     {{#patient}}
-    <title>Cypress Certification Patient Test Record: {{{given_name}}} {{familyName}}</title>
+    <title>Cypress Certification Patient Test Record: {{given_name}} {{familyName}}</title>
     {{/patient}}
     {{#include_style?}}
       {{> _header_css}}
@@ -11,12 +11,12 @@
   </head>
   <body>
     {{#patient}}
-    <h1 class="h1center">Cypress Certification Patient Test Record: {{{given_name}}} {{familyName}}</h1>
+    <h1 class="h1center">Cypress Certification Patient Test Record: {{given_name}} {{familyName}}</h1>
     <div class="div-table">
       <div class="div-table-body">
         <div class="div-head-row patient_narr_tr panel panel-default patient-details">
           <div class="div-table-head patient_narr_th panel-heading"><span class="td_label">Patient</span></div>
-          <div class="div-table-head">{{{given_name}}} {{familyName}}</div>
+          <div class="div-table-head">{{given_name}} {{familyName}}</div>
           <div class="div-table-head patient_narr_th panel-heading"><span class="td_label">Sex</span></div>
           <div class="div-table-head">{{{gender}}}</div>
         </div>
@@ -24,14 +24,14 @@
           <div class="div-table-head patient_narr_th panel-heading"><span class="td_label">Date of birth</span></div>
           <div class="div-table-head">{{{birthdate}}}</div>
           <div class="div-table-head patient_narr_th panel-heading"><span class="td_label">Date of expiration</span></div>
-          <div class="div-table-head"></div>
+          <div class="div-table-head">{{{expiration}}}</div>
         </div>
         <div class="div-head-row patient_narr_tr panel panel-default patient-details">
           <div class="div-table-head patient_narr_th panel-heading"><span class="td_label">Race</span></div>
           <div class="div-table-head">{{{race}}}</div>
           <div class="div-table-head patient_narr_th panel-heading"><span class="td_label">Ethnicity</span></div>
           <div class="div-table-head">{{{ethnic_group}}}</div>
-        </div>  
+        </div>
         <div class="div-head-row patient_narr_tr panel panel-default patient-details">
           <div class="div-table-head patient_narr_th panel-heading"><span class="td_label">Insurance Providers</span></div>
           <div class="div-table-head">{{{payer}}}</div>
@@ -39,8 +39,10 @@
           <div class="div-table-head">{{{mrn}}} Cypress</div>
         </div>
         <div class="div-head-row patient_narr_tr panel panel-default patient-details">
-          <div class="div-table-head patient_narr_th panel-heading"><span class="td_label">Contact info</span></div>
-          <div class="div-table-head"></div>
+          <div class="div-table-head patient_narr_th panel-heading"><span class="td_label">Address</span></div>
+          <div class="div-table-head">{{{patient_addresses}}}</div>
+          <div class="div-table-head patient_narr_th panel-heading"><span class="td_label">Telecom</span></div>
+          <div class="div-table-head">{{{patient_telecoms}}}</div>
         </div>
       </div>
     </div>

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

@@ -1,6 +1,7 @@
 require 'mustache'
 class QdmPatient < Mustache
   include Qrda::Export::Helper::PatientViewHelper
+  include HQMF::Util::EntityHelper
 
   self.template_path = __dir__
 
@@ -8,6 +9,36 @@ class QdmPatient < Mustache
     @include_style = include_style
     @patient = patient
     @qdmPatient = patient.qdmPatient
+    @patient_addresses = patient['addresses']
+    @patient_telecoms = patient['telecoms']
+  end
+
+  def patient_addresses
+    @patient_addresses ||= [CQM::Address.new(
+      use: 'HP',
+      street: ['202 Burlington Rd.'],
+      city: 'Bedford',
+      state: 'MA',
+      zip: '01730',
+      country: 'US'
+    )]
+    address_str = ""
+    @patient_addresses.each do |address|
+      # create formatted address
+      address_str += "<address>"
+      address['street'].each { |street| address_str += "#{street}<br>" }
+      address_str += "#{address['city']}, #{address['state']} #{address['zip']}<br> #{address['country']} </address>"
+    end
+    address_str
+  end
+
+  def patient_telecoms
+    @patient_telecoms ||= [CQM::Telecom.new(
+      use: 'HP',
+      value: '555-555-2003'
+    )]
+    # create formatted telecoms
+    @patient_telecoms.map { |telecom| "(#{telecom['use']}) #{telecom['value']}" }.join("<br>")
   end
 
   def include_style?
@@ -17,17 +48,50 @@ class QdmPatient < Mustache
   def data_elements
     de_hash = {}
     @qdmPatient.dataElements.each do |data_element|
+      data_element['methodCode'] = data_element['method'] if data_element['method']
       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
 
   def unit_string
+    return "#{self['value']} " if !self['unit'] || self['unit'] == '1'
     "#{self['value']} #{self['unit']}"
   end
 
+  def entity_string
+    if care_partner_entity?
+      "</br>&nbsp; Care Partner: #{identifier_for_element(self['identifier'])}
+      </br>&nbsp; Care Partner Relationship: #{code_for_element(self['relationship'])}"
+    elsif organization_entity?
+      "</br>&nbsp; Organization: #{identifier_for_element(self['identifier'])}
+      </br>&nbsp; Organization Type: #{code_for_element(self['type'])}"
+    elsif patient_entity?
+      "</br>&nbsp; Patient: #{identifier_for_element(self['identifier'])}"
+    elsif practitioner_entity?
+      "</br>&nbsp; Practitioner: #{identifier_for_element(self['identifier'])}
+      </br>&nbsp; Practitioner Role: #{code_for_element(self['role'])},
+      </br>&nbsp; Practitioner Specialty: #{code_for_element(self['specialty'])},
+      </br>&nbsp; Practitioner Qualification: #{code_for_element(self['qualification'])}"
+    else
+      "</br>&nbsp; Entity: #{identifier_for_element(self['identifier'])}"
+    end
+  end
+
+  def identifier_string
+    identifier_for_element(self)
+  end
+
+  def identifier_for_element(identifier)
+    "#{identifier['value']} (#{identifier['namingSystem']})"
+  end
+
   def code_code_system_string
-    "#{self['code']} (#{HQMF::Util::CodeSystemHelper.code_system_for(self['system'])})"
+    code_for_element(self)
+  end
+
+  def code_for_element(element)
+    "#{element['code']} (#{HQMF::Util::CodeSystemHelper.code_system_for(element['system'])})"
   end
 
   def code_system_name
@@ -35,14 +99,14 @@ class QdmPatient < Mustache
   end
 
   def result_string
-    return unit_string if self['unit']
+    return unit_string if self['value']
     return code_code_system_string if self['code']
 
-    ''
+    self['result']
   end
 
-  def facility_string
-    "#{self['code']['code']} (#{self['code']['codeSystem']})"
+  def nested_code_string
+    code_for_element(self['code'])
   end
 
   def end_time?